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= = Academic publications ( incomplete ) = =
" Fabrication of mercuric iodide radiation detectors " , Lodewijk van den Berg and Ron D. Vigil , Nuclear Instruments and Methods in Physics Research Section A : Accelerators , <unk> , Detectors and Associated Equipment , Volume 458 , Issues 1 @-@ 2 , 1 February 2001 , Pages 148 @-@ 151
" Improved yield of high resolution mercuric iodide gamma @-@ ray spectrometers " , Vernon <unk> and Lodewijk van den Berg , Nuclear Instruments and Methods in Physics Research Section A : Accelerators , <unk> , Detectors and Associated Equipment , Volume 299 , Issues 1 @-@ 3 , 20 December 1990 , Pages 41 @-@ 44
" Vapor growth of <unk> by periodic source or crystal temperature oscillation " , by M. Schieber βˆ— , W.F. <unk> , L. Van den Berg . Journal of Crystal Growth , Volume 33 , Issue 1 , April 1976 , Pages 125 – 135
= Wrigley Square =
Wrigley Square is a public square located in the northwest section of Millennium Park in the Historic Michigan Boulevard District of the Loop area of Chicago in Cook County , Illinois , United States . The square is located at the southeast corner of the intersection of East Randolph Street and North Michigan Avenue . It contains the Millennium Monument , a nearly full @-@ sized replica of the semicircle of paired Roman Doric @-@ style columns ( called a peristyle ) that originally sat in this area of Grant Park , near Michigan Avenue and Randolph Street , between 1917 and 1953 . The square also contains a large lawn and a public fountain .
= = Detail = =
Lying between Lake Michigan to the east and the Loop to the west , Grant Park has been Chicago 's front yard since the mid 19th century . Its northwest corner , north of Monroe Street and the Art Institute , east of Michigan Avenue , south of Randolph Street , and west of Columbus Drive , had been Illinois Central rail yards and parking lots until 1997 , when it was made available for development by the city as Millennium Park . Today , Millennium Park trails only Navy Pier as a Chicago tourist attraction .
The square is a tree @-@ lined section of Millennium Park with a large lawn . The area broadcasts free wifi wireless technology . The square has earned a reputation as an outdoor culture spot by hosting a wide range of cultural events such as local and international art and photography exhibitions , as well as occasional live musical performances . This reputation is reminiscent of the earlier neo @-@ classical meeting place . When Mayor of Chicago Richard M. Daley dedicated the square , it was dedicated to the donors , known as the Founders Group , who funded Millennium Park .
In 2005 , Millennium Park was marked for updates and improvements . Benches were to be added to the 56 original benches . Landscape architect Kathryn Gustafson designed 14 new 320 @-@ pound ( 145 @.@ 1 kg ) , aluminum β€œ Maggie benches ” benches in Millennium Park , mostly in Wrigley square , in honor of Mayor Daley ’ s wife .
The square was intended to serve as an exhibit space for outdoor sculpture as well as small cultural performances , according to Christopher <unk> , vice president of the Wrigley Square Foundation . The square 's peristyle monument is in remembrance of the corporation , foundations , and individuals who made Millennium Park possible .
An architectural model of Wrigley Square and Millennium Monument , designed by O 'Donnell , <unk> , Pigozzi and Peterson Architects , Inc . ( OWP & P ) in 2000 , is on display at the Harold Washington Library Center .
= = = Original peristyle = = =
In 1917 , the original peristyle was designed by renowned Chicago planner Edward H. Bennett , who was Daniel Burnham 's partner in the Plan of Chicago and who was known for designing the nearby Buckingham Fountain . It was located in Grant Park in the same location as the current Wrigley Square . The original peristyle rose to 40 feet ( 12 @.@ 2 m ) and had a diameter of 100 feet ( 30 @.@ 5 m ) . The original was made of concrete , which did not stand up to the Lake Michigan lakefront weather . In 1953 it was razed to make way for the Grant Park North Garage . The original peristyle was on a promenade with balustrades .
