2HK4

Dimeric solution structure of the cyclic octamer d(CCGTCCGT)

Summary for 2HK4

• Entry DOI: 10.2210/pdb2hk4/pdb
• Related: 184D 1EU2 1EU6 1N96 284D
• Descriptor: 5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' (1 entity in total)
• Functional Keywords: cyclic oligonucleotide, quadruplex, minor groove tetrads, dna
• Total number of polymer chains: 2
• Total formula weight: 4757.13

Authors

Escaja, N.,Gomez-Pinto, I.,Pedroso, E.,Gonzalez, C. (deposition date: 2006-07-03, release date: 2007-03-20, Last modification date: 2024-05-29)

Primary citation

Escaja, N.,Gomez-Pinto, I.,Pedroso, E.,Gonzalez, C.
Four-stranded DNA structures can be stabilized by two different types of minor groove G:C:G:C tetrads.
J.Am.Chem.Soc., 129:2004-2014, 2007

PubMed Abstract: Four-stranded nucleic acid structures are central to many processes in biology and in supramolecular chemistry. It has been shown recently that four-stranded DNA structures are not only limited to the classical guanine quadruplex but also can be formed by tetrads resulting from the association of Watson-Crick base pairs. Such an association may occur through the minor or the major groove side of the base pairs. Structures stabilized by minor groove tetrads present distinctive features, clearly different from the canonical guanine quadruplex, making these quadruplexes a unique structural motif. Within our efforts to study the sequence requirements for the formation of this unusual DNA motif, we have determined the solution structure of the cyclic oligonucleotide dpCCGTCCGT by two-dimensional NMR spectroscopy and restrained molecular dynamics. This molecule self-associates, forming a symmetric dimer stabilized by two G:C:G:C tetrads with intermolecular G-C base pairs. Interestingly, although the overall three-dimensional structure is similar to that found in other cyclic and linear oligonucleotides of related sequences, the tetrads that stabilize the structure of dpCCGTCCGT are different to other minor groove G:C:G:C tetrads found earlier. Whereas in previous cases the G-C base pairs aligned directly, in this new tetrad the relative position of the two base pairs is slipped along the axis defined by the base pairs. This is the first time that a quadruplex structure entirely stabilized by slipped minor groove G:C:G:C tetrads is observed in solution or in the solid state. However, an analogous arrangement of G-C base pairs occurs between the terminal residues of contiguous duplexes in some DNA crystals. This structural polymorphism between minor groove GC tetrads may be important in stabilization of higher order DNA structures.

PubMed: 17260988
DOI: 10.1021/ja066172z

Experimental method

SOLUTION NMR