2022
DOI: 10.1021/acs.jpcb.2c01138
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Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations

Abstract: The thermodynamic stability of double-stranded (ds)­DNA depends on its sequence. It is influenced by the base pairing and stacking with neighboring bases along DNA molecules. Semiempirical schemes are available that allow us to predict the thermodynamic stability of DNA sequences based on empirically derived nearest-neighbor contributions of base pairs formed in the context of all possible nearest-neighbor base pairs. Current molecular dynamics (MD) simulations allow one to simulate the dynamics of DNA molecul… Show more

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Cited by 3 publications
(2 citation statements)
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“…Interactions such as hydrogen bonding and pi-pi stacking in DNA and protein complexes play important roles in determining which of the large number of possible conformations are populated by the molecules under a given set of conditions, 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 at 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 strong signal can simplify the time and effort required to collect a complete set of thermodynamic increments.…”
mentioning
confidence: 99%
“…Interactions such as hydrogen bonding and pi-pi stacking in DNA and protein complexes play important roles in determining which of the large number of possible conformations are populated by the molecules under a given set of conditions, 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 at 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 strong signal can simplify the time and effort required to collect a complete set of thermodynamic increments.…”
mentioning
confidence: 99%
“…[31][32][33][34] 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. [35][36][37][38][39][40] 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.…”
mentioning
confidence: 99%