Structure and Dynamics of GNA: A Molecular Dynamics Study
Glycol nucleic acid (GNA) is a newly discovered, non-natural nucleic acid consisting of an acyclic propylene glycol phosphodiester backbone. This highly simplified nucleic acid is capable of forming stable duplexes far exceeding the thermodynamic stability of DNA. To this date, the only structure available contains modified nucleobases. In this study we utilize molecular dynamics simulations in order to explore the structure and dynamics of both the modified and unmodified GNA. MD simulations show periodic fluctuations in the backbone RMSDs which are attributed to a “breathing mode” involving a twisting/ untwisting mode. This observation is consistent with thermodynamic analysis which shows the GNA duplex formation is entropically more favorable than DNA. The inherent flexibility of the GNA duplex in comparison to the DNA duplex is discussed in relation to entropic penalties upon annealing.
Johnson, Andrew T.; Wiest, Olaf; Essen, Lars-Oliver; and Meggers, Eric, "Structure and Dynamics of GNA: A Molecular Dynamics Study" (2010). CUP Faculty Research. 135.
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