Primary Citation PubMed: 8081740
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Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal.
(2005) Nucleic Acids Res 33
PubMed: 16106044 | PubMedCentral: PMC1187823 | DOI: 10.1093/nar/gki782
Molecular dynamics simulations The d[AGGG(TTAGGG) 3 ] crystal structure (PDB code 1KF1) and NMR structure (143d) were used directly for molecular dynamics calculations.
Publication Year: 2005
Quadruplex DNA: sequence, topology and structure.
(2006) Nucleic Acids Res 34
PubMed: 17012276 | PubMedCentral: PMC1636468 | DOI: 10.1093/nar/gkl655
In each case two views are shown ( a ) one of the deposited structures of the Na + form, determined by NMR (PDB entry 143D) ( 54 ), with a diagonal and two lateral 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
NMR-based ( a ) folding topology and ( b ) solution structure of the four-repeat human telomere unimolecular G-quadruplex formed by the d[AG 3 (T 2 AG 3 ) 3 ] sequence in Na + solution (coordinates de... osition: 143D) ( 9 ).
Publication Year: 2007
Structural polymorphism of intramolecular quadruplex of human telomeric DNA: effect of cations, quadruplex-binding drugs and flanking sequences.
(2008) Nucleic Acids Res 36
PubMed: 18535007 | PubMedCentral: PMC2475613 | DOI: 10.1093/nar/gkn351
Average distances (in angstroms) from the C1′ of the G22 to the sugars of the guanines in the core for three different conformations of the G-quadruplex; open diamonds—(3+1) type 1, PD... ID 2GKU ( 18 ); black squares—propeller, PDB ID 1KF1 ( 24 ); black circles—basket PDB ID 143D ( 16 ).
Publication Year: 2008
Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures.
PubMed: 18567908 | PubMedCentral: PMC2475619 | DOI: 10.1093/nar/gkn379
Cartoon showing the folding topology of ODN1 in Na + [G 3 (T 2 AG 3 ) 3 , PDB id 143D, ( A )] and ODN1 [T 2 G 3 (T 2 AG 3 ) 3 A, PDB id 2GKU] in K + ( B ).
The figures were drawn using the molecular graphics program Chimera ( 65 ) from NMR-derived coordinates for the first conformer listed in pdb files 143D ( 24 ) and 2GKU ( 28 ).
Stability and kinetics of G-quadruplex structures.
PubMed: 18718931 | PubMedCentral: PMC2553573 | DOI: 10.1093/nar/gkn517
Loop distances as defined by O3′-O5′ distances a PDB Code Sequence Loop 1 Loop 2 Loop 3 143D dA(GGGTTA) 3 GGG ( 39 ) type: antiparallel basket 12.1 l 19.7 d 14.3 l 148D d(GGTTGGTGTGGTT... G) ( 36 ) type: antiparallel chair 12.3 l 13.8 l 12.0 l 1I34 dGGTTTTGGCAG GGTTTTGGT) ( 40 ) type: hybrid 19.0 d 11.3 r 20.4 d 1KF1 dA(GGGTTA) 3 GGG) ( 35 ) type: parallel 10.8 r 11.3 r 9.7 r 2HY9 dAAA(GGGTTA) 3 GGGAA ( 41 ) type: hybrid 11.1 r 16.2 l 11.5 l 2JPZ dTTA(GGGTTA) 3 GGGTT ( 42 ) type: hybrid 15.8 l 12.6 l 11.9 r 2F8U d(GGGCGCGGGA GGAATTGGGCGGG) ( 37 ) 15.8 l 12.8 l 6.0 r 2GKU d(TTA(GGGTTA) 3 GGGA) ( 38 ) type: hybrid 11.9 r 17.2 l 8.8 l a These are taken from the first structure in the PDB files for NMR structures, therefore are part of the ensemble of structures that satisfy the spatial constraints.
Natural isoflavones regulate the quadruplex-duplex competition in human telomeric DNA.
(2009) Nucleic Acids Res 37
PubMed: 19261597 | PubMedCentral: PMC2677859 | DOI: 10.1093/nar/gkp055
3 Molecular modeling Three experimental structures are chosen as starting models, including the antiparallel basket-type NMR structure (PDB 143D), the parallel propeller-type X-ray structure (PDB 1KF1... , and the mixed hybrid-type NMR structure deduced from a 26-nt DNA sequence (PDB 2HY9) through removal of two terminal adenines from each end of the 26-nt sequence ( 42 , 43 ).
Therefore, three experimental structures are chosen as starting models in our simulations, including antiparallel basket-type G-quadruplex (PDB 143D), hybrid-type G-quadruplex (PDB 2HY9) and parallel propeller-type G-quadruplex (PDB 1KF1) separately ( 43 ).
