Primary Citation PubMed: 8263919
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Effects of abasic sites on structural, thermodynamic and kinetic properties of quadruplex structures.
(2010) Nucleic Acids Res 38
PubMed: 20026588 | PubMedCentral: PMC2847214 | DOI: 10.1093/nar/gkp1087
The initial coordinates for the starting model of the quadruplex [d(TGGGGGT)] 4 were taken from the NMR solution structure of the quadruplex [d(TTGGGGT)] 4 (Protein Data Bank entry number 139D), choos... ng randomly one of the four available structures.
Publication Year: 2010
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
(2011) Nucleic Acids Res 39
PubMed: 21296760 | PubMedCentral: PMC3105399 | DOI: 10.1093/nar/gkr031
The (3SAA + 1SSA) model was built from the human telomeric G-quadruplex 2GKU ( 34 ); AAA was built from the first three G-quartets of the NMR parallel structure 139D ( 35 ).
The respective coordinates were taken from the first and the second G-quartets of the parallel quadruplex d(TTGGGGT) 4 NMR solution structure [( 35 ); PDB: 139D; the first model was used].
Publication Year: 2011
Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.
(2011) J Am Chem Soc 133
PubMed: 21761922 | PubMedCentral: PMC3168932 | DOI: 10.1021/ja107805r
( 56 ) Methods Starting Structures All of the L n , L w , D , and P 3 a models were built from the NMR structure 2GKU ;( 56 ) the P 2 a models were built from the 1L34 structure;( 57 ) the P 4 a stems... were built from the crystal structure 1JPQ with two loop K + ions removed from the initial structure;( 58 ) and the stem structures of the P 3 p / P 4 p models were obtained from the first three/four G-quartets of the 139D structure, respectively.
The insertion of two 8-methyl-2'-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands.
(2012) Nucleic Acids Res 40
PubMed: 21908403 | PubMedCentral: PMC3245916 | DOI: 10.1093/nar/gkr670
In all cases, with the exception of F13 , the initial coordinates for the starting models of the quadruplexes [d(TGGGGT)] 4 and [d(TGGGT)] 4 (for the G4-run and G3-run series, respectively) were taken... from the NMR solution structure of the quadruplex [d(TTGGGGT)] 4 (Protein Data Bank entry number 139D), with one of the four available structures chosen randomly.
Publication Year: 2012
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