Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations
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-DN...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/22/14452 |
| _version_ | 1797464947882459136 |
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| author | Amedeo Capobianco Alessandro Landi Andrea Peluso |
| author_facet | Amedeo Capobianco Alessandro Landi Andrea Peluso |
| author_sort | Amedeo Capobianco |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T18:15:25Z |
| format | Article |
| id | doaj.art-2020b9ff64ec45f48f5de5c69f47a17b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T18:15:25Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2020b9ff64ec45f48f5de5c69f47a17b2023-11-24T08:44:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123221445210.3390/ijms232214452Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical ComputationsAmedeo Capobianco0Alessandro Landi1Andrea Peluso2Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, ItalyDipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, ItalyDipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, ItalyMolecular 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.https://www.mdpi.com/1422-0067/23/22/14452single-stranded DNADNADNA secondary structure |
| spellingShingle | Amedeo Capobianco Alessandro Landi Andrea Peluso Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations International Journal of Molecular Sciences single-stranded DNA DNA DNA secondary structure |
| title | Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations |
| title_full | Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations |
| title_fullStr | Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations |
| title_full_unstemmed | Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations |
| title_short | Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations |
| title_sort | duplex dna retains the conformational features of single strands perspectives from md simulations and quantum chemical computations |
| topic | single-stranded DNA DNA DNA secondary structure |
| url | https://www.mdpi.com/1422-0067/23/22/14452 |
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