the section of dna being used to make the strand of rna is known as
a gene
97580
codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons (4 combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA, and TAG codons. Cell division is essential for an organism to
DNA
2763147
Coding strand When referring to DNA transcription, the coding strand is the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil). It is this strand which contains codons, while the non-coding strand contains anticodons. During transcription, RNA Pol II binds the non-coding strand, reads the anti-codons, and transcribes their sequence to synthesize an RNA transcript with complementary bases. By convention, the coding strand is the strand used when displaying a DNA sequence. It is presented in the 5' to 3' direction. Wherever a gene exists on a DNA
Coding strand
335527
Promoter (genetics) In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 3' region of the anti-sense strand). Promoters can be about 100–1000 base pairs long. For transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors
Promoter (genetics)
6847433
Removing the inducer stops transcription. Because a small inducer molecule is required, the increased expression of the target gene is called induction. The lactose operon is one example of an inducible system. Repressor proteins bind to the DNA strand and prevent RNA polymerase from being able to attach to the DNA and synthesize mRNA. Inducers bind to repressors, causing them to change shape and preventing them from binding to DNA. Therefore, they allow transcription, and thus gene expression, to take place. For a gene to be expressed, its DNA sequence must be copied (in a process known as transcription) to
Inducer
8007418
strand and the "antisense" strand. The DNA sense strand looks like the messenger RNA (mRNA) and can be used to read the expected protein code; for example, ATG in the sense DNA may correspond to an AUG codon in the mRNA, encoding the amino acid methionine. However, the DNA sense strand itself is not used to make protein by the cell. It is the DNA antisense strand which serves as the source for the protein code, because, with bases complementary to the DNA sense strand, it is used as a template for the mRNA. Since transcription results in an RNA
Sense (molecular biology)
2763148
molecule, one strand is the coding strand (or sense strand), and the other is the noncoding strand (also called the antisense strand, anticoding strand, template strand or transcribed strand). During transcription, RNA polymerase unwinds a short section of the DNA double helix near the start of the gene (the transcription start site). This unwound section is known as the transcription bubble. The RNA polymerase, and with it the transcription bubble, travels along the noncoding strand in the opposite, 3' to 5', direction, as well as polymerizing a newly synthesized strand in 5' to 3' or downstream direction. The DNA double
Coding strand
4711225
replication. DNA polymerase can only connect new DNA nucleotides to a pre-existing chain of nucleotides. Therefore, replication begins as an enzyme called primase assembles an RNA primer at the origin of replication. The RNA primer consists of a short sequence of RNA nucleotides, complementary to a small, initial section of the DNA strand being prepared for replication. DNA polymerase is then able to add DNA nucleotides to the RNA primer and thus begin the process of constructing a new complementary strand of DNA. Later the RNA primer is enzymatically removed and replaced with the appropriate sequence of DNA nucleotides. Because
Nuclear DNA
8007420
not because it will be used to make protein (it won't be), but because it has a sequence that looks like the protein codon sequence. In biology and research, short antisense molecules can interact with complementary strands of nucleic acids, modifying expression of genes. See the section on "antisense oligonucleotides" below. DNA strand 1: antisense strand (transcribed to)→ RNA strand (sense) DNA strand 2: sense strand Some regions within a double strand of DNA code for genes, which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites, noncoding introns, and other
Sense (molecular biology)
17917656
it is removed from the DNA strand. Base flipping is used to repair mutations such as 8-Oxoguanine (oxoG) and thymine dimers created by UV radiation. DNA replication and RNA transcription both make use of base flipping. DNA polymerase is an enzyme that carries out replication. It can be thought of as a hand that grips the DNA single strand template. As the template passes across the palm region of the polymerase, the template bases are flipped out of the helix and away from the dNTP binding site. During transcription, RNA polymerase catalyzes RNA synthesis. During the initiation phase, two bases
DNA base flipping
10620193
target RNA sequences are amplified exponentially into DNA copies. For this to occur, however, the RNA of the virus must first be transcribed to DNA by means of a reverse transcriptase polymerase. This polymerase synthesizes a DNA strand using the RNA as template. This results in a DNA/RNA complex. For synthesis of a DNA strand from the RNA template only the reverse primer is required since the RNA is a single strand arranged from 5’ to 3’. Subsequently, the newly synthesized DNA strand is used as a template for traditional PCR. Different types of reverse transcriptase polymerases are available to
Potato virus Y
2748569
short RNA or DNA segments known as primers. In order for DNA polymerization to take place, two requirements must be met. First of all, all DNA polymerases must have both a template strand and a primer strand. Unlike RNA, DNA polymerases cannot synthesize DNA from a template strand. Synthesis must be initiated by a short RNA segment, known as RNA primer, synthesized by Primase in the 5' to 3' direction. DNA synthesis then occurs by the addition of a dNTP to the 3' hydroxyl group at the end of the preexisting DNA strand or RNA primer. Secondly, DNA polymerases can
DNA polymerase I
112534
strand is synthesized in the 5′ to 3′ direction—this is often confused). Four distinct mechanisms for DNA synthesis are recognized: The first is the best known of these mechanisms and is used by the cellular organisms. In this mechanism, once the two strands are separated, primase adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand is continuously extended from the primer by a DNA polymerase with high processivity, while the lagging strand is extended discontinuously from each primer forming Okazaki fragments. RNase removes the primer RNA
DNA replication
656169
initiation site. This causes the formation of Okazaki fragments. More RNA primers attach further on the DNA strand and DNA polymerase comes along and continues to make a new DNA strand.Eventually, the last RNA primer attaches, and DNA polymerase, RNA nuclease, and DNA ligase come along to convert the RNA (of the primers) to DNA and to seal the gaps in between the Okazaki fragments. But, in order to change RNA to DNA, there must be another DNA strand in front of the RNA primer. This happens at all the sites of the lagging strand, but it does not happen
Telomere
1447639
