Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations

Int J Mol Sci. 2022 Nov 21;23(22):14452. doi: 10.3390/ijms232214452.

Abstract

Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.

Keywords: DNA; DNA secondary structure; single-stranded DNA.

MeSH terms

  • DNA* / chemistry
  • DNA, B-Form*
  • DNA, Single-Stranded
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation

Substances

  • DNA
  • DNA, Single-Stranded
  • DNA, B-Form