NMR structure of a parallel-stranded DNA duplex at atomic resolution

• Published in: Nucleic acids research 2002-04, Vol.30 (7), p.1500-1511
• Main Authors: Parvathy, V. Rani, Bhaumik, Sukesh R., Chary, Kandala V. R., Govil, Girjesh, Liu, Keliang, Howard, Frank B., Miles, H. Todd
• Format: Article
• Language: English
• Subjects: Base Pairing; DNA - chemistry; Hydrogen Bonding; Hydrogen-Ion Concentration; Magnetic Resonance Spectroscopy - methods; Models, Molecular; molecular dynamics; Nucleic Acid Conformation; Nucleic Acid Denaturation; Temperature; Thermodynamics
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/30.7.1500

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.