CUP Faculty Research
Title
Structure and Dynamics of GNA: A Molecular Dynamics Study
Document Type
Poster
Publication Date
1-1-2010
Abstract
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.
Recommended Citation
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.
https://digitalcommons.csp.edu/cup_commons_faculty/135
Source
CU Commons -- Math and Science Department Faculty Research
Comments
Publication Information.
Johnson, A. T., Wiest, O., Essen, L.-O., & Meggers, E. (2010). Structure and dynamics of GNA: A molecular dynamics study. Poster presented at the 239th ACS National Meeting, San Francisco, CA. Abstract retrieved from acselb-529643017.us-west-2.elb.amazonaws.com/chem/239nm/program/view.php?obj_id=13605