Primary Citation PubMed: 17895279
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Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution.
(2007) Nucleic Acids Res 35
PubMed: 17895279 | PubMedCentral: PMC2095816 | DOI: 10.1093/nar/gkm706
Accession Nos PDB2JSK 2JSL 2JSM 2JSQ INTRODUCTION Guanine-rich DNA sequences can form G-quadruplex structures in vitro through stacking of planar G·G·G·G tetrads ( 1–5 ... .
Data deposition The coordinates for four quadruplex structures formed by the 23-nt and 25-nt natural and Br G-substituted human telomere sequences have been deposited in the Protein Data Bank (accession codes natural-Form 1: 2JSM ; Br G16-Form 1: 2JSK ; natural-Form 2: 2JSL ; Br G15-Form 2: 2JSQ ).
Publication Year: 2007
Applications of isothermal titration calorimetry in biophysical studies of G-quadruplexes.
(2009) Int J Mol Sci 10
PubMed: 19742177 | PubMedCentral: PMC2738904 | DOI: 10.3390/ijms10072935
(c) NMR structure of the G-quadruplex formed by the d[TAG 3 (T 2 AG 3 ) 3 ] sequence (hybrid-1) in K + solution (pdb code: 2JSM).
Publication Year: 2009
Molecular models for intrastrand DNA G-quadruplexes.
(2009) BMC Struct Biol 9
PubMed: 19811654 | PubMedCentral: PMC2768733 | DOI: 10.1186/1472-6807-9-64
143D , 186D , 1KF1 , 1XAV , 230D , 2F8U , 2GKU , 2HY9 , 2JPZ , 2JSL , 2JSM , 2O3M , 201D , 3CDM ), including 230D which contains the nucleotides uridine and inosine-phosphate.
1KF1 , 2GKU , 2HY9 , 2JPZ , 2JSL , 2JSM and 3CDM all contain the core sequence GGGTTAGGGTTAGGGTTAGGG and adopt three different topologies: namely -p-p-p, -l-l-p, -p-l-l.
Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops.
(2013) PLoS One 8
PubMed: 24367632 | PubMedCentral: PMC3867476 | DOI: 10.1371/journal.pone.0084113
Molecular modeling analysis The PDB X-ray structure 1KF1 [ 9 ] and the NMR models 143D [ 7 ], 2HY9 [ 33 ], 2JPZ [ 34 ], 2JSL and 2JSM [ 12 ] related to the telomeric sequence d [AG 3 (T 2 AG 3 ) 3 ], ... ere downloaded from the Protein Data Bank [ 35 ]; http://www.rcsb.org/pdb} to analyze the G-quadruplex structures in wt sequence.
In order to select the mixed model to use as starting point for our calculations, we evaluated the energetic stability of globally 80 receptor structures, since we included both original and optimized experimentally determined conformations of 2HY9 (10 original structures + 10 energy optimized structures), 2JPZ (10 original structures + 10 energy optimized structures), 2JSL (10 original structures + 10 energy optimized structures) and 2JSM (10 original structures + 10 energy optimized structures) NMR models.
Publication Year: 2013
PubMed ID is not available.
Published in 2014
The calibration was done using previously reported NMR structures (PDB ID: 143D, 2GKU, 2HY9, 2JPZ, 2JSL, 2JSM, and 2KF8).
Publication Year: 2014
Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding.
(2014) Nucleic Acids Res 42
PubMed: 25428355 | PubMedCentral: PMC4267657 | DOI: 10.1093/nar/gku1245
Structures of ( a ) hybrid-1 (PDB ID: 2jsm ), and ( b ) hybrid-2 (PDB ID: 2jsl ) quadruplex topology with detailed view of the adenine bases located in the edgewise loops of both structures.
Published in 2015
MATERIALS AND METHODS Structure preparation The initial structure of human telomeric hybrid [3 + 1] form-one G-quadruplex was retrieved from PDB data bank with the entry ID of 2JSM (Phan et al.
Publication Year: 2015
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