Predicting nucleic acid energetics and thermodynamic properties in duplexes is essential for a physical understanding of their cellular functions and biological applications in fields of medical diagnostics and biotechnology such as PCR techniques, sequencing by hybridization, antigen targeting, and Southern blotting. The nucleobases in the sequence of a genome must be correctly ordered and paired to their opposing complementary bases in the duplex for DNA binding molecules to bind and accurately read the instructions to produce a set of proteins and biomolecules required by the cell. Therefore, having accurate DNA thermodynamics is fundamental to the function of cellular processes, as the amount of energy required for many DNA binding molecules to open the duplex and interact with the nucleobase is a critical factor in its molecular recognition. Interactions such as hydrogen bonding and pi-pi stacking in DNA and protein complexes play important roles in determining which of the possibilities of active and non-active conformations are populated under a given set of conditions by these large biomolecules, as their energetic landscape is sensitive to the physicochemical conditions they experience. Therefore, detecting and measuring the strengths of these noncovalent interactions to determine their contributions to the stability of the whole nucleic acid assembly is of substantial interest for optimizing duplex hybridization reactions. Prediction of the melting temperature for even short duplexes from primary sequence information alone remains an active area of research due to dependencies of the total melting temperature on nearest neighbor interactions exhibited by these biopolymers. While substantial work was performed to measure the contribution of sequence order to duplex structural stability, few "thermometers" exist that are small enough to measure transitions of individual base pairs located at specified duplex positions, as this would require a minimum molecular-level spatial resolution of the probe. Fluorophores are a well-known probe for sensing local environments in duplexes, and their high signal can simplify the time and effort required to collect a complete set of thermodynamic increments. However, incorporating these fluorescent probes alters the molecular structure of the sensitive duplex, and the detection method is no longer label-free. While NMR has been applied for this purpose, it remains experimentally challenging to measure local values for a transition temperature at an arbitrary sequence proton due to the size and chemical exchange of the protons. Infrared spectroscopy (IR) has a long history of applications performing solution-state temperature-dependent measurements of nucleic acid melting. The vibrations of DNA duplexes are wellknown to exhibit temperature dependence, and both IR and Raman spectroscopy have been used to measure the global transition temperature of short duplexes. The fact that normal modes in some bases are at unique frequencies in a duplexed spectrum is exploited to obtain more localized measurements of local structural stability with carefully designed sequences. However, these polymeric biomolecules contain a large amount of vibrational degrees of freedom, resulting in an overlapped and congested duplex IR spectrum, limiting the spatial resolution of the measurement. Nucleobase isotope editing is an underdeveloped method for measuring the frequencies of vibrations of bases at specific locations in a given DNA sequence. Isotope editing methodologies overcome the limitations of linear IR by utilizing spectral subtraction to locate a signal from a specific base in a given sequence. In these experiments, the IR of a DNA structure containing an isotopically labeled atom in one of its bases is subtracted from the spectrum of the molecule that is identical in sequence but contains all light atoms. Signals from normal modes that do not involve displacement of the atom at the labeled position are mostly canceled out, and the signals from a few atoms in the high molecular weight duplex structure can be identified as positive and negative features in the isotopic difference spectrum.