= = = Millennium Monument = = =
A gift from the William Wrigley , Jr . Company , the limestone replica peristyle rises to a height of nearly 40 feet ( 12 @.@ 2 m ) ( one source says the columns were planned to rise to 36 feet ( 11 @.@ 0 m ) ) , restoring a classical elegance to Grant Park . The William Wrigley , Jr . Foundation contributed $ 5 million to the monument , and the entire square , which cost $ 5 million to build , was named in its honor . The Millennium Monument is a tribute to the individual , corporate and foundation benefactors of Millennium Park . The pedestal of the peristyle is inscribed with the names of the 115 financial donors ( including Oprah Winfrey ) who made the 91 contributions of at least $ 1 million each to help pay for Millennium Park . The New York Times describes the pedestal as French marble , but other sources mention the use of French limestone . These 115 donors are referred to as the founders of Millennium Park in official park brochures published by the City of Chicago and distributed at the visitor 's centers as well as in other press accounts . Their contributions not only paid for the construction of the park , but also provide for its ongoing conservation .
The David Dillon and Michael Patrick Sullivan ( of OWP & P ) design is based on original drawings by Bennett found in the Chicago Park District 's archive .
The naming rights of the space belong to Wm . Wrigley Jr , the foundation that created the world ’ s famous chewing gum . Wrigley Company officials , including William Wrigley , Jr . II , wanted to contribute to Millennium Park , and the historic aspect of the peristyle was attractive to them partly because the original peristyle was constructed around the same time as the Wrigley Building , the corporate headquarters located a few blocks to the north , and because the classical architectural styles of both are similar .
The 24 paired , fluted columns are the same height as the original peristyle . However , the structure was scaled down to an 80 @-@ foot ( 24 @.@ 4 m ) diameter in order to accommodate the accessible ramp that runs behind the monument . Each of the limestone columns is cut from an Indiana quarry and made of five 2 @,@ 200 pounds ( 997 @.@ 9 kg ; 157 @.@ 1 st ) sections reinforced by steel rods and plates . The fountain in front of the monument is a bronze @-@ cast replica of the finials that adorn the Wrigley Building . The brass spout was made from a mold of a terra cotta <unk> on the Wrigley Building .
The front of the monument has a dedication plaque ( pictured left ) . In addition , on the reverse side in approximately the same location , the monument has a special plaque commemorating John H. Bryan 's contribution as the head of fundraising for the Park .
The original model of the Millennium Monument was the starting point of the Peristyle appearance in Chicago . To this day , it is said to not compare to the once β€œ commanding presence ” that once stood in its place , before being demolished and replaced with an underground parking garage . The new monument was downsized by approximately 15 % to accommodate a wheel @-@ chair ramp for the disabled in a tight space . It also includes a β€œ classical ” take on the original , incorporating a fountain at the base of the limestone , Doric , column monument . The monument , despite being relatively small in comparison to the rest of Grant Park , makes it presence known as the central focus to shape Wrigley Square and the surrounding landscape . Wrigley Square is unique for its fountain that , unlike Buckingham Fountain , which is fenced off , remains open with a circular ledge to allow park @-@ goers the freedom to sit next to the open water to enjoy the atmosphere .
= Homologous recombination =
Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA . It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA , known as double @-@ strand breaks . Homologous recombination also produces new combinations of DNA sequences during meiosis , the process by which eukaryotes make gamete cells , like sperm and egg cells in animals . These new combinations of DNA represent genetic variation in offspring , which in turn enables populations to adapt during the course of evolution . Homologous recombination is also used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses .
Although homologous recombination varies widely among different organisms and cell types , most forms involve the same basic steps . After a double @-@ strand break occurs , sections of DNA around the 5 ' ends of the break are cut away in a process called resection . In the strand invasion step that follows , an overhanging 3 ' end of the broken DNA molecule then " invades " a similar or identical DNA molecule that is not broken . After strand invasion , the further sequence of events may follow either of two main pathways discussed below ( see Models ) ; the DSBR ( double @-@ strand break repair ) pathway or the SDSA ( synthesis @-@ dependent strand annealing ) pathway . Homologous recombination that occurs during DNA repair tends to result in non @-@ crossover products , in effect restoring the damaged DNA molecule as it existed before the double @-@ strand break .
Homologous recombination is conserved across all three domains of life as well as viruses , suggesting that it is a nearly universal biological mechanism . The discovery of genes for homologous recombination in protists β€” a diverse group of eukaryotic microorganisms β€” has been interpreted as evidence that meiosis emerged early in the evolution of eukaryotes . Since their dysfunction has been strongly associated with increased susceptibility to several types of cancer , the proteins that facilitate homologous recombination are topics of active research . Homologous recombination is also used in gene targeting , a technique for introducing genetic changes into target organisms . For their development of this technique , Mario Capecchi , Martin Evans and Oliver Smithies were awarded the 2007 Nobel Prize for Physiology or Medicine ; Capecchi and Smithies independently discovered applications to mouse embryonic stem cells , however the highly conserved mechanisms underlying the DSB repair model , including uniform homologous integration of transformed DNA ( gene therapy ) , were first shown in plasmid experiments by Orr @-@ Weaver , <unk> and Rothstein . Researching the plasmid @-@ induced DSB , using Ξ³ @-@ irradiation in the 1970 's @-@ 1980 's , led to later experiments using endonucleases ( e.g. I @-@ <unk> ) to cut chromosomes for genetic engineering of mammalian cells , where <unk> recombination is more frequent than in yeast .
= = History and discovery = =
In the early 1900s , William Bateson and Reginald Punnett found an exception to one of the principles of inheritance originally described by Gregor Mendel in the 1860s . In contrast to Mendel 's notion that traits are independently assorted when passed from parent to child β€” for example that a cat 's hair color and its tail length are inherited independent of each other β€” Bateson and Punnett showed that certain genes associated with physical traits can be inherited together , or genetically linked . In 1911 , after observing that linked traits could on occasion be inherited separately , Thomas Hunt Morgan suggested that " crossovers " can occur between linked genes , where one of the linked genes physically crosses over to a different chromosome . Two decades later , Barbara McClintock and Harriet Creighton demonstrated that chromosomal crossover occurs during meiosis , the process of cell division by which sperm and egg cells are made . Within the same year as McClintock 's discovery , Curt Stern showed that crossing over β€” later called " recombination " β€” could also occur in somatic cells like white blood cells and skin cells that divide through mitosis .
In 1947 , the microbiologist Joshua Lederberg showed that bacteria β€” which had been assumed to reproduce only asexually through binary fission β€” are capable of genetic recombination , which is more similar to sexual reproduction . This work established E. coli as a model organism in genetics , and helped Lederberg win the 1958 Nobel Prize in Physiology or Medicine . Building on studies in fungi , in 1964 Robin Holliday proposed a model for recombination in meiosis which introduced key details of how the process can work , including the exchange of material between chromosomes through Holliday junctions . In 1983 , Jack Szostak and colleagues presented a model now known as the DSBR pathway , which accounted for observations not explained by the Holliday model . During the next decade , experiments in Drosophila , budding yeast and mammalian cells led to the emergence of other models of homologous recombination , called SDSA pathways , which do not always rely on Holliday junctions .
= = In eukaryotes = =
Homologous recombination ( HR ) is essential to cell division in eukaryotes like plants , animals , fungi and protists . In cells that divide through mitosis , homologous recombination repairs double @-@ strand breaks in DNA caused by ionizing radiation or DNA @-@ damaging chemicals . Left unrepaired , these double @-@ strand breaks can cause large @-@ scale rearrangement of chromosomes in somatic cells , which can in turn lead to cancer .
