2K90

Dimeric solution structure of the DNA loop d(TGCTTCGT)

Summary for 2K90

• Entry DOI: 10.2210/pdb2k90/pdb
• Related: 2k8z 2k97
• NMR Information: BMRB: 16054
• Descriptor: 5'-D(*TP*GP*CP*TP*TP*CP*GP*T)-3' (1 entity in total)
• Functional Keywords: dna, quadruplex, dna-loop, minor groove tetrad
• Total number of polymer chains: 2
• Total formula weight: 4817.18

Authors

Viladoms, J.,Escaja, N.,Frieden, M.,Gomez-Pinto, I.,Pedroso, E.,Gonzalez, C. (deposition date: 2008-09-29, release date: 2009-04-28, Last modification date: 2024-05-08)

Primary citation

Viladoms, J.,Escaja, N.,Frieden, M.,Gomez-Pinto, I.,Pedroso, E.,Gonzalez, C.
Self-association of short DNA loops through minor groove C:G:G:C tetrads.
Nucleic Acids Res., 37:3264-3275, 2009

PubMed Abstract: In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes.

PubMed: 19321501
DOI: 10.1093/nar/gkp191

Experimental method

SOLUTION NMR