RNA polymerase can only add nucleotides to the 3' end of the growing mRNA chain. This use of only the 3' → 5' DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, as is the case in DNA replication. The "non"-template (sense) strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). This is the strand that is used by convention when presenting
Transcription (biology)
656168
in the 3' to 5' direction, one finds a leading and a lagging strand on the DNA molecule being replicated. On the leading strand, DNA polymerase can make a complementary DNA strand without any difficulty because it reads the template strand from 3' to 5'. However, there is a problem going in the other direction on the lagging strand. To counter this, short sequences of RNA acting as primers attach to the lagging strand a short distance ahead of where the initiation site was. The DNA polymerase can start replication at that point and go to the end of the
Telomere
1447645
formed. Mechanistically, promoter escape occurs through DNA scrunching, providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter. In bacteria, upon and following promoter clearance, the σ factor is released according to a stochastic model. In eukaryotes, at an RNA polymerase II-dependent promoter, upon promoter clearance, TFIIH phosphorylates serine 5 on the carboxy terminal domain of RNA polymerase II, leading to the recruitment of capping enzyme (CE). The exact mechanism of how CE induces promoter clearance in eukaryotes is not yet known. One strand of the DNA, the "template strand" (or noncoding strand), is used as
Transcription (biology)
20944240
Toehold mediated strand displacement Toehold mediated strand displacement (TMSD) is an enzyme-free molecular tool to exchange one strand of DNA or RNA (output) with another strand (input). It is based on the hybridization of two complementary strands of DNA or RNA via Watson-Crick base pairing (A-T/U and C-G) and makes use of a process called branch migration . Although branch migration has been known to the scientific community since the 1970s, TMSD has not been introduced to the field of DNA nanotechnology until 2000 when Yurke et al. was the first who took advantage of TMSD . He used the
Toehold mediated strand displacement
2754311
of Dna2 Endonuclease and FEN1 are partially responsible in Okazaki fragment maturation. Newly synthesized DNA, otherwise known as Okazaki fragments, are bound by DNA ligase, which forms a new strand of DNA. There are two strands that are created when DNA is synthesized. The leading strand is continuously synthesized and is elongated during this process to expose the template that is used for the lagging strand (Okazaki fragments). During the process of DNA replication, DNA and RNA primers are removed from the lagging strand of DNA to allow Okazaki fragments to bind to. Since this process is so common, Okazaki
Okazaki fragments
1630324
is long, complex, and highly regulated. In "Escherichia coli" bacteria, more than 100 transcription factors have been identified, which modify the activity of RNAP. RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain, which is complementary to the template DNA strand. The process of adding nucleotides to the RNA strand is known as elongation; in eukaryotes, RNAP can build chains as long as 2.4 million nucleotides (the full length of the dystrophin gene). RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes, which are
RNA polymerase
1391887
5' → 3' DNA strand. Therefore, the resulting 5' → 3' RNA strand is identical to the coding DNA strand with the exception that Thymines are replaced with uracils (U) in the RNA. A coding DNA strand reading "ATG" is indirectly transcribed through the non-coding strand as "UAC" in RNA. In prokaryotes, transcription is carried out by a single type of RNA polymerase, which needs a DNA sequence called a Pribnow box as well as a sigma factor (σ factor) to start transcription. In eukaryotes, transcription is performed by three types of RNA polymerases, each of which needs a special
Gene expression
348222
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and DNA are nucleic acids, and, along with lipids, proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information (using the nitrogenous bases of guanine, uracil, adenine, and cytosine, denoted by the
RNA
8351917
Chimeraplasty Chimeraplasty is a non-viral method of gene therapy. Chimeraplasty changes DNA sequences using a synthetic strand of RNA and DNA. This strand of RNA and DNA is known as a chimeraplast. The chimeraplast enters a cell and attaches itself to the target gene. The DNA of the chimeraplast and the cell complement each other except in the middle of the strand, where the chimeraplast's sequence is different from that of the cell. The DNA repair enzymes then replace the cell's DNA with that of the chimeraplast. This leaves the chimeraplast's new sequence in the cell's DNA and the replaced
Chimeraplasty
9835968
all RNA primers are removed and nicks are repaired. During DNA replication, the replisome will unwind the parental duplex DNA into a two single-stranded DNA template replication fork in a 5' to 3' direction. The leading strand is the template strand that is being replicated in the same direction as the movement of the replication fork. This allows the newly synthesized strand complementary to the original strand to be synthesized 5' to 3' in the same direction as the movement of the replication fork. Once an RNA primer has been added by a primase to the 3' end of the
Eukaryotic DNA replication
1391886
RNA transcript, and the "coding strand," which includes the DNA version of the transcript sequence. (Perhaps surprisingly, the "coding strand" is not physically involved in the coding process because it is the "template strand" that is read during transcription.) The production of the RNA copy of the DNA is called transcription, and is performed in the nucleus by RNA polymerase, which adds one RNA nucleotide at a time to a growing RNA strand as per the complementarity law of the bases. This RNA is complementary to the template 3' → 5' DNA strand, which is itself complementary to the coding
Gene expression
319026
transcription of its RNA. However, the HIV-encoded reverse transcriptase has its own ribonuclease activity that degrades the viral RNA during the synthesis of cDNA, as well as DNA-dependent DNA polymerase activity that copies the sense cDNA strand into "antisense" DNA to form a double-stranded DNA intermediate. DNA sequencing is used to determine the nucleotides in a DNA strand. The Sanger chain termination method of sequencing uses a primer to start the chain reaction. In PCR, primers are used to determine the DNA fragment to be amplified by the PCR process. The length of primers is usually not more than 30
Primer (molecular biology)
4187248
transcribed to produce a variety of RNA products to be translated into functional proteins for cellular use. To initiate the transcription process in a cell's nucleus, DNA double helices are unwound and hydrogen bonds connecting compatible nucleic acids of DNA are broken to produce two unconnected single DNA strands. One strand of the DNA template is used for transcription of the single-stranded primary transcript mRNA. This DNA strand is bound by an RNA polymerase at the promoter region of the DNA. In eukaryotes, three kinds of RNA—rRNA, tRNA, and mRNA—are produced based on the activity of three distinct RNA polymerases,
Primary transcript
8088499
