A ZIPPER-LIKE DUPLEX IN DNA - THE CRYSTAL-STRUCTURE OF D(GCGAAAGCT) AT 2.1 ANGSTROM RESOLUTION

Background: The replication origin of the single-stranded (ss)DNA bact eriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GA AA), which also occurs in conserved repetitive sequences of centromeri c DNA, ssDNA analogues of these sequences often show exceptional stabi lity which is associated with hairpin loops or unusual duplexes, and m ay be important in DNA replication and centromere function. Nuclear ma gnetic resonance (NMR) studies indicate that the GCGAAAGC sequence for ms 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 derivati ve in the presence of cobalt hexammine, The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the br omine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheare d GA mismatches, are intercalated and stacked on top of each other wit hout any interstrand Watson-Crick base pairing, The cobalt hexammine c ation appears to participate only in crystal cohesion. Conclusions: Th e GAAA consensus sequence can dimerise into a stable zipper-like duple x 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 ha irpin, should be considered as a structural option in modelling DNA an d as a potential binding site, where it could have a role in DNA repli cation, nuclease resistance, ssDNA genome packaging and centromere fun ction.