In addition to repairing DNA , homologous recombination also helps produce genetic diversity when cells divide in meiosis to become specialized gamete cells β€” sperm or egg cells in animals , pollen or ovules in plants , and spores in fungi . It does so by facilitating chromosomal crossover , in which regions of similar but not identical DNA are exchanged between homologous chromosomes . This creates new , possibly beneficial combinations of genes , which can give offspring an evolutionary advantage . Chromosomal crossover often begins when a protein called Spo11 makes a targeted double @-@ strand break in DNA . These sites are non @-@ randomly located on the chromosomes ; usually in intergenic promoter regions and preferentially in GC @-@ rich domains These double @-@ strand break sites often occur at recombination hotspots , regions in chromosomes that are about 1 @,@ 000 – 2 @,@ 000 base pairs in length and have high rates of recombination . The absence of a recombination hotspot between two genes on the same chromosome often means that those genes will be inherited by future generations in equal proportion . This represents linkage between the two genes greater than would be expected from genes that independently assort during meiosis .
= = = Timing within the mitotic cell cycle = = =
Double @-@ strand breaks can be repaired through homologous recombination or through non @-@ homologous end joining ( NHEJ ) . NHEJ is a DNA repair mechanism which , unlike homologous recombination , does not require a long homologous sequence to guide repair . Whether homologous recombination or NHEJ is used to repair double @-@ strand breaks is largely determined by the phase of cell cycle . Homologous recombination repairs DNA before the cell enters mitosis ( M phase ) . It occurs during and shortly after DNA replication , in the S and G2 phases of the cell cycle , when sister chromatids are more easily available . Compared to homologous chromosomes , which are similar to another chromosome but often have different alleles , sister chromatids are an ideal template for homologous recombination because they are an identical copy of a given chromosome . In contrast to homologous recombination , NHEJ is predominant in the G1 phase of the cell cycle , when the cell is growing but not yet ready to divide . It occurs less frequently after the G1 phase , but maintains at least some activity throughout the cell cycle . The mechanisms that regulate homologous recombination and NHEJ throughout the cell cycle vary widely between species .
<unk> @-@ dependent kinases ( <unk> ) , which modify the activity of other proteins by adding phosphate groups to ( that is , <unk> ) them , are important regulators of homologous recombination in eukaryotes . When DNA replication begins in budding yeast , the cyclin @-@ dependent kinase <unk> begins homologous recombination by <unk> the Sae2 protein . After being so activated by the addition of a phosphate , Sae2 uses its endonuclease activity to make a clean cut near a double @-@ strand break in DNA . This allows a three @-@ part protein known as the MRX complex to bind to DNA , and begins a series of protein @-@ driven reactions that exchange material between two DNA molecules .
= = = Models = = =
Two primary models for how homologous recombination repairs double @-@ strand breaks in DNA are the double @-@ strand break repair ( DSBR ) pathway ( sometimes called the double Holliday junction model ) and the synthesis @-@ dependent strand annealing ( SDSA ) pathway . The two pathways are similar in their first several steps . After a double @-@ strand break occurs , the MRX complex ( MRN complex in humans ) binds to DNA on either side of the break . Next a resection , in which DNA around the 5 ' ends of the break is cut back , is carried out in two distinct steps . In the first step of resection , the MRX complex recruits the Sae2 protein . The two proteins then trim back the 5 ' ends on either side of the break to create short 3 ' overhangs of single @-@ strand DNA . In the second step , 5 ' β†’ 3 ' resection is continued by the Sgs1 helicase and the <unk> and <unk> nucleases . As a helicase , Sgs1 " <unk> " the double @-@ strand DNA , while <unk> and <unk> 's nuclease activity allows them to cut the single @-@ stranded DNA produced by Sgs1 .