is about 60 Å in length in eukaryotic RTs, corresponding to nearly two helical turns. When eukaryotic RT extends a conventional primer, the growing DNA/RNA double helix spirals along the cleft, and as the double helix passes the RNase H domain, the template RNA is digested to release the nascent strand of cDNA. In the case of msDNA primer extension, however, a long strand of RNA remains attached to the 3'-OH of the priming G. Although it is possible to model an RT-primer template complex which would make the 2'-OH accessible for the priming reaction, further extension of the DNA
Multicopy single-stranded DNA
5116504
homologous recombination factors at double-strand breaks within actively transcribed regions. It appears that transcription is coupled to repair of DNA double-strand breaks by RNA templated homologous recombination. This repair process efficiently and accurately rejoins double-strand breaks in genes being actively transcribed by RNA polymerase II. RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II
RNA polymerase II
7276719
DNA gene and its final protein product. The gene's DNA is used as a template to generate a complementary mRNA. The mRNA matches the sequence of the gene's DNA coding strand because it is synthesised as the complement of the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription, the polymerase first recognizes and binds a promoter region of the gene. Thus, a major mechanism of gene regulation is the blocking or sequestering the promoter
Gene
4037739
ability to bind to the largest subunit of RNA polymerase II at the phosphorylated C-terminal domain. Once RNA polymerase II begins making the new RNA strand, SR proteins move from the C-terminal domain of the RNA polymerase II to the new RNA stand. The movement of SR proteins from the RNA polymerase II to the new RNA strand prevents the new RNA strand, which is complementary to the template DNA strand, from binding to the template DNA strand thus preventing R loops. SR proteins can also stabilize DNA during transcription through an interaction with Topoisomerase I. When Topoisomerase I, Topo
SR protein
6847434
make a smaller, mobile molecule called messenger RNA (mRNA), which carries the instructions for making a protein to the site where the protein is manufactured (in a process known as translation). Many different types of proteins can affect the level of gene expression by promoting or preventing transcription. In prokaryotes (such as bacteria), these proteins often act on a portion of DNA known as the operator at the beginning of the gene. The promoter is where RNA polymerase, the enzyme that copies the genetic sequence and synthesizes the mRNA, attaches to the DNA strand. Some genes are modulated by activators,
Inducer
6385998
has two strands that are complementary, one strand must be 5'→3' while the other is 3'→5'. This inability to synthesize in the 3'→5' directionality is compensated with the use of Okazaki fragments, short pieces of DNA that are synthesized 5'→3' from the 3'→5' as the replication fork moves. As DNA polymerase requires RNA primers for DNA binding in order to commence replication, each Okazaki fragment is thus preceded by an RNA primer on the strand being synthesized. When the end of the chromosome is reached, the final RNA primer is placed upon this nucleotide region, and it is inevitably removed.
Dyskeratosis congenita
9835985
are intricately folded into a nucleosome within the cell. As previously mentioned, linear chromosomes face another issue that is not seen in circular DNA replication. Due to the fact that an RNA primer is required for initiation of DNA synthesis, the lagging strand is at a disadvantage in replicating the entire chromosome. While the leading strand can use a single RNA primer to extend the 5' terminus of the replicating DNA strand, multiple RNA primers are responsible for lagging strand synthesis, creating Okazaki fragments. This leads to an issue due to the fact that DNA polymerase is only able to
Eukaryotic DNA replication
188450
appear to package their RNA differently. HIV-1 will bind to any appropriate RNA. HIV-2 will preferentially bind to the mRNA that was used to create the Gag protein itself. Two RNA genomes are encapsidated in each HIV-1 particle (see Structure and genome of HIV). Upon infection and replication catalyzed by reverse transcriptase, recombination between the two genomes can occur. Recombination occurs as the single-strand, positive-sense RNA genomes are reverse transcribed to form DNA. During reverse transcription, the nascent DNA can switch multiple times between the two copies of the viral RNA. This form of recombination is known as copy-choice. Recombination
HIV
8893941
synthesize the new strand of RNA. The addition and pairing of nitrogenous bases are the two main processes that take place in the transcription bubble, and both of these processes are controlled by the RNA Polymerase enzyme. These processes take place in the elongation phase of the RNA strand. As RNA polymerase progresses down the DNA template strand in the 3' to 5' direction (the DNA coding strand in the 5' to 3' direction), more of the double stranded DNA is unwound downstream of the polymerase (towards the 5' end of the template strand or 3' end of the coding
Transcription bubble
16334988
with a size ladder is used to identify a section of the gel containing RNA of the appropriate size, reducing the amount of material ultimately sequenced. This step does not have to be necessarily carried out before the ligation and reverse transcription steps outlined below. Ligation The ligation step adds DNA adaptors to both ends of the small RNAs, which act as primer binding sites during reverse transcription and PCR amplification. An adenylated single strand DNA 3’adaptor followed by a 5’adaptor is ligated to the small RNAs using a ligating enzyme such as T4 RNA ligase2. The adaptors are also
MicroRNA sequencing
1787572
original DNA molecule. This pairing always occurs in specific combinations, with cytosine along with guanine, and thymine along with adenine, forming two separate pairs, respectively. By contrast, RNA polymerases synthesize RNA from ribonucleotides from either RNA or DNA. When synthesizing new DNA, DNA polymerase can add free nucleotides only to the 3' end of the newly forming strand. This results in elongation of the newly forming strand in a 5'–3' direction. No known DNA polymerase is able to begin a new chain ("de novo"); it can only add a nucleotide onto a pre-existing 3'-OH group, and therefore needs a primer
DNA polymerase
20944241
technique to open and close a set of DNA tweezers made of two DNA helices using an auxiliary strand of DNA as fuel . Since its first use, the technique has been modified for the construction of autonomous molecular motors, catalytic amplifiers, reprogrammable DNA nanostructures and molecular logic gates . It has also been used in conjunction with RNA for the production of kinetically-controlled ribosensors . TMSD starts with a double-stranded DNA complex composed of the original strand and the protector strand . The original strand has an overhanging region the so-called “toehold” which is complementary to a third strand
Toehold mediated strand displacement
2582066
