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- Title
Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.
- Authors
Capobianco, Amedeo; Landi, Alessandro; Peluso, Andrea
- 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.
- Subjects
QUANTUM computing; DOUBLE helix structure; MOLECULAR dynamics; SINGLE-stranded DNA; DNA; BASE pairs; CYTOSINE
- Publication
International Journal of Molecular Sciences, 2022, Vol 23, Issue 22, p14452
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms232214452