DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

Abstract

DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, we obtain a nearly 1/3 reduction but only at low salt concentrations. At higher salt concentrations, terminal adenine-thymine (AT) pair has almost the same hydrogen bond strength than interior bases. The calculated terminal stacking interaction parameters display some peculiarly contrasting behavior. While there is mostly no perceptible difference to internal stacking, for some cases, we observe an unusually strong dependence with salt concentration which does not appear follow any pattern or trend.

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

“…Explicitly, it is known that the interaction potential emanating from the formation of HBs between basepairs stabilizes the canonical B-DNA structure, and consequently the breaking of HBs gives rise to a melted DNA [73]. Thus, the number of HBs is an important quantity in monitoring conformational changes that occur during the pulling of B-DNA.…”

Twist-stretch profiles of DNA chains

“…This has also been suggested more recently by molecular dynamics simulations [78] and analysis of (un)looping probabilities in short chains based on single molecule fluorescence resonance energy transfer [79]. While the polymer flexibility can be directly related to the average bending angles between any two distant monomers [80,81], computation of persistence length has shown that linear short sequences have an intrinsic flexibility mainly ascribed to their terminal base pairs [42,82].…”

Molecular dynamics simulation of a DNA duplex labeled with triarylmethyl spin radicals

“…This process is often referred to as "fraying", which occurs for pairs of complementary bases. Study of this phenomenon is the subject of many experimental investigations [18][19][20][21], as well as of theoretical ones and of computer simulation [22][23][24][25][26][27][28][29].…”