Publication Year: 2009
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
(a) NMR structure of the anti-parallel G-quadruplex formed by the d[AG 3 (T 2 AG 3 ) 3 ] sequence in Na+ solution (pdb code: 143D).
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.
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
The initial structures of TTA- L n , TTA- L w , and TTA- P 3 a were obtained by keeping the third, second, and first loop of 2GKU , respectively; TTA- D was built by connecting the diagonal TTA loop f... om 143D ( 62 ) with the 2GKU stem; the TTA- P 2 a / P 3 p / P 4 p / P 4 a models were built by connecting the first loop of the 2GKU structure with the appropriate stems as stated above.
Publication Year: 2011
The effects of molecular crowding on the structure and stability of g-quadruplexes with an abasic site.
(2011) J Nucleic Acids 2011
PubMed: 21949901 | PubMedCentral: PMC3178115 | DOI: 10.4061/2011/857149
1 Zimmerman SB Minton AP Macromolecular crowding: biochemical, biophysical, and physiological consequences Annual Review of Biophysics and Biomolecular Structure 1993 22 27 65 2 Minton AP The influenc... of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media Journal of Biological Chemistry 2001 276 14 10577 10580 11279227 3 Ellis RJ Minton AP Cell biology: join the crowd Nature 2003 425 6953 27 28 12955122 4 Medalia O Weber I Frangakis AS Nicastro D Gerisch G Baumeister W Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography Science 2002 298 5596 1209 1213 12424373 5 Ellis RJ Macromolecular crowding: an important but neglected aspect of the intracellular environment Current Opinion in Structural Biology 2001 11 1 114 119 11179900 6 Davis-Searles PR Saunders AJ Erie DA Winzor DJ Pielak GJ Interpreting the effects of small uncharged solutes on protein-folding equilibria Annual Review of Biophysics and Biomolecular Structure 2001 30 271 306 7 Wenner JR Bloomfield VA Crowding effects on EcoRV kinetics and binding Biophysical Journal 1999 77 6 3234 3241 10585945 8 Sasaki Y Miyoshi D Sugimoto N Regulation of DNA nucleases by molecular crowding Nucleic Acids Research 2007 35 12 4086 4093 17567601 9 Spink CH Chaires JB Selective stabilization of triplex DNA by poly(ethylene glycols) Journal of the American Chemical Society 1995 117 51 12887 12888 10 Goobes R Minsky A Thermodynamic aspects of triplex DNA formation in crowded environments Journal of the American Chemical Society 2001 123 50 12692 12693 11741440 11 Nakano S Karimata H Ohmichi T Kawakami J Sugimoto N The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability Journal of the American Chemical Society 2004 126 44 14330 14331 15521733 12 Miyoshi D Karimata H Sugimoto N Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions Journal of the American Chemical Society 2006 128 24 7957 7963 16771510 13 Miyoshi D Nakamura K Tateishi-Karimata H Ohmichi T Sugimoto N Hydration of watson crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions Journal of the American Chemical Society 2009 131 10 3522 3531 19236045 14 Miller MC Buscaglia R Chaires JB Lane AN Trent JO Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3′ sequence of d(AG 3 (TTAG 3 ) 3 ) Journal of the American Chemical Society 2010 132 48 17105 17107 15 Olsen CM Lee HT Marky LA Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops Journal of Physical Chemistry B 2009 113 9 2587 2595 16 Arora A Maiti S Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents Journal of Physical Chemistry B 2009 113 25 8784 8792 17 Rajendran A Nakano S Sugimoto N Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH Chemical Communications 2010 46 8 1299 1301 20449283 18 Nakano S Karimata HT Kitagawa Y Sugimoto N Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes Journal of the American Chemical Society 2009 131 46 16881 16888 19874030 19 Todd AK Johnston M Neidle S Highly prevalent putative quadruplex sequence motifs in human DNA Nucleic Acids Research 2005 33 9 2901 2907 15914666 20 Allsopp RC Vaziri H Patterson C Telomere length predicts replicative capacity of human fibroblasts Proceedings of the National Academy of Sciences of the United States of America 1992 89 21 10114 10118 1438199 21 Klobutcher LA Swanton MT Donini P Prescott DM All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3′ terminus Proceedings of the National Academy of Sciences of the United States of America 1981 78 5 3015 3019 6265931 22 Williamson JR G-quartet structures in telomeric DNA Annual Review of Biophysics and Biomolecular Structure 1994 23 703 730 23 Huppert