1JUU

NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution

Summary for 1JUU

• Entry DOI: 10.2210/pdb1juu/pdb
• NMR Information: BMRB: 5164
• Descriptor: 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3', 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3' (2 entities in total)
• Functional Keywords: parallel stranded, dna duplex, dna
• Total number of polymer chains: 2
• Total formula weight: 7162.74

Authors

Parvathy, V.R.,Bhaumik, S.R.,Chary, K.V.R.,Govil, G.,Liu, K.,Howard, F.B.,Miles, H.T. (deposition date: 2001-08-28, release date: 2002-04-03, Last modification date: 2024-05-22)

Primary citation

Parvathy, V.R.,Bhaumik, S.R.,Chary, K.V.,Govil, G.,Liu, K.,Howard, F.B.,Miles, H.T.
NMR structure of a parallel-stranded DNA duplex at atomic resolution.
Nucleic Acids Res., 30:1500-1511, 2002

PubMed 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.

PubMed: 11917010
DOI: 10.1093/nar/30.7.1500

Experimental method

SOLUTION NMR