resolution. Helicase polarity, which is also deemed "directionality", is defined as the direction (characterized as 5'→3' or 3'→5') of helicase movement on the DNA/RNA single-strand along which it is moving. This determination of polarity is vital in f.ex. determining whether the tested helicase attaches to the DNA leading strand, or the DNA lagging strand. To characterize this helicase feature, a partially duplex DNA is used as the substrate that has a central single-strand DNA region with different lengths of duplex regions of DNA (one short region that runs 5'→3' and one longer region that runs 3'→5') on both sides of
Helicase
319034
dna polymerase I There are a number of programs available to perform these primer predictions: Primer (molecular biology) A primer is a short single strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3′-end of the primer, and copies the opposite strand. In vivo DNA replication utilizes short strands of RNA called RNA primers to initiate DNA synthesis on
Primer (molecular biology)
319021
Primer (molecular biology) A primer is a short single strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3′-end of the primer, and copies the opposite strand. In vivo DNA replication utilizes short strands of RNA called RNA primers to initiate DNA synthesis on both the leading and lagging strands – DNA primers are not seen in vivo in
Primer (molecular biology)
1447646
a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose
Transcription (biology)
5637071
In situ hybridization "In situ" hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue ("in situ"), or, if the tissue is small enough (e.g., plant seeds, "Drosophila" embryos), in the entire tissue (whole mount ISH), in cells, and in circulating tumor cells (CTCs). This is distinct from immunohistochemistry, which usually localizes proteins in tissue sections. In situ hybridization is used to reveal the location of specific nucleic acid sequences on chromosomes or in
In situ hybridization
15939473
is carried out by the host's own DNA polymerase. The host's RNA polymerase binds to the viral genome and syntheses RNA. Some of this RNA is translated and the remainder is used to initiate DNA replication. This is initiated when a viral endonuclease (gp2) nicks the double stranded intermediate. This nicking site is specific and the sequence around the site highly symmetrical. The activity of gp2 is regulated by two other viral proteins: gp5 (single strand binding protein) and gp1# New viral genomes are produced via the rolling circle mechanism. These new single strand DNA sequences become templates for further
Plectrovirus
2733941
the DNA and downstream transcript through an unclear mechanism; there are two basic models for this event known as the torpedo and allosteric models. After the mRNA is completed and cleaved off at the poly-A signal sequence, the left-over (residual) RNA strand remains bound to the DNA template and the RNA polymerase II unit, continuing to be transcribed. After this cleavage, a so-called exonuclease binds to the residual RNA strand and removes the freshly transcribed nucleotides one at a time (also called 'degrading' the RNA), moving towards the bound RNA polymerase II. This exonuclease is XRN2 (5'-3' Exoribonuclease 2) in
Terminator (genetics)
14447296
pucker which determines the shape of the a-helix, whether the helix will exist in the A-form or in the B-form, occurs at the C2'-endo. A-DNA, is a form of the DNA duplex observed under dehydrating conditions. It is shorter and wider than B-DNA. RNA adopts this double helical form, and RNA-DNA duplexes are mostly A-form, but B-form RNA-DNA duplexes have been observed. In localized single strand dinucleotide contexts, RNA can also adopt the B-form without pairing to DNA. A-DNA has a deep, narrow major groove which does not make it easily accessible to proteins. On the other hand, its wide,
Nucleic acid structure
2394525
Primase DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA (or DNA in some organisms ) segment called a primer complementary to a ssDNA (single-stranded DNA) template. Primase is of key importance in DNA replication because no known replicative DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation). After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA. In bacteria, primase binds to
Primase
8007421
complicating details. For a cell to use this information, one strand of the DNA serves as a template for the synthesis of a complementary strand of RNA. The template DNA strand is called the transcribed strand with antisense sequence and the mRNA transcript is said to be sense sequence (the complement of antisense). Because the DNA is double-stranded, the strand complementary to the antisense sequence is called the non-transcribed strand and has the same sense sequence as the mRNA transcript (though T bases in DNA are substituted with U bases in RNA). "A note on the confusion between "sense" and
Sense (molecular biology)
2748550
and dsDNA-RT viruses, which replicate their double-stranded DNA genomes through an RNA "pregenome" intermediate. Pathogenic examples include human immunodeficiency virus and hepatitis B virus, respectively. Both encode large multifunctional reverse transcriptase (RT) proteins containing RNase H domains. Retroviral RT proteins from HIV-1 and murine leukemia virus are the best-studied members of the family. Retroviral RT is responsible for converting the virus' single-stranded RNA genome into double-stranded DNA. This process requires three steps: first, RNA-dependent DNA polymerase activity produces minus-strand DNA from the plus-strand RNA template, generating an RNA:DNA hybrid intermediate; second, the RNA strand is destroyed; and third, DNA-dependent DNA
Ribonuclease H
1787573
at which it can add the first nucleotide. Primers consist of RNA or DNA bases (or both). In DNA replication, the first two bases are always RNA, and are synthesized by another enzyme called primase. Helicase and topoisomerase II are required to unwind DNA from a double-strand structure to a single-strand structure to facilitate replication of each strand consistent with the semiconservative model of DNA replication. It is important to note that the directionality of the newly forming strand (the daughter strand) is opposite to the direction in which DNA polymerase moves along the template strand. Since DNA polymerase requires
DNA polymerase
10492924
Aspergillus nuclease S1 Aspergillus nuclease S1 is an endonuclease enzyme derived from "Aspergillus oryzae" that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides. This enzyme catalyses the following chemical reaction Although its primary substrate is single-stranded, it can also occasionally introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. The enzyme hydrolyses single stranded region in duplex DNA such as loops or gaps. Alternative names include , endonuclease S1 (Aspergillus), single-stranded-nucleate endonuclease, deoxyribonuclease S1, deoxyribonuclease S1, nuclease S1, Neurospora crassa single-strand specific endonuclease, S1 nuclease, single-strand endodeoxyribonuclease, single-stranded DNA specific endonuclease, single-strand-specific endodeoxyribonuclease, single strand-specific DNase
Aspergillus nuclease S1
8893942
