284D

THE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF

Summary for 284D

• Entry DOI: 10.2210/pdb284d/pdb
• Descriptor: DNA (5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3'), SODIUM ION, BARIUM ION, ... (4 entities in total)
• Functional Keywords: cyclic b-dna, quadruple helix, bi-loop, dna
• Total number of polymer chains: 2
• Total formula weight: 6286.77

Authors

Salisbury, S.A.,Wilson, S.E.,Powell, H.R.,Kennard, O.,Lubini, P.,Sheldrick, G.M.,Escaja, N.,Alazzouzi, E.,Grandas, A.,Pedroso, E. (deposition date: 1996-09-11, release date: 1997-06-11, Last modification date: 2024-02-14)

Primary citation

Salisbury, S.A.,Wilson, S.E.,Powell, H.R.,Kennard, O.,Lubini, P.,Sheldrick, G.M.,Escaja, N.,Alazzouzi, E.,Grandas, A.,Pedroso, E.
The bi-loop, a new general four-stranded DNA motif.
Proc.Natl.Acad.Sci.USA, 94:5515-5518, 1997

PubMed Abstract: The crystal structure of the cyclic octanucleotide d contains two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking. A virtually identical quadruplex composed of G.C pairs was found by earlier x-ray analysis of the linear heptamer d(GCATGCT), when the DNA was looped in the crystal. The close correspondence between these two structures of markedly dissimilar oligonucleotides suggests that they are both examples of a previously unrecognized motif. Their nucleotide sequences have little in common except for two separated 5'-purine-pyrimidine dinucleotides forming the quadruplex, and by implication these so-called "bi-loops" could occur widely in natural DNA. Such structures provide a mechanism for noncovalent linking of polynucleotides in vivo. Their capacity to associate by base stacking, demonstrated in the crystal structure of d(GCATGCT), creates a compact molecular framework made up of four DNA chains within which strand exchange could take place.

PubMed: 9159103
DOI: 10.1073/pnas.94.11.5515

Experimental method

X-RAY DIFFRACTION (1.1 Å)