5M1W

Structure of a stable G-hairpin

Summary for 5M1W

• Entry DOI: 10.2210/pdb5m1w/pdb
• NMR Information: BMRB: 34053
• Descriptor: DNA (5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3') (1 entity in total)
• Functional Keywords: g-hairpin g:g base pairs nmr spectroscopy conformational exchange, dna
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 3476.25

Authors

Gajarsky, M.,Zivkovic, M.L.,Stadlbauer, P.,Pagano, B.,Fiala, R.,Amato, J.,Tomaska, L.,Sponer, J.,Plavec, J.,Trantirek, L. (deposition date: 2016-10-11, release date: 2017-03-01, Last modification date: 2024-05-15)

Primary citation

Gajarsky, M.,Zivkovic, M.L.,Stadlbauer, P.,Pagano, B.,Fiala, R.,Amato, J.,Tomaska, L.,Sponer, J.,Plavec, J.,Trantirek, L.
Structure of a Stable G-Hairpin.
J. Am. Chem. Soc., 139:3591-3594, 2017

PubMed Abstract: In this study, we report the first atomic resolution structure of a stable G-hairpin formed by a natively occurring DNA sequence. An 11-nt long G-rich DNA oligonucleotide, 5'-d(GTGTGGGTGTG)-3', corresponding to the most abundant sequence motif in irregular telomeric DNA from Saccharomyces cerevisiae (yeast), is demonstrated to adopt a novel type of mixed parallel/antiparallel fold-back DNA structure, which is stabilized by dynamic G:G base pairs that transit between N1-carbonyl symmetric and N1-carbonyl, N7-amino base-pairing arrangements. Although the studied sequence first appears to possess a low capacity for base pairing, it forms a thermodynamically stable structure with a rather complex topology that includes a chain reversal arrangement of the backbone in the center of the continuous G-tract and 3'-to-5' stacking of the terminal residues. The structure reveals previously unknown principles of the folding of G-rich oligonucleotides that could be applied to the prediction of natural and/or the design of artificial recognition DNA elements. The structure also demonstrates that the folding landscapes of short DNA single strands is much more complex than previously assumed.

PubMed: 28217994
DOI: 10.1021/jacs.6b10786

Experimental method

SOLUTION NMR