strand) while DNA upstream of the polymerase (towards the 3' end of the template strand or 5' end of the coding strand) re-anneals. Since DNA has a helical structure, the movement of transcription bubble during RNA synthesis requires the DNA strand to be consistently rotated. This process is also controlled by RNA Polymerase. The process of elongation is very fast. For example, transcription takes place at around 50 to 90 nucleotides per second in E. Coli. The process of elongation takes place until the RNA Polymerase comes across a terminator. This halts the process, which causes both the template DNA
Transcription bubble
19040350
is then processed by RNaseH to produce the 3' OH primer that DNA polymerase I uses to initiate leading strand DNA synthesis. RNA I serves as a major plasmid-encoded inhibitor of this process whose concentration is proportional to plasmid copy number. RNA I is exactly complementary to the 5' end of the RNA II (because it is transcribed from the opposite strand of the same region of DNA as RNA II). RNA I and RNA II first form a weak interaction called a kissing complex. The kissing complex is stabilized by a protein called Rop (repressor of primer) and a
Plasmid copy number
14015356
to the next on the looped lagging strand. Leading strand synthesis begins with the synthesis of a short RNA primer at the replication origin by the enzyme Primase (DnaG protein). Deoxynucleotides are then added to this primer by a single DNA polymerase III dimer, in an integrated complex with DnaB helicase. Leading strand synthesis then proceeds continuously, while the DNA is concurrently unwound at the replication fork. In contrast, lagging strand synthesis is accomplished in short Okazaki fragments. First, an RNA primer is synthesized by primase, and, like that in leading strand synthesis, DNA Pol III binds to the RNA
Circular bacterial chromosome
8007417
protein coding and non-coding RNAs can be transcribed from the sense strand. Additionally, the terms "sense" and "antisense" are relative to the RNA transcript in question and not to the DNA strand as a whole. In other words, either DNA strand can serve as the sense or antisense strand for a particular RNA transcript. In some cases, RNA transcripts can be transcribed in both directions (i.e. on either strand) from a common promoter region, or be transcribed from within introns on either strand (see "ambisense" below). The two complementary strands of double-stranded DNA (dsDNA) are usually differentiated as the "sense"
Sense (molecular biology)
3356424
amounts of viral components. In the case of DNA viruses, the DNA transcribes itself into messenger RNA (mRNA) molecules that are then used to direct the cell's ribosomes. One of the first polypeptides to be translated destroys the host's DNA. In retroviruses (which inject an RNA strand), a unique enzyme called reverse transcriptase transcribes the viral RNA into DNA, which is then transcribed again into RNA. Once the viral DNA has taken control it induces the host cell's machinery to synthesize viral DNA, protein and starts multiplying. The biosynthesis is (e.g. T4) regulated in three phases of mRNA production followed
Lytic cycle
157102
are separated, new partner strands can be reconstructed for each based on the sequence of the old strand. This property is what gives DNA its semi-conservative nature where one strand of new DNA is from an original parent strand. Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls the process of protein production. It was discovered that the cell uses DNA as a template to create matching messenger RNA, molecules with nucleotides very similar to DNA. The
Genetics
2754304
DNA in the 5’ to 3’ direction. DNA polymerase is essential for both the leading strand which is made as a continuous strand and lagging strand which is made in small pieces in DNA Synthesis. This process happens for extension of the newly synthesized fragment and expulsion of the RNA and DNA segment. Synthesis occurs in 3 phases with two different polymerases, DNA polymerase α-primase and DNA polymerase δ. This process starts with polymer α-primase displacing from the RNA and DNA primer by the clamp loader replication affect, this affect leads the sliding clamp onto the DNA. After this, DNA
Okazaki fragments
5343297
to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences. Stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As
Stem-loop
15099069
of terminal sequences that are lost in each round of DNA replication. Before telomerase was identified, its activity was predicted on the basis of a molecular understanding of DNA replication, which indicated that the DNA polymerases known at that time could not replicate the 3' end of a linear chromosome, due to the absence of a template strand. Telomerase was shown to be a ribonucleoprotein enzyme that contains an RNA component that serves as a template strand, and a protein component that has reverse transcriptase activity and adds nucleotides to the chromosome ends using the internal RNA template. For years,
History of RNA biology
348347
play vital roles, such as that of the ribosome, an RNA-protein complex responsible for protein synthesis. Many other ribozyme functions exist; for example, the hammerhead ribozyme performs self-cleavage and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template. Among the enzymatic properties important for the beginning of life are: RNA is a very similar molecule to DNA, with only two major chemical differences (the backbone of RNA uses ribose instead of deoxyribose and its nucleobases include uracil instead of thymine). The overall structure of RNA and DNA are immensely similar—one strand of DNA and
RNA world
2763150
of base-pairs in the hybrid is under investigation, but it has been suggested that the hybrid is formed from the last 10 nucleotides added. Coding strand When referring to DNA transcription, the coding strand is the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil). It is this strand which contains codons, while the non-coding strand contains anticodons. During transcription, RNA Pol II binds the non-coding strand, reads the anti-codons, and transcribes their sequence to synthesize an RNA transcript with complementary bases. By convention, the coding strand is
Coding strand
2394535
a bacterial multifunctional complex composed of fused helicase and primase domains. The enzyme has both primase and polymerase functions in addition to helicase function. Primase DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA (or DNA in some organisms ) segment called a primer complementary to a ssDNA (single-stranded DNA) template. Primase is of key importance in DNA replication because no known replicative DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA
Primase
8007419
product complementary to the DNA template strand, the mRNA is complementary to the DNA antisense strand. The mRNA is what is used for translation (protein synthesis).Hence, a base triplet 3'-TAC-5' in the DNA antisense strand can be used as a template which will result in an 5'-AUG-3' base triplet in mRNA (AUG is the codon for methionine, the start codon). The DNA sense strand will have the triplet ATG, which looks just like AUG but will not be used to make methionine because it will not be used to make mRNA. The DNA sense strand is called a "sense" strand
Sense (molecular biology)
1630340
combinations of the above techniques. RNA polymerase RNA polymerase (ribonucleic acid polymerase), both abbreviated RNAP or RNApol, official name DNA-directed RNA polymerase, is a member of a family of enzymes that are essential to life: they are found in all living organisms and many viruses. RNAP locally opens the double-stranded DNA (usually about four turns of the double helix) so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called
