1OCI

[3.2.0]bcANA:DNA

Summary for 1OCI

• Entry DOI: 10.2210/pdb1oci/pdb
• Descriptor: 5'-D(*CP*TP*GP*A TLBP*AP*TP*GP*CP)-3', 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*GP)-3' (2 entities in total)
• Functional Keywords: deoxyribonucleic acid, arabino nucleic acid, dna, rnase h
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 5498.65

Authors

Tommerholt, H.V.,Christensen, N.K.,Nielsen, P.,Wengel, J.,Stein, P.C.,Jacobsen, J.P.,Petersen, M. (deposition date: 2003-02-07, release date: 2003-07-14, Last modification date: 2024-05-15)

Primary citation

Tommerholt, H.V.,Christensen, N.K.,Nielsen, P.,Wengel, J.,Stein, P.C.,Jacobsen, J.P.,Petersen, M.
NMR Solution Structure of a DsDNA Containing a Bicyclic D-Arabino-Configured Nucleotide Fixed in an O4'-Endo Sugar Conformation
Org.Biomol.Chem., 1:1790-1797, 2003

PubMed Abstract: [3.2.0]bcANA is a D-arabino-configured bicyclic nucleotide with a 2'-O,3'-C-methylene bridge. We here present the high-resolution NMR structure of a [3.2.0]bcANA modified dsDNA nonamer with one modified nucleotide incorporated. NOE restraints were obtained by analysis of NOESY cross peak intensities using a full relaxation matrix approach, and subsequently these restraints were incorporated into a simulated annealing scheme for the structure determination. In addition, the furanose ring puckers of the deoxyribose moieties were determined by analysis of COSY cross peaks. The modified duplex adopts a B-like geometry with Watson-Crick base pairing in all base pairs and all glycosidic angles in the anti range. The stacking arrangement of the nucleobases appears to be unperturbed relative to the normal B-like arrangement. The 2'-O,3'-C-methylene bridge of the modified nucleotide is located at the brim of the major groove where it fits well into the B-type duplex framework. The sugar pucker of the [3.2.0]bcANA nucleotide is O4'-endo and this sugar conformation causes a change in the delta backbone angle relative to the C2'-endo deoxyribose sugar pucker. This change is absorbed locally by slight changes in the epsilon and zeta angles of the modified nucleotide. Overall, the [3.2.0]bcANA modifications fits very well into a B-like duplex framework and only small and local perturbations are observed relative to the unmodified dsDNA of identical base sequence.

PubMed: 12926371
DOI: 10.1039/B300848G

Experimental method

SOLUTION NMR