TY - JOUR
T1 - Thermodynamics of DNA Hybridization from Atomistic Simulations
AU - Zerze, Gül H.
AU - Stillinger, Frank H.
AU - Debenedetti, Pablo G.
N1 - Funding Information:
G.H.Z. thanks Daniel Kozuch and Dr. Pablo Piaggi for useful discussions. P.G.D. acknowledges the support of the National Science Foundation (grant CHE-1856704). The simulations presented in this work are performed on computational resources managed and supported by Princeton Research Computing, a consortium of groups including the Princeton Institute for Computational Science and Engineering (PICSciE) and the Office of Information Technology’s High Performance Computing Center and Visualization Laboratory at Princeton University.
Publisher Copyright:
©
PY - 2021/1/28
Y1 - 2021/1/28
N2 - Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- A nd l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
AB - Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- A nd l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
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U2 - 10.1021/acs.jpcb.0c09237
DO - 10.1021/acs.jpcb.0c09237
M3 - Article
C2 - 33434025
AN - SCOPUS:85099977274
SN - 1089-5647
VL - 125
SP - 771
EP - 779
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 3
ER -