RNA polymerase
1630318
RNA polymerase RNA polymerase (ribonucleic acid polymerase), both abbreviated RNAP or RNApol, official name DNA-directed RNA polymerase, is a member of a family of enzymes that are essential to life: they are found in all living organisms and many viruses. RNAP locally opens the double-stranded DNA (usually about four turns of the double helix) so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP
RNA polymerase
331610
DNA strand from the 3-prime (3') end to the 5-prime (5') end, while it synthesizes a single strand of messenger RNA in the 5'-to-3' direction. The general RNA structure is very similar to the DNA structure, but in RNA the nucleotide uracil takes the place that thymine occupies in DNA. The single strand of mRNA leaves the nucleus through nuclear pores, and migrates into the cytoplasm. The first product of transcription differs in prokaryotic cells from that of eukaryotic cells, as in prokaryotic cells the product is mRNA, which needs no post-transcriptional modification, whereas, in eukaryotic cells, the first product
Protein biosynthesis
8088500
strand presents a problem: as DNA synthesis progresses, the bulky RNA strand extending from the 3'-OH needs somehow to spiral down the binding cleft without being blocked by steric hindrance. To overcome this issue, the msDNA reverse transcriptase clearly would require special features not shared by other RTs. Multicopy single-stranded DNA Before the discovery of msDNA in myxobacteria, a group of swarming, soil-dwelling bacteria, it was thought that the enzymes known as reverse transcriptases (RT) existed only in eukaryotes and viruses. The discovery led to an increase in research of the area. As a result, msDNA has been found to
Multicopy single-stranded DNA
1447638
As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Only one of the two DNA strands serve as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3' end to the 5' end during transcription (3' → 5'). The complementary RNA is created in the opposite direction, in the 5' → 3' direction, matching the sequence of the sense strand with the exception of switching uracil for thymine. This directionality is because
Transcription (biology)
4008732
replication: the leading strand, which is synthesized continuously and grows towards the replication fork, and the lagging strand, which is made discontinuously in Okazaki fragments and grows away from the replication fork. Okazaki fragments are covalently joined by DNA ligase to form a continuous strand. Then, to complete DNA replication, RNA primers are removed, and the resulting gaps are replaced with DNA and joined via DNA ligase. A protein is a polymer that is composed from amino acids that are linked by peptide bonds. There are more than 300 amino acids found in nature of which only twenty, known as
Biosynthesis
11004029
Upstream and downstream (DNA) In molecular biology and genetics, upstream and downstream both refer to relative positions of genetic code in DNA or RNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for the carbon position on the deoxyribose (or ribose) ring. By convention, upstream and downstream relate to the 5' to 3' direction respectively in which RNA transcription takes place. Upstream is toward the 5' end of the RNA molecule and downstream is toward the 3' end. When considering double-stranded DNA, upstream is toward the 5' end of the coding strand
Upstream and downstream (DNA)
2673648
to copy the DNA. At some point during the replication process, the polymerase dissociates from the DNA and replication stalls. When the polymerase reattaches to the DNA strand, it aligns the replicating strand to an incorrect position and incidentally copies the same section more than once. Replication slippage is also often facilitated by repetitive sequences, but requires only a few bases of similarity. During the cellular invasion by a replicating retroelement or retrovirus, viral proteins copy their genome by reverse transcribing RNA to DNA. If viral proteins aberrantly attach to cellular mRNA, they can reverse transcribe copies of genes to
Gene duplication
2748795
in bacterial DNA replication because DNA polymerase cannot initiate the synthesis of a DNA strand, but can only add nucleotides to a preexisting strand. DnaG synthesizes a single RNA primer at the origin of replication. This primer serves to prime leading strand DNA synthesis. For the other parental strand, the lagging strand, DnaG synthesizes an RNA primer every few kilobases (kb). These primers serve as substrates for the synthesis of Okazaki fragments. In "E. coli" DnaG associates through noncovalent interactions with bacterial replicative helicase DnaB to perform its primase activity, with three DnaG primase proteins associating with each DnaB helicase
DnaG
112529
synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand. DNA polymerase adds a new strand of DNA by extending the 3' end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds. The energy for this process of DNA polymerization comes from hydrolysis of the high-energy phosphate (phosphoanhydride) bonds between the three phosphates attached to each
DNA replication
2748555
which eukaryotic homologs became obligate heterotrimers, is unclear; the B and C subunits have no apparent homologs in prokaryotes. Because RNase H specifically degrades only the RNA in double-stranded RNA:DNA hybrids, it is commonly used as a laboratory reagent in molecular biology. Purified preparations of "E. coli" RNase HI and HII are commercially available. RNase HI is often used to destroy the RNA template after first-strand complementary DNA (cDNA) synthesis by reverse transcription. It can also be used to cleave specific RNA sequences in the presence of short complementary segments of DNA. Highly sensitive techniques such as surface plasmon resonance
Ribonuclease H
8243238
but independent from, sense. Transcription of single-stranded RNA from a double-stranded DNA template requires the selection of one strand of the DNA template as the template strand that directly interacts with the nascent RNA due to complementary sequence. The other strand is not copied directly, but necessarily its sequence will be similar to that of the RNA. Transcription initiation sites generally occur on both strands of an organism's DNA, and specify the location, direction, and circumstances under which transcription will occur. If the transcript encodes one or (rarely) more proteins, translation of each protein by the ribosome will proceed in
Directionality (molecular biology)
97558
called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein. The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands can contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear. One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing. A few DNA sequences in prokaryotes and
DNA
43647
Protein synthesis generally consists of two major steps: transcription and translation. Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol, where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets
Cell (biology)
14460477
