title: Structure of a Stable G-Hairpin.
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.
authors.affiliation: Central European Institute of Technology, Masaryk University , Kamenice 753/5, 62500 Brno, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Gajarský
authors.affiliation: Slovenian NMR Centre, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
authors.forename: Martina Lenarčič
authors.initials: ML
authors.lastname: Živković
authors.affiliation: Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic , Kralovopolska 135, 61265 Brno, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Stadlbauer
authors.affiliation: Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, I-80131 Naples, Italy.
authors.forename: Bruno
authors.initials: B
authors.lastname: Pagano
authors.affiliation: Central European Institute of Technology, Masaryk University , Kamenice 753/5, 62500 Brno, Czech Republic.
authors.forename: Radovan
authors.initials: R
authors.lastname: Fiala
authors.affiliation: Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, I-80131 Naples, Italy.
authors.forename: Jussara
authors.initials: J
authors.lastname: Amato
authors.affiliation: Department of Genetics, Faculty of Natural Sciences, Comenius University , Mlynska dolina B-1, Ilkovicova 6, 84215 Bratislava, Slovakia.
authors.forename: L'ubomír
authors.initials: L
authors.lastname: Tomáška
authors.affiliation: Central European Institute of Technology, Masaryk University , Kamenice 753/5, 62500 Brno, Czech Republic.|Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic , Kralovopolska 135, 61265 Brno, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Šponer
authors.affiliation: Slovenian NMR Centre, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.|EN-FIST Centre of Excellence , Trg Osvobodilne fronte 13, SI-1001 Ljubljana, Slovenia.|Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia.
authors.forename: Janez
authors.initials: J
authors.lastname: Plavec
authors.affiliation: Central European Institute of Technology, Masaryk University , Kamenice 753/5, 62500 Brno, Czech Republic.
authors.forename: Lukáš
authors.identifier: 0000-0001-5948-4837
authors.initials: L
authors.lastname: Trantírek
mesh_terms: D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D016615:Telomere / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D006147:Guanine; D004247:DNA