Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations

Understanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selectively switched off the hydrogen bonds (one specific bond or their combinations in all the base pairs at a time) via manipulating the force fields for A-T and G-C base pairs. We studied 12 systems in total via all-atom explicit-solvent molecular dynamics simulations (200 ns each). The MD output structures were compared with the control system by means of structural, dynamic, and energetic properties to monitor the overall consequences of removing H-bond(s) on the B-DNA characteristics of the model systems. Our findings suggest that all the individual hydrogen bonds involved in base pairing are vital for maintaining the DNA structural integrity as any possible alteration in Watson-Crick hydrogen bond(s) leads to the disintegration/collapse of DNA strands resulting in unfolded states.

Automated summary

Understanding the role of base pairing and stacking is crucial for understanding the structure of DNA. Computational and experimental studies suggest that base pairing is more important than stacking for duplex stability. This study selectively turned off hydrogen bonds and found that all individual hydrogen bonds are vital for maintaining the structural integrity of DNA.