living cells using the DNA ‘cage’. A DNA tetrahedron was used to deliver RNA Interference (RNAi) in a mouse model, reported a team of researchers in MIT. Delivery of the interfering RNA for treatment has showed some success using polymer or lipid, but there are limits of safety and imprecise targeting, in addition to short shelf life in the blood stream. The DNA nanostructure created by the team consists of six strands of DNA to form a tetrahedron, with one strand of RNA affixed to each of the six edges. The tetrahedron is further equipped with targeting protein, three folate
DNA nanotechnology
13887538
these four NNRTIs several other are in clinical development. Reverse transcriptase (RT) is an enzyme that controls the replication of the genetic material of HIV and other retroviruses. The enzyme has two enzymatic functions. Firstly it acts as a polymerase where it transcribes the single-stranded RNA genome into single-stranded DNA and subsequently builds a complementary strand of DNA. This provides a DNA double helix which can be integrated in the host cell's chromosome. Secondly it has ribonuclease H (Rnase H) activity as it degrades the RNA strand of RNA-DNA intermediate that forms during viral DNA synthesis. The HIV-1 RT is
Discovery and development of non-nucleoside reverse-transcriptase inhibitors
15345713
use one strand as a template to construct the other. This principle plays an important role in DNA replication, setting the foundation of heredity by explaining how genetic information can be passed down to the next generation. Complementarity is also utilized in DNA transcription, which generates an RNA strand from a DNA template. DNA repair mechanisms such as proof reading are complementarity based and allow for error correction during DNA replication by removing mismatched nucleobases. Nucleic acids strands may also form hybrids in which single stranded DNA may readily anneal with complementary DNA or RNA. This principle is the basis
Complementarity (molecular biology)
319024
Okazaki fragments. Along the lagging strand's template, primase builds RNA primers in short bursts. DNA polymerases are then able to use the free 3′-OH groups on the RNA primers to synthesize DNA in the 5′→3′ direction. The RNA fragments are then removed by DNA polymerase I for prokaryotes or DNA polymerase δ for eukaryotes (different mechanisms are used in eukaryotes and prokaryotes) and new deoxyribonucleotides are added to fill the gaps where the RNA was present. DNA ligase then joins the deoxyribonucleotides together, completing the synthesis of the lagging strand. In eukaryotic primer removal, DNA polymerase δ extends the Okazaki
Primer (molecular biology)
15636084
folds into a secondary structure which stabilises the interaction between the nascent RNA and the origin's DNA. This hybrid is attacked by RNase H, which cleaves the RNA strand, exposing a 3' hydroxyl group. This allows the extension of the leading strand by DNA Polymerase I. Lagging strand synthesis is later initiated by a primase encoded by the host cell.1 Replication is carried out entirely by host proteins (RNA polymerase, DNA polymerase I and RNase H) so that inhibition of translation will stop the growth of the cells, but not the replication of ColE1. Since the translation of Rop protein
ColE1
2754303
that at which DNA polymerase synthesizes DNA on the leading strand. DNA polymerase on the lagging strand also has to be continually recycled to construct Okazaki fragments following RNA primers. This makes the speed of lagging strand synthesis much lower than that of the leading strand. To solve this, primase acts as a temporary stop signal, briefly halting the progression of the replication fork during DNA replication. This molecular process prevents the leading strand from overtaking the lagging strand. DNA polymerase is such a critical part of this because new DNA is made during this phase by enzymes which synthesize
Okazaki fragments
8035619
Sense strand In genetics, a sense strand, or coding strand, is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'. The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein. The antisense strand is thus responsible for the RNA that is later translated to protein, while the sense strand possesses a nearly identical
Sense strand
15345714
of commonly performed laboratory techniques such as the polymerase chain reaction, PCR. Two strands of complementary sequence are referred to as sense and anti-sense. The sense strand is, generally, the transcribed sequence of DNA or the RNA that was generated in transcription. While the anti-sense strand is the strand that is complementary to the sense sequence. Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double-strand like structure. Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, junctions, bulges
Complementarity (molecular biology)
348350
binds uracil or thymine. Uracil is, however, one product of damage to cytosine that makes RNA particularly susceptible to mutations that can replace a GC base pair with a GU (wobble) or AU base pair. RNA is thought to have preceded DNA, because of their ordering in the biosynthetic pathways. The deoxyribonucleotides used to make DNA are made from ribonucleotides, the building blocks of RNA, by removing the 2'-hydroxyl group. As a consequence a cell must have the ability to make RNA before it can make DNA. The chemical properties of RNA make large RNA molecules inherently fragile, and they
RNA world
20835536
either located very far away or on the opposite DNA strand, and these cases tend to argue against a cis-regulatory function. Assuming that the RNA is cis regulatory, the genes that would be regulated by the RNAs lack specific functional annotations, which makes it difficult to develop a hypothesis for the RNA's function. COG3943 RNA motif The COG3943 RNA motif is a conserved RNA structure that was discovered by bioinformatics. COG3943 motifs are found in unknown bacteria whose genomic DNA was isolated from cow rumen. As of 2018, there is no specific, classified organism that is known to contain a
COG3943 RNA motif
8007427
can produce antisense RNA molecules naturally, called microRNA, which interact with complementary mRNA molecules and inhibit their expression. In virology, the genome of an RNA virus can be said to be either positive-sense, also known as a "plus-strand", or negative-sense, also known as a "minus-strand". In most cases, the terms "sense" and "strand" are used interchangeably, making such terms as "positive-strand" equivalent to "positive-sense", and "plus-strand" equivalent to "plus-sense". Whether a virus genome is positive-sense or negative-sense can be used as a basis for classifying viruses. Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may
Sense (molecular biology)
4759812
substrate of viral DNA polymerase. When used as a substrate for viral DNA polymerase, ara-ATP competitively inhibits dATP leading to the formation of ‘faulty’ DNA. This is where ara-ATP is incorporated into the DNA strand replacing many of the adenosine bases. This results in the prevention of DNA synthesis, as phosphodiester bridges can no longer to be built, destabilizing the strand. Vidarabine triphosphate (ara-ATP) also inhibits RNA polyadenylation; preventing polyadenylation essential for HIV-1 and other retroviruses; and S-adenosylhomocysteine hydrolase, preventing transmethylation reactions. Uniquely to vidarabine, the diphosphorylated vidarabine (ara-ADP) also has an inhibitory effect. Other nucleoside analogs need to be
