Structure And Dynamics Of Nucleic Acids

  • K.V.R. Chary
  • Girjesh Govil
Part of the Focus on Structural Biology book series (FOSB, volume 6)

Keywords

Codon Amide Oligomer Adenine Triad 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

9.1 Further Reading

  1. J. D. Watson and F. H. C. Crick, Molecular Structure of nucleic acids: a structure for deoxyribose nucleic acid, Nature (London) 171, 737–738 (1953).CrossRefGoogle Scholar
  2. J. D. Watson and F. H. C. Crick, Genetical implications of the structure of deoxyribonucleic acid, Nature (London) 171, 964–967 (1953).Google Scholar

9.2 Books

  1. W. Saenger, Principles of Nucleic Acid Structure, Springer, New York, Berlin, Heidelberg, and Tokyo, 315 (1984).Google Scholar
  2. T.M. Jovin, K. Rippe, N.B. Ramsing, R. Klement, W. Elhorst, and M. Vojtiskova, Structure and Methods, Vol. 3: DNA and RNA (R.H. Sarma and M.H. Sarma, eds.), Adenine Press, Schenectady, New York, 155 (1990).Google Scholar
  3. T.L. James (ed.) Methods in Enzymology. Nuclear Magnetic Resonance and Nucleic Acids, Academic Press, San Diego (1995).Google Scholar
  4. V.N. Soyfer, and V.N. Potaman, Triple-Helical Nucleic Acids, Springer - Verlag New York (1996).Google Scholar
  5. V.A. Bloomfield, D. Crothers, I. Tinoco and J. Hearst, Nucleic Acids: Structures, Properties and Functions, University Science Books (2000).Google Scholar
  6. David L. Nelson, David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd BK & CD edition, W.H. Freeman & Company (2000).Google Scholar
  7. B. Lewin, Genes, 7th edition, Oxford University Press (2000).Google Scholar
  8. Lubert Stryer, Jeremy M. Berg and John L. Tymoczko, Biochemistry, 5th Ed. W.H.Freeman & Co Ltd. (2002).Google Scholar

9.3 DNA Structure

  1. G. Lipari and A. Szabo, Nuclear magnetic resonance relaxation in nucleic acid fragments: models for internal motion, Biochemistry 20, 6250–6256 (1981).Google Scholar
  2. J. Feigon, J.M. Wright, W.A. Denny, W. Leupin, and D.R. Kearns, Use of two dimensional NMR in the study of a double-stranded DNA decamer, J. Am. Chem. Soc. 104, 5540–5541 (1982).CrossRefGoogle Scholar
  3. D.J. Patel. A. Pardi and K. Itakura, DNA conformation, dynamics and interactions in solution, Science 216, 581–590 (1982).CrossRefGoogle Scholar
  4. D.R. Hare, D.E. Wemmer, S.H. Chou, G. Drobny and B.R. Reid, Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-T-T-C-G-C-G) using two dimensional nuclear magnetic resonance methods, J. Mol. Biol. 171, 319–336 (1983).CrossRefGoogle Scholar
  5. D.J. Patel, S.A. Kozlowski, S. Ikura, K. Bhatt and D.R. Hare, NMR studies of DNA conformation and dynamics in solution, Cold Spring Harb. Symp. Quant. Biol. 47, 197–206 (1983).Google Scholar
  6. K.V.R. Chary and S. Mody, Analysis of intrasugar interproton NOESY cross-peaks as an aid to determine sugar geometries in DNA fragments, FEBS Lett. 233, 319 (1988).CrossRefGoogle Scholar
  7. K.V.R. Chary, S. Mody, R.V. Hosur, G. Govil, C. Chen and H.T. Miles, Quantification of DNA structure from NMR data: Conformation of d-ACATCGATGT, Biochemistry 28, 5240 (1989).CrossRefGoogle Scholar
  8. B.R. Reid, K. Banks, P. Flynn and W. Nerdal, NMR distance measurements in DNA duplexes: sugars and bases have the same correlation times, Biochemistry 28, 10001–10007 (1989).CrossRefGoogle Scholar
  9. K.V.R. Chary, DNA structure from NMR data, Magnetic Resonance-Current Trends; Eds. C.L. Khetrapal and G. Govil, Narosa Publishing House, New Delhