Molecular Dynamics Simulations of DNA Triple-Helices. Does The Triplex d(A)₁₀·d(T)₁₀·d(T)₁₀ Have A-Form or B-form Geometry?

References

• Felsenfeld , G. , Davies , D. R. and Rich , A. 1957 . Formation of a Three-Stranded Polynucleotide Molecule . J. Amer. Chem. Soc. , 79 : 2023
   Web of Science ®Google Scholar
• Frank-Kaminetskii , M. D. 1990 . DNA Toplogy and its Biological Effects , Edited by: Cozzarelli , N. R. and Wang , J. C. 185 – 215 . Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press .
   Google Scholar
• Helene , C. 1991 . The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides . Anticancer Drug Des. , 6 : 569
   PubMedGoogle Scholar
• Strobel , S. A. and Dervan , P. B. 1991 . Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation . Nature , 350 : 172
   PubMed Web of Science ®Google Scholar
• Orson , F. M. , Thomas , D. W. , McShan , W. M. , Kessler , D. J. and Hogan , M. E. 1991 . Oligonucleotide inhibition of IL2R alpha mRNA transcription by promoter region collinear triplex formation in lymphocytes . Nucl. Acids Res , 19 : 3435
   PubMed Web of Science ®Google Scholar
• Arnott , S. and Selsing , E. 1974 . Structures of the polynucleotide complexes poly(dA)·poly(dT) and poly(dT)·poly(dA)·poly(dT) . J. Mol. Biol. , 88 : 509
   PubMed Web of Science ®Google Scholar
• Arnott , S. , Bond , P. J. , Selsing , E. and Smith , P. J.C. 1976 . Models of triple-stranded polynucleotides with optimised stereochemistry. . Nucl. Acids Res. , 11 : 4141
   Web of Science ®Google Scholar
• Radhakrishnan , I. and Patel , D. J. 1992 . Solution Conformation of a G·TA Triple in an Intramolecular Pyrimidine·Purine·Pyrimidine DNA Triplex . J. Amer. Chem. Soc. , 144 : 6913
   Google Scholar
• Macaya , R. F. , Schultze , P. and Feigon , J. 1992 . Sugar Conformations in Intramolecular DNA Triplexes Determined by Coupling Constants Obtained by Automated Simulation of P. COSY Cross Peaks. . J. Amer. Chem. Soc. , 114 : 781
   Web of Science ®Google Scholar
• Howard , F. B. , Miles , H. T. , Liu , K. , Frazier , J. , Raghunathan , G. and Sasisekharan , V. 1992 . Structure of d(T)n·d(A)n·d(T)n: the DNA triple helix has B-form geometry with C2′-endo sugar pucker . Biochemistry , 31 : 10671
   PubMed Web of Science ®Google Scholar
• Raghunathan , G. , Miles , H. T. and Sasisekharan , V. 1993 . Symmetry and molecular structure of a DNA triple helix: d(T)n·d(A)n·d(T)n . Biochemistry , 32 : 455
   PubMed Web of Science ®Google Scholar
• Tidor , B. , Irikura , K. K. , Brooks , B. R. and Karplus , M. 1983 . Dynamics of DNA Oligomers . J. Biomol. Struct. Dyn. , 1 : 231
   PubMed Web of Science ®Google Scholar
• Orozco , M. , Laughton , C. A. , Herzyk , P. and Neidle , S. 1990 . Molecular-mechanics modelling of drug-DNA structures; the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model . J. Biomol Struct Dyn. , 8 : 359
   PubMed Web of Science ®Google Scholar
• Laughton , C. A. and Neidle , S. 1992 . Prediction of the structure of the Y+·R−·R+-type DNA triple helix by molecular modelling . Nucl. Acids Res. , 20 : 6535
   PubMed Web of Science ®Google Scholar
• Laughton , C. A. and Neidle , S. 1992 . Molecular dynamics simulation of the DNA triplex d(TC)5·d(GA)5· d(C+ T)5 . J. Mol. Biol. , 223 : 519
   PubMed Web of Science ®Google Scholar
• Hausheer , F. H. , Singh , U. C. , Saxe , J. D. , Colvin , O. M. and Tsu , P. O. 1990 . Can oligonucleoside methylphosphonates form a stable triplet with a double DNA helix? . Anticancer Drug Des. , 5 : 159
   PubMedGoogle Scholar
• Pearlman , D. A. , Case , D. A. , Caldwell , J. C. , Seibel , G. L. , Singh , U. C. , Weiner , P. and Kollman , P. A. 1991 . San Francisco, , USA : University of California . AMBER 4.0
   Google Scholar
• Weiner , S. J. , Kollman , P. A. , Nguyen , D. T. and Case , D. A. 1986 . An All Atom Force Field for Simulations of Proteins and Nucleic Acids . J. Comp. Chem. , 7 : 230
   PubMed Web of Science ®Google Scholar
• Ferrin , T. E. , Huang , C. C. , Jarvis , L. E. and Langridge , R. 1988 . The MIDAS display system . J. Mol. Graphics , 6 : 13
   Google Scholar
• Callahan , T. and Lybrand , T. P. 1991 . Available from the Quantum Chemistry Program Exchange , Bloomington : Indiana University . MD Display, QCPE program 623, IN 47405, USA
   Google Scholar
• Dickérson , R. E. 1992 . Upton : Brookhaven National Laboratory . Newhelix92, available from the Protein Data Bank, NY 11973, USA
   Google Scholar
• Lavery , R. and Sklenar , H. 1988 . The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids. . J. Biomol. Struct. Dyn. , 6 : 63
   PubMed Web of Science ®Google Scholar
• Miaskiewicz , K. , Osman , R. and Weinstein , H. 1993 . Molecular Dynamics Simulation of the Hydrated d(CGCGAATTCGCG)2 Dodecamer . J. Amer. Chem. Soc. , 115 : 1526
   Web of Science ®Google Scholar
• Swaminathan , S. , Ravishanker , G. and Beveridge , D. L. 1991 . Molecular Dynamics of B-DNA Including Water and Counterions: A 140-ps Trajectory for d(CGCGAATTCGCG) Based on the GROMOS Force Field. . J. Amer. Chem. Soc. , 113 : 5027
   Web of Science ®Google Scholar
• Mooren , M. M. , Pulleyblank , D. E. , Wijmenga , S. S. , Blommers , M. J. and Hilbers , C. W. 1990 . Polypurine/polypyrimidine halŕpins form a triple helix structure at low pH . Nucl. Acids Res. , 18 : 6523
   PubMed Web of Science ®Google Scholar