Vidarabine
11004030
for the gene in question and downstream is toward the 3' end. Due to the anti-parallel nature of DNA, this means the 3' end of the template strand is upstream of the gene and the 5' end is downstream. Some genes on the same DNA molecule may be transcribed in opposite directions. This means the upstream and downstream areas of the molecule may change depending on which gene is used as the reference. Upstream and downstream (DNA) In molecular biology and genetics, upstream and downstream both refer to relative positions of genetic code in DNA or RNA. Each strand of
Upstream and downstream (DNA)
8035621
contains a sequence of nucleotides that is identical to that of the sense strand. The exception to this is that uracil is used for nucleotide sequencing of RNA molecules rather than thymine. Most eukaryotic RNA transcripts undergo additional editing prior to being translated for protein synthesis. This process typically involves removal of introns from the initial RNA transcript, the addition of a methylated guanine nucleotide cap at the 5' end, and the addition of a poly-A tail at the 3' end. This deletion process is known as splicing. The end product is known as a mature mRNA. Prokaryotic mRNA does
Sense strand
4711226
the two complementary strands of the DNA molecule are oriented in opposite directions and the DNA polymerase can only accommodate replication in one direction, two different mechanisms for copying the strands of DNA are employed. One strand is replicated continuously towards the unwinding, separating portion of the original DNA molecule; while the other strand is replicated discontinuously in the opposite direction with the formation of a series of short DNA segments called Okazaki fragments. Each Okazaki fragment requires a separate RNA primer. As the Okazaki fragments are synthesized, the RNA primers are replaced with DNA nucleotides and the fragments are
Nuclear DNA
9850050
next phase of transcription: elongation. Transcription elongation is a processive process. Double stranded DNA that enters from the front of the enzyme is unzipped to avail the template strand for RNA synthesis. For every DNA base pair separated by the advancing polymerase, one hybrid RNA:DNA base pair is immediately formed. DNA strands and nascent RNA chain exit from separate channels; the two DNA strands reunite at the trailing end of the transcription bubble while the single strand RNA emerges alone. Among the proteins recruited to polymerase are elongation factors, thus called because they stimulate transcription elongation. There are different classes
Eukaryotic transcription
91968
a provirus. The term "cDNA" is also used, typically in a bioinformatics context, to refer to an mRNA transcript's sequence, expressed as DNA bases (GCAT) rather than RNA bases (GCAU). cDNA is derived from mRNA, so it contains only exons but no introns. Although there are several methods for doing so, cDNA is most often synthesized from mature (fully spliced) mRNA using the enzyme reverse transcriptase. This enzyme, which naturally occurs in retroviruses, operates on a single strand of mRNA, generating its complementary DNA based on the pairing of RNA base pairs (A, U, G and C) to their DNA
Complementary DNA
2748817
the 3'OH of the primer: DNA polymerase III will then synthesize a continuous or discontinuous strand of DNA, depending if this is occurring on the leading or lagging strand (Okazaki fragment) of the DNA. DNA polymerase III has a high processivity and therefore, synthesizes DNA very quickly. This high processivity is due in part to the β-clamps that "hold" onto the DNA strands. After replication of the desired region, the RNA primer is removed by DNA polymerase I via the process of nick translation. The removal of the RNA primer allows DNA ligase to ligate the DNA-DNA nick between the
DNA polymerase III holoenzyme
9835970
can be anywhere between 100–400 nucleotides long in eukaryotes. At the end of Okazaki fragment synthesis, DNA polymerase δ runs into the previous Okazaki fragment and displaces its 5' end containing the RNA primer and a small segment of DNA. This generates an RNA-DNA single strand flap, which must be cleaved, and the nick between the two Okazaki fragments must be sealed by DNA ligase I. This process is known as Okazaki fragment maturation and can be handled in two ways: one mechanism processes short flaps, while the other deals with long flaps. DNA polymerase δ is able to displace
Eukaryotic DNA replication
1630328
stabilized, RNA polymerase synthesizes an RNA strand to establish a DNA-RNA heteroduplex (~8-9 bp) at the active center, which stabilizes the elongation complex. In order to accomplish RNA synthesis, RNA polymerase must maintain promoter contacts while unwinding more downstream DNA for synthesis, "scrunching" more downstream DNA into the initiation complex. During the promoter escape transition, RNA polymerase is considered a "stressed intermediate." Thermodynamically the stress accumulates from the DNA-unwinding and DNA-compaction activities. Once the DNA-RNA heteroduplex is long enough, RNA polymerase releases its upstream contacts and effectively achieves the promoter escape transition into the elongation phase. However, promoter escape is
RNA polymerase
11254899
can be created with positive sense viral RNA. The 5' section on the newly created strand matches that of the template strand, and this section on the template strand is referred to as the "nested set". 3' 5' This complex method of transcription is generally restricted to viruses, especially those of the single-stranded, positive-sense RNA or Class IV viruses using the Baltimore Classification System, e.g. viruses of the order Nidovirales. It is primarily used for compacting more genetic information into a shorter amount of genetic material. Subgenomic mRNA Subgenomic mRNA's are essentially smaller sections of the original transcribed template strand.
Subgenomic mRNA
355033
is unusual because reverse transcriptase synthesize DNA from 3’ end of the primer in the 5’ to 3’ direction (with respect to the newly synthesized DNA strand). Therefore, the primer and reverse transcriptase must be relocated to 3’ end of viral RNA. In order to accomplish this reposition, multiple steps and various enzymes including DNA polymerase, ribonuclease H(RNase H) and polynucleotide unwinding are needed. The HIV reverse transcriptase also has ribonuclease activity that degrades the viral RNA during the synthesis of cDNA, as well as DNA-dependent DNA polymerase activity that copies the sense cDNA strand into an "antisense" DNA to
Reverse transcriptase
1447655
synthesizing a complementary DNA strand (cDNA) to the viral RNA genome. The enzyme ribonuclease H then digests the RNA strand, and reverse transcriptase synthesises a complementary strand of DNA to form a double helix DNA structure ("cDNA"). The cDNA is integrated into the host cell's genome by the enzyme integrase, which causes the host cell to generate viral proteins that reassemble into new viral particles. In HIV, subsequent to this, the host cell undergoes programmed cell death, or apoptosis of T cells. However, in other retroviruses, the host cell remains intact as the virus buds out of the cell. Some
Transcription (biology)