JL Balasubramanian S Prevalence of quadruplexes in the human genome Nucleic Acids Research 2005 33 9 2908 2916 15914667 24 Blackburn EH Challoner PB Identification of a telomeric DNA sequence in Trypanosoma brucei Cell 1984 36 2 447 457 6319025 25 Blackburn EH Structure and function of telomeres Nature 1991 350 6319 569 573 1708110 26 Patel DJ Phan AT Kuryavyi V Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics Nucleic Acids Research 2007 35 22 7429 7455 17913750 27 Vallur AC Maizels N Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions Proceedings of the National Academy of Sciences of the United States of America 2008 105 43 16508 16512 18940926 28 Szostak JW Blackburn EH Cloning yeast telomeres on linear plasmid vectors Cell 1982 29 1 245 255 6286143 29 Greider CW Blackburn EH The telomere terminal transferase of tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity Cell 1987 51 6 887 898 3319189 30 Baker ES Lee JT Sessler JL Bowers MT Cyclo[n]pyrroles: size and site-specific binding to G-quadruplexes Journal of the American Chemical Society 2006 128 8 2641 2648 16492050 31 Seenisamy J Bashyam S Gokhale V Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure Journal of the American Chemical Society 2005 127 9 2944 2959 15740131 32 Shirude PS Gillies ER Ladame S Macrocyclic and helical oligoamides as a new class of G-quadruplex ligands Journal of the American Chemical Society 2007 129 39 11890 11891 17845042 33 Yaku H Murashima T Miyoshi D Sugimoto N Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes Chemical Communications 2010 46 31 5740 5742 20596577 34 van Steensel B Smogorzewska A De Lange T TRF2 protects human telomeres from end-to-end fusions Cell 1998 92 3 401 413 9476899 35 Lindahl T Instability and decay of the primary structure of DNA Nature 1993 362 6422 709 715 8469282 36 Lindahl T Nyberg B Rate of depurination of native deoxyribonucleic acid Biochemistry 1972 11 19 3610 3618 4626532 37 Tchou J Kasai H Shibutani S 8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity Proceedings of the National Academy of Sciences of the United States of America 1991 88 11 4690 4694 2052552 38 Esposito V Martino L Citarella G Effects of abasic sites on structural, thermodynamic and kinetic properties of quadruplex structures Nucleic Acids Research 2009 38 6 2069 2080 20026588 39 Školáková P Bednářová K Vorlíčková M Sagi J Quadruplexes of human telomere dG 3 (TTAG 3 ) 3 sequences containing guanine abasic sites Biochemical and Biophysical Research Communications 2010 399 2 203 208 20643102 40 Sugimoto N Nakano S Katoh M Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes Biochemistry 1995 34 35 11211 11216 7545436 41 Nakano S Kanzaki T Sugimoto N Influences of Ribonucleotide on a duplex conformation and its thermal stability: study with the chimeric RNA-DNA strands Journal of the American Chemical Society 2004 126 4 1088 1095 14746477 42 Mergny JL Li J Lacroix L Amrane S Chaires JB Thermal difference spectra: a specific signature for nucleic acid structures Nucleic Acids Research 2005 33 16 p. e138 43 Wang Y Patel DJ Solution structure of the human telomeric repeat d[AG 3 (T 2 AG 3 ) 3 ] G-tetraplex Structure 1993 1 4 263 282 8081740 44 Sugimoto N Nakano M Nakano S Thermodynamics—structure relationship of single mismatches in RNA/DNA duplexes Biochemistry 2000 39 37 11270 11281 10985772 45 Vasilevskaya VV Khokhlov AR Matsuzawa Y Yoshikawa K Collapse of single DNA molecule in poly(ethylene glycol) solutions The Journal of Chemical Physics 1995 102 16 6595 6602 46 Chen Z Zheng KW Hao YH Tan Z Reduced or diminished stabilization of the telomere G-quadruplex and inhibition of telomerase by small chemical ligands under molecular crowding condition Journal of the American Chemical Society 2009 131 30 10430 10438 19588966 47 Sági J Hang B Singer B Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases Chemical Research in Toxicology 1999 12 10 917 923 10525266 48 Sági J Guliaev AB Singer B 15-Mer DNA duplexes containing an abasic site are thermodynamically more stable with adjacent purines than with pyrimidines Biochemistry 2001 40 13 3859 3868 11300765 49 Gelfand CA Plum GE Grollman AP Johnson F Breslauer KJ Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence Biochemistry 1998 37 20 7321 7327 9585546 50 Goobes R Kahana N Cohen O Minsky A Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance Biochemistry 2003 42 8 2431 2440 12600210 Figure 1 (a) Structure of human telomere (5′-A(G 3 T 2 A) 3 G 3 -3′) G-quadruplex in the presence of Na + (PDB ID: 143D).
