Primary Citation PubMed: 12050675
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Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.
(2006) Nucleic Acids Res 34
PubMed: 16641317 | PubMedCentral: PMC1449907 | DOI: 10.1093/nar/gkl182
Parallel structures were generated from the d(TAG 3 T 2 AG 3 T) 2 crystal structure, (PDB code 1K8P) ( 1 ) in which a fourth G-quartet was added to the stem after removal of the loops.
Publication Year: 2006
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
(2007) Nucleic Acids Res 35
PubMed: 17913750 | PubMedCentral: PMC2190718 | DOI: 10.1093/nar/gkm711
( a ) X-ray structure of the two-repeat human telomere bimolecular G-quadruplex formed by the d(TAGGGTTAGGGT) sequence for crystals grown from K + solution (coordinates deposition: 1K8P) ( 17 ).
Publication Year: 2007
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex.
(2010) Nucleic Acids Res 38
PubMed: 20413582 | PubMedCentral: PMC2938214 | DOI: 10.1093/nar/gkq259
This mix of C3′- endo and C2′- endo puckering is consistent with the NMR model and with the DNA crystal structure (2KBP and 1K8P respectively), and was also observed in the r(UGGGGU) i... termolecular parallel-stacked quadruplex refined to 0.61 Å resolution ( 46 ).
Sugar puckers consistent between 3IBK and 1K8P are shaded dark grey.
Comparison of the rms deviation between the two RNA models [2KBP—determined by NMR (model 1) and 3IBK determined by X-ray diffraction], and between the two crystal structures (1K8P–DNA quadruplex and 3IBK–RNA quadruplex) rmsd (Å) Whole model Quartets only 3IBK v 1K8P (DNA) 0.990 (470 atoms) 0.539 (232 atoms) 3IBK v 2KBP (NMR) 2.971 (473 atoms) 1.011 (246 atoms) The rms deviations are generated from structural alignments, which can be seen in Figure 1 c and d Crystal packing interactions The two 5′ nts U Br 1 and A2 associate together in the crystal lattice through a 2-fold crystallographic symmetry element forming two stacked U Br AU Br *A* tetrads, to generate a 5′ to 5′ stacked arrangement of two quadruplexes.
Sugar pucker conformations for the 12-mer DNA crystal structure (1K8P), the 12-mer RNA crystal structure (3IBK) and the 12-mer NMR structure (2KBP, model 1) Linking U6 U7 and A8 residues for the B strands have been excluded for the crystal structures.
A MD simulation of the equivalent 12-mer DNA quadruplex (PDB 1K8P; resolution 2.40 Å) was performed for 18 ns in order to highlight the differences between RNA and DNA quadruplexes.
Hydroxyl group interactions are linked to sugar pucker conformation, and appear to affect the hydration structure and overall stability of the RNA quadruplex The sugar pucker arrangement in our structure for the guanine G 3 stack has C2′- endo puckers at the ends and a C3′- endo for the central guanine, an arrangement consistent with the RNA quadruplex (PDB ID 2KBP) in NMR solution, but quite different from the two equivalent DNA quadruplex structures (PDB ID 1K8P and PDB ID 1KF1).
( c ) Overlay of the bimolecular RNA quadruplex (PDB 3IBK) (blue) with the equivalent bimolecular DNA quadruplex (PDB 1K8P) (red).
RNA (PDB 3IBK), solid black trace with squares; DNA (1K8P), grey dashed trace with diamonds.
MD simulations: stability and ligand binding In order to assess the comparative conformational stability of the telomeric RNA quadruplex, a 20ns MD simulation was performed on both the RNA 12-mer and the DNA 12-mer quadruplex structures (PDB IDs 3IBK and 1K8P respectively).
Structure determination and refinement The structure was solved by molecular replacement using the Phaser program ( 22 ) (CCP4), using the bimolecular DNA quadruplex structure, PDB 1K8P, as a model, and refined using Refmac5 ( 23 ).
Publication Year: 2010
Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.
(2012) Nucleic Acids Res 40
PubMed: 22287624 | PubMedCentral: PMC3378867 | DOI: 10.1093/nar/gks023
The G-quartets extracted from the human telomeric quadruplex crystal structure (PDB code 1K8P) were modified to obtain an initial model for electron-density fitting.
Publication Year: 2012
PubMed ID is not available.
Published in 2015
Pucker distributions for TTA/UUAs of all type-1 loops 1KF1-a 1KF1-b 1KF1-c 1K8P 3IBK 3CDM-a 3CDM-b 3CDM-c 3CDM-d 3CE5 3SC8 3UYH 3T5E-a T C1’- exo C1’- exo C1’- exo C1’-... exo C1’- exo C1’- exo C4’- exo C1’- exo C1’- exo C1’- exo C1’- exo C1’- exo C2’- endo T C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo A C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C1’- exo C2’- endo C2’- endo C2’- endo C2’- endo 3T5E-b 3T5E-c 4DA3 4DAQ 3R6R-a 3R6R-b 3R6R-c 4FXM-a 4FXM-b 4FXM-c 4G0F-a 4G0F-b 4G0F-c T C1’- exo C2’- endo C1’- exo C1’- exo C1’- exo C1’- exo C4’- exo C2’- endo C1’- exo C1’- exo C2’- endo C2’- endo C2’- endo T C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo C3’- endo A C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C2’- endo C1’- exo C1’- exo C2’- endo Yellow indicates a sugar which deviates from the consensus pucker conformation.
Qualitative TTA/UUA loop descriptors in terms of base stacking Loop type Stacked bases Mutually perpendicular bases Orientation of 3 rd base 1 T1, A3 T2, A3 T2 close to A3 2 T1, T2 - A3 away from T1, T2 3 T2, A3 T1, A3 T1 close to A3 4 - T2, A3 T1 away from T2, A3 5 T2, A3 - T1 close to T2, A3 6 T2, A3 T1 T1 away from T2, A3 7 T2, A3 T1 close to T2 8 U2, A3 U1 U1 away from U2, A3 9 No stacking - All away from each other 10 T2, A3 - T1 away from T2, A3 11 No stacking T1, T2 A3 close to T1 12 T2, A3 - T1 away from T2, A3 Type-1 propeller loops By far the most commonly observed loop type is the intercalated ‘TAT’ loop found in the native telomeric DNA structures (PDB IDs 1KF1 and 1K8P), termed type-1 loops.
Publication Year: 2015
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