1BWT

NMR SOLUTION STRUCTURE OF [D(GCGAATCGC)2]

Summary for 1BWT

• Entry DOI: 10.2210/pdb1bwt/pdb
• NMR Information: BMRB: 4235
• Descriptor: DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*GP*C)-3') (1 entity in total)
• Functional Keywords: ecori recognition site, dna
• Total number of polymer chains: 2
• Total formula weight: 6090.01

Authors

Aramini, J.M.,Mujeeb, A.,Germann, M.W. (deposition date: 1998-09-28, release date: 1999-01-06, Last modification date: 2024-05-22)

Primary citation

Aramini, J.M.,Mujeeb, A.,Germann, M.W.
NMR solution structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its unmodified control.
Nucleic Acids Res., 26:5644-5654, 1998

PubMed Abstract: We present the high-resolution solution structures of a self-complementary DNA decamer duplex featuring a single alpha-anomeric nucleotide per strand encompassed by a set of 3'-3' and 5'-5' phosphodiester linkages, d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2, alphaT, and its unmodified control, d(GCGAATTCGC)2, obtained by restrained molecular dynamics. Interproton distance and deoxyribose ring torsion angle restraints were deduced from homonuclear NOESY and DQF-COSY data, respectively. For both the control and alphaT duplexes, excellent global convergence was observed from two different (A- and B-) starting models. The final average structures of the two duplexes are highly homologous, and overall possess the traits characteristic of right-handed B-DNA duplexes. However, localized differences between the two structures stem from the enhanced conformational exchange in the deoxyribose ring of the cytidine following the 5'-5' linkage, the C3'- exo pseudorotation phase angle of the alpha-nucleotide, and unusual backbone torsions in the 3'-3' and 5'-5' phosphodiester linkages. The structural data reported here are relevant to the design of antisense therapeutics comprised of these modifications.

PubMed: 9837995
DOI: 10.1093/nar/26.24.5644

Experimental method

SOLUTION NMR