Effect of the Base-Pair Sequence on B-DNA Thermal Conductivity

V Mahalingam and D Harursampath, JOURNAL OF PHYSICAL CHEMISTRY B, 125, 10652-10656 (2021).

DOI: 10.1021/acs.jpcb.1c04318

The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing the base pair (bp) on the thermal conductivity of dsDNA needed investigation at a molecular level. Hence, four sequences, viz., poly(A), poly(G), poly(CG), and poly(AT), were initially analyzed in this work. First, the length of these sequences was varied from 4 to 40 bp at 300 K, and the respective thermal conductivity (kappa) was computed. Second, the temperature-dependent thermal conductivities between 100 and 400 K were obtained in 50 K steps at 28 bp length. The Miiller-Plathe reverse nonequilibrium molecular dynamics (RNEMD) was employed to set a thermal gradient and obtain all thermal conductivities in this work. Moreover, mixed sequences using AT and CG sequences, namely, A(CG)(n)T (n = 3-7), ACGC(AT)(m)GCGT (m = 0-5), and ACGC(AT)(n)AGCGT (n = 1-4), were investigated based on the hypothesis that these sequences could be better thermoelectrics. One- dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate the Fourier law. These follow the power law, where kappa proportional to L-beta. At longer lengths, the exponent beta needs to satisfy the condition beta > 1/3 for divergent thermal conductivity. We find no such significant Fourier law violation through divergence of thermal conductivities at 80 bp lengths or 40 bp lengths. Also, in the case of the second study, the presence of short (m <= 2) encapsulated AT sequences within CG sequences shows an increasing trend. These results are important for engineering DNA-based thermal devices.

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