ArticleNucleic acids research2002
NMR structure of a parallel-stranded DNA duplex at atomic resolution.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Assessment of binding interaction to salmon sperm DNA of two antiviral agents and ecofriendly nanoparticles: comprehensive spectroscopic study.BMC chemistry · 2023Article
- Biophysical Reviews' "Meet the Councilor Series"-a profile of Kandala V. R. Chary.Biophysical reviews · 2021Article
- Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair.Molecules (Basel, Switzerland) · 2020Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms.Scientific reports · 2018Article
- The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwRSC advances · 2018Article
- Structural properties and gene-silencing activity of chemically modified DNA-RNA hybrids with parallel orientation.Nucleic acids research · 2018Article
- Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments.Journal of molecular modeling · 2018Article
- Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.Frontiers in chemistry · 2018Article
- Article
- A bouquet of DNA structures: Emerging diversity.Biochemistry and biophysics reports · 2016Review
- Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides.PloS one · 2015Article
- The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum.PLoS genetics · 2014Article
- Mechanisms of antisense transcription initiation from the 3' end of the GAL10 coding sequence in vivo.Molecular and cellular biology · 2013Article
- Electron correlated ab initio study of amino group flexibility for improvement of molecular mechanics simulations on nucleic acid conformations and interactions.Journal of biological physics · 2007Article
- Hoogsteen-paired homopurine [RP-PS]-DNA and homopyrimidine RNA strands form a thermally stable parallel duplex.Biophysical journal · 2007Article
- Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.Nucleic acids research · 2007Article
- Transcription and translation in an RNA world.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2006Article
- Unusual DNA duplex and hairpin motifs.Nucleic acids research · 2003Review
- Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.Nucleic acids research · 2002Article
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different.
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