Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA


Autoria(s): Heinemann, U; Alings, C; Bansal, Manju
Data(s)

01/05/1992

Resumo

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Formato

application/pdf

Identificador

http://eprints.iisc.ernet.in/35269/1/emboj00090-0259.pdf

Heinemann, U and Alings, C and Bansal, Manju (1992) Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA. In: The EMBO Journal, 11 (5). 1931-1939 .

Publicador

Oxford University Press

Relação

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC556652/?tool=pubmed

http://eprints.iisc.ernet.in/35269/

Palavras-Chave #Molecular Biophysics Unit
Tipo

Journal Article

PeerReviewed