Disordering of human telomeric G-quadruplex with novel antiproliferative anthrathiophenedione.
(2011) PLoS One 6
PubMed: 22102877 | PubMedCentral: PMC3216923 | DOI: 10.1371/journal.pone.0027151
Computer modeling of binding of 2 to TelQ Na Fig. 6A shows the results of docking of 2 to the rigid structure of TelQ Na (  , PDB ID: 143D).
Molecular modeling The coordinates of the atomic positions of TelQ were taken from NMR (PDB ID: 143D).
Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy.
(2013) Nucleic Acids Res 41
PubMed: 23303789 | PubMedCentral: PMC3575832 | DOI: 10.1093/nar/gks1341
The antiparallel G-quadruplex structure solved by NMR is shown in the illustration (PDB code 143D).
Publication Year: 2013
Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions.
PubMed: 23396442 | PubMedCentral: PMC3616730 | DOI: 10.1093/nar/gkt038
( C ) The best-matching G-quadruplex (PDB: 143D) with a highlighted triangle.
The RMSD between these two data sets ( Figure 2 B) reveals the best-matching structure is indeed the basket G-quadruplex (PDB: 143D, Figure 2 C), which has been shown to populate in the core (GGGTTA) 3 GGG sequence in the same buffer by NMR studies ( 10 ).
V-shaped dinuclear Pt(II) complexes: selective interaction with human telomeric G-quadruplex and significant inhibition towards telomerase.
(2013) Sci Rep 3
PubMed: 23792883 | PubMedCentral: PMC3690394 | DOI: 10.1038/srep02060
(a) a G-tetrad consists of four guanines, (b) the wild-type 22-mer crystal with K + (parallel structure, PDB ID: 1KF1), (c) the modified 20-mer in K + solution (mixed-type “(3 + 1) hybrid... 1d; structure, PDB ID: 2KZD), (d) the wild-type 22-mer in Na + solution (basket-type “(2 + 2) hybrid” structure, PDB ID: 143D).
Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
(2013) PLoS One 8
PubMed: 23951152 | PubMedCentral: PMC3738534 | DOI: 10.1371/journal.pone.0071380
Results In the present work, we chose anti-parallel structure (PDB code, 143D) and [3+1] hybrid structure (PDB code, 2GKU) for simulations ( Figure 1 ).
PDB ID ions type force field time(ns) abbreviation 143D Na + parm99 1000 anti_99 2GKU K + parm99 1000 hybrid_99 143D Na + parmbsc0 1000 anti_bsc0 2GKU K + parmbsc0 1000 hybrid_bsc0 143D Na + parmbsc0 5 anti_stem a 2GKU K + parmbsc0 5 hybrid_stem a a In these two structures, loop bases are deleted and just G-quartets left.
Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops.
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.
Targeting human telomeric G-quadruplex DNA and inhibition of telomerase activity with [(dmb)2Ru(obip)Ru(dmb)2](4+).
PubMed: 24386376 | PubMedCentral: PMC3874006 | DOI: 10.1371/journal.pone.0084419
Molecular docking studies Both the antiparallel basket quadruplex (PDB ID 143D) and the mixed parallel/antiparallel structure (PDB ID 2E4I) (Waters were removed from the DNA PDB file) were used as an ... nitial model to study the interaction between [(dmb) 2 Ru(obip)Ru(dmb) 2 ] 4+ and 22-mer telomeric G-quadruplex DNA.
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).
For 143D, 6 poses were deposited in the PDB record.
Publication Year: 2014
Native electrospray mass spectrometry of DNA G-quadruplexes in potassium solution.
(2014) J Am Soc Mass Spectrom 25
PubMed: 24781455 | PubMedCentral: PMC4055847 | DOI: 10.1007/s13361-014-0890-3
(c) NMR structure of the antiparallel G-quadruplex form of d(A(GGGTTA) 3 GGG) in Na + solution [ 13 ] (PDB ID: 143D).
Published in 2015
The items used are the following: the parallel intramolecular DNA with PDB id:1KF1 ( 12 ) (obtained by X-ray diffraction); the hybrid intramolecular DNA with PDB id:2HY9 ( 17 ) (obtained by NMR) and t... e antiparallel intramolecular DNA with PDB id:143D ( 13 ) (obtained by NMR).
Top: All atom representation of the PDB files: 1KF1 ↑↑- parallel DNA, 2HY9 ↑↑↓ - hybrid I, 143D ↑↓ - antiparallel DNA.
Publication Year: 2015
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