W. Shepard

A ZIPPER-LIKE DUPLEX IN DNA: THE CRYSTAL STRUCTURE OF D(GCGAAAGCT)

William Shepard^¹ , William B.T. Cruse^² , Roger Fourme^¹, Eric de la Fortelle^³ & Thierry Prangé^{^1,2}

¹ LURE, Bât.209d, Université Paris-Sud, 91405-ORSAY Cedex, France.
² Chimie Structurale Biomoléculaire, 93017-BOBIGNY Cedex, France.
³ Laboratory of Molecular Biology, MRC, Hills road, CB2 2QH Cambridge, UK.

The initiation site at the replication origin of the single-stranded DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence d(GCGAAAGC). This sequence comprises of a purine-rich motif (GAAA) which also occurs in centromeric DNA, such as in the CENP-B box and in the highly conserved GNAAT repetitive sequences. Single-stranded DNA analogues of these sequences often show exceptional thermal stabilities which are thought to be associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. NMR studies indicate that the d(GCGAAAGC) sequence forms a hairpin loop in solution [1], while centromere-like analogues dimerise into unusual duplexes [2].

The nonamer d(GC[Br]GAAAGCT) was crystallised as a bromo-5-cytosine-2 derivative in the presence of cobalt hexammine. The crystal structure, solved by the 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 are intercalated and stacked on top of each other, without interstrand Watson-Crick base pairing. The motif is flanked by two sheared G-A mismatches, and the conformation shows some similarities with centromere-like oligonucleotides. The cobalt hexammine cation appears to participate only in crystal cohesion.

Single-stranded DNAs containing the GAAA consensus can form a stable zipper-like duplex as well as a hairpin loop. The arrangement of the phosphate backbone closes the minor groove and exposes the intercalated, unpaired adenines to the solvent or any potential DNA-binding proteins. Such a motif could play a functional role in systems involving single-stranded DNA, palindromes or tandem repeats, and should be considered as an option in DNA secondary structure.

1. Hirao et al. Nucleic Acid Res. 17 (1989) 2223-2231
2. Chou et al. J. Mol. Biol. 267 (1997) 1055-1067