The RPA protein , which has high affinity for single @-@ stranded DNA , then binds the 3 ' overhangs . With the help of several other proteins that mediate the process , the Rad51 protein ( and Dmc1 , in meiosis ) then forms a filament of nucleic acid and protein on the single strand of DNA coated with RPA . This nucleoprotein filament then begins searching for DNA sequences similar to that of the 3 ' overhang . After finding such a sequence , the single @-@ stranded nucleoprotein filament moves into ( invades ) the similar or identical recipient DNA duplex in a process called strand invasion . In cells that divide through mitosis , the recipient DNA duplex is generally a sister chromatid , which is identical to the damaged DNA molecule and provides a template for repair . In meiosis , however , the recipient DNA tends to be from a similar but not necessarily identical homologous chromosome . A displacement loop ( D @-@ loop ) is formed during strand invasion between the invading 3 ' overhang strand and the homologous chromosome . After strand invasion , a DNA polymerase extends the end of the invading 3 ' strand by synthesizing new DNA . This changes the D @-@ loop to a cross @-@ shaped structure known as a Holliday junction . Following this , more DNA synthesis occurs on the invading strand ( i.e. , one of the original 3 ' overhangs ) , effectively restoring the strand on the homologous chromosome that was displaced during strand invasion .
= = = = DSBR pathway = = = =
After the stages of resection , strand invasion and DNA synthesis , the DSBR and SDSA pathways become distinct . The DSBR pathway is unique in that the second 3 ' overhang ( which was not involved in strand invasion ) also forms a Holliday junction with the homologous chromosome . The double Holliday junctions are then converted into recombination products by nicking endonucleases , a type of restriction endonuclease which cuts only one DNA strand . The DSBR pathway commonly results in crossover , though it can sometimes result in non @-@ crossover products ; the ability of a broken DNA molecule to collect sequences from separated donor loci was shown in mitotic budding yeast using plasmids or endonuclease induction of chromosomal events . Because of this tendency for chromosomal crossover , the DSBR pathway is a likely model of how crossover homologous recombination occurs during meiosis .
Whether recombination in the DSBR pathway results in chromosomal crossover is determined by how the double Holliday junction is cut , or " resolved " . Chromosomal crossover will occur if one Holliday junction is cut on the crossing strand and the other Holliday junction is cut on the non @-@ crossing strand ( in Figure 4 , along the horizontal purple arrowheads at one Holliday junction and along the vertical orange arrowheads at the other ) . Alternatively , if the two Holliday junctions are cut on the crossing strands ( along the horizontal purple arrowheads at both Holliday junctions in Figure 4 ) , then chromosomes without crossover will be produced .
= = = = SDSA pathway = = = =
Homologous recombination via the SDSA pathway occurs in cells that divide through mitosis and meiosis and results in non @-@ crossover products . In this model , the invading 3 ' strand is extended along the recipient DNA duplex by a DNA polymerase , and is released as the Holliday junction between the donor and recipient DNA molecules slides in a process called branch migration . The newly synthesized 3 ' end of the invading strand is then able to anneal to the other 3 ' overhang in the damaged chromosome through complementary base pairing . After the strands anneal , a small flap of DNA can sometimes remain . Any such flaps are removed , and the SDSA pathway finishes with the resealing , also known as ligation , of any remaining single @-@ stranded gaps .
During mitosis , the major homologous recombination pathway for repairing DNA double @-@ strand breaks appears to be the SDSA pathway ( rather than the DSBR pathway ) . The SDSA pathway produces non @-@ crossover recombinants ( Figure 4 ) . During meiosis non @-@ crossover recombinants also occur frequently and these appear to arise mainly by the SDSA pathway as well . Non @-@ crossover recombination events occurring during meiosis likely reflect instances of repair of DNA double @-@ strand damages or other types of DNA damages .
= = = = SSA pathway = = = =
The single @-@ strand annealing ( SSA ) pathway of homologous recombination repairs double @-@ strand breaks between two repeat sequences . The SSA pathway is unique in that it does not require a separate similar or identical molecule of DNA , like the DSBR or SDSA pathways of homologous recombination . Instead , the SSA pathway only requires a single DNA duplex , and uses the repeat sequences as the identical sequences that homologous recombination needs for repair . The pathway is relatively simple in concept : after two strands of the same DNA duplex are cut back around the site of the double @-@ strand break , the two resulting 3 ' overhangs then align and anneal to each other , restoring the DNA as a continuous duplex .
As DNA around the double @-@ strand break is cut back , the single @-@ stranded 3 ' overhangs being produced are coated with the RPA protein , which prevents the 3 ' overhangs from sticking to themselves . A protein called <unk> then binds each of the repeat sequences on either side of the break , and aligns them to enable the two complementary repeat sequences to anneal . After annealing is complete , leftover non @-@ homologous flaps of the 3 ' overhangs are cut away by a set of nucleases , known as <unk> / <unk> , which are brought to the flaps by the <unk> and <unk> proteins . New DNA synthesis fills in any gaps , and ligation restores the DNA duplex as two continuous strands . The DNA sequence between the repeats is always lost , as is one of the two repeats . The SSA pathway is considered mutagenic since it results in such deletions of genetic material .
= = = = BIR pathway = = = =
During DNA replication , double @-@ strand breaks can sometimes be encountered at replication forks as DNA helicase <unk> the template strand . These defects are repaired in the break @-@ induced replication ( BIR ) pathway of homologous recombination . The precise molecular mechanisms of the BIR pathway remain unclear . Three proposed mechanisms have strand invasion as an initial step , but they differ in how they model the migration of the D @-@ loop and later phases of recombination .
The BIR pathway can also help to maintain the length of telomeres ( regions of DNA at the end of eukaryotic chromosomes ) in the absence of ( or in cooperation with ) telomerase . Without working copies of the telomerase enzyme , telomeres typically shorten with each cycle of mitosis , which eventually blocks cell division and leads to senescence . In budding yeast cells where telomerase has been inactivated through mutations , two types of " survivor " cells have been observed to avoid senescence longer than expected by elongating their telomeres through BIR pathways .
Maintaining telomere length is critical for cell immortalization , a key feature of cancer . Most cancers maintain telomeres by <unk> telomerase . However , in several types of human cancer , a BIR @-@ like pathway helps to sustain some tumors by acting as an alternative mechanism of telomere maintenance . This fact has led scientists to investigate whether such recombination @-@ based mechanisms of telomere maintenance could thwart anti @-@ cancer drugs like telomerase inhibitors .
= = In bacteria = =
Homologous recombination is a major DNA repair process in bacteria . It is also important for producing genetic diversity in bacterial populations , although the process differs substantially from meiotic recombination , which repairs DNA damages and brings about diversity in eukaryotic genomes . Homologous recombination has been most studied and is best understood for Escherichia coli . Double @-@ strand DNA breaks in bacteria are repaired by the RecBCD pathway of homologous recombination . Breaks that occur on only one of the two DNA strands , known as single @-@ strand gaps , are thought to be repaired by the RecF pathway . Both the RecBCD and RecF pathways include a series of reactions known as branch migration , in which single DNA strands are exchanged between two intercrossed molecules of duplex DNA , and resolution , in which those two intercrossed molecules of DNA are cut apart and restored to their normal double @-@ stranded state .
= = = RecBCD pathway = = =
The RecBCD pathway is the main recombination pathway used in many bacteria to repair double @-@ strand breaks in DNA , and the proteins are found in a broad array of bacteria . These double @-@ strand breaks can be caused by UV light and other radiation , as well as chemical mutagens . Double @-@ strand breaks may also arise by DNA replication through a single @-@ strand nick or gap . Such a situation causes what is known as a collapsed replication fork and is fixed by several pathways of homologous recombination including the RecBCD pathway .
In this pathway , a three @-@ subunit enzyme complex called RecBCD initiates recombination by binding to a blunt or nearly blunt end of a break in double @-@ strand DNA . After RecBCD binds the DNA end , the RecB and <unk> subunits begin unzipping the DNA duplex through helicase activity . The RecB subunit also has a nuclease domain , which cuts the single strand of DNA that emerges from the unzipping process . This unzipping continues until RecBCD encounters a specific nucleotide sequence ( 5 ' <unk> @-@ 3 ' ) known as a Chi site .
Upon encountering a Chi site , the activity of the RecBCD enzyme changes drastically . DNA unwinding pauses for a few seconds and then resumes at roughly half the initial speed . This is likely because the slower RecB helicase unwinds the DNA after Chi , rather than the faster <unk> helicase , which unwinds the DNA before Chi . Recognition of the Chi site also changes the RecBCD enzyme so that it cuts the DNA strand with Chi and begins loading multiple RecA proteins onto the single @-@ stranded DNA with the newly generated 3 ' end . The resulting RecA @-@ coated nucleoprotein filament then searches out similar sequences of DNA on a homologous chromosome . The search process induces stretching of the DNA duplex , which enhances homology recognition ( a mechanism termed conformational proofreading ) . Upon finding such a sequence , the single @-@ stranded nucleoprotein filament moves into the homologous recipient DNA duplex in a process called strand invasion . The invading 3 ' overhang causes one of the strands of the recipient DNA duplex to be displaced , to form a D @-@ loop . If the D @-@ loop is cut , another swapping of strands forms a cross @-@ shaped structure called a Holliday junction . Resolution of the Holliday junction by some combination of RuvABC or <unk> can produce two recombinant DNA molecules with reciprocal genetic types , if the two interacting DNA molecules differ genetically . Alternatively , the invading 3 ’ end near Chi can prime DNA synthesis and form a replication fork . This type of resolution produces only one type of recombinant ( non @-@ reciprocal ) .
= = = RecF pathway = = =
Bacteria appear to use the RecF pathway of homologous recombination to repair single @-@ strand gaps in DNA . When the RecBCD pathway is inactivated by mutations and additional mutations inactivate the <unk> and <unk> nucleases , the RecF pathway can also repair DNA double @-@ strand breaks . In the RecF pathway the <unk> helicase unwinds the DNA and the <unk> nuclease degrades the strand with a 5 ’ end , leaving the strand with the 3 ’ end intact . RecA protein binds to this strand and is either aided by the RecF , <unk> , and <unk> proteins or stabilized by them . The RecA nucleoprotein filament then searches for a homologous DNA and exchanges places with the identical or nearly identical strand in the homologous DNA .
Although the proteins and specific mechanisms involved in their initial phases differ , the two pathways are similar in that they both require single @-@ stranded DNA with a 3 ’ end and the RecA protein for strand invasion . The pathways are also similar in their phases of branch migration , in which the Holliday junction slides in one direction , and resolution , in which the Holliday junctions are cleaved apart by enzymes . The alternative , non @-@ reciprocal type of resolution may also occur by either pathway .
= = = Branch migration = = =
Immediately after strand invasion , the Holliday junction moves along the linked DNA during the branch migration process . It is in this movement of the Holliday junction that base pairs between the two homologous DNA duplexes are exchanged . To catalyze branch migration , the RuvA protein first recognizes and binds to the Holliday junction and recruits the RuvB protein to form the <unk> complex . Two sets of the RuvB protein , which each form a ring @-@ shaped ATPase , are loaded onto opposite sides of the Holliday junction , where they act as twin pumps that provide the force for branch migration . Between those two rings of RuvB , two sets of the RuvA protein assemble in the center of the Holliday junction such that the DNA at the junction is sandwiched between each set of RuvA . The strands of both DNA duplexes β€” the " donor " and the " recipient " duplexes β€” are unwound on the surface of RuvA as they are guided by the protein from one duplex to the other .
= = = Resolution = = =