376d

[[Image:376d.gif|left|200px]]<br /><applet load="376d" size="350" color="white" frame="true" align="right" spinBox="true"

caption="376d, resolution 2.100&Aring;" />

'''A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)'''<br />

==Overview==

BACKGROUND: The replication origin of the single-stranded (ss)DNA, bacteriophage G4 has been proposed to fold into a hairpin loop containing, the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA., ssDNA analogues of these sequences often show exceptional stability which, is associated with hairpin loops or unusual duplexes, and may be important, in DNA replication and centromere function. Nuclear magnetic resonance, (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in, solution, while centromere-like repeats dimerise into unusual duplexes., The factors stabilising these unusual secondary structure elements in, ssDNA, however, are poorly understood. RESULTS: The nonamer d(GCGAAAGCT), was crystallised as a bromocytosine derivative in the presence of cobalt, hexammine. The crystal structure, solved by the multiple wavelength, anomalous dispersion (MAD) method at the bromine K-edge, reveals an, unexpected zipper-like motif in the middle of a standard B-DNA duplex., Four central adenines, flanked by two sheared G.A mismatches, are, intercalated and stacked on top of each other without any interstrand, Watson-Crick base pairing. The cobalt hexammine cation appears to, participate only in crystal cohesion. CONCLUSIONS: The GAAA consensus, sequence can dimerise into a stable zipper-like duplex as well as forming, a hairpin loop. The arrangement closes the minor groove and exposes the, intercalated, unpaired, adenines to the solvent and DNA-binding proteins., Such a motif, which can transform into a hairpin, should be considered as, a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA, genome packaging and centromere function.

 

==About this Structure==

376D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=376D OCA].

 

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution., Shepard W, Cruse WB, Fourme R, de la Fortelle E, Prange T, Structure. 1998 Jul 15;6(7):849-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9687367 9687367]

[[Category: Protein complex]]

[[Category: Cruse, W.B.T.]]

[[Category: Fourme, R.]]

[[Category: Prange, T.]]

[[Category: Shepard, W.]]

[[Category: delalFortelle, E.]]