Article

Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.

Department of Chemistry, University of York, Heslington, York YO1 5DD, England.
Acta Crystallographica Section D Biological Crystallography (impact factor: 12.62). 12/1998; 54(Pt 6 Pt 2):1273-84.
Source: PubMed

ABSTRACT The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.

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    Article: Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.
    James H Thorpe, Susana C M Teixeira, Benjamin C Gale, Christine J Cardin
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    ABSTRACT: Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.
    Nucleic Acids Research 03/2003; 31(3):844-9. · 8.03 Impact Factor
Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.

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Keywords

'pure spermine form' [Egli
 
A. Hexamer duplexes
 
al
 
cobalt hexammine molecules
 
different cell dimensions
 
interactions
 
metal cations Na+
 
metal ions
 
Nucleic Acid Database
 
observed pattern
 
phosphate binding
 
reported structure
 
small proportion
 
water structure
 
X-ray crystal structure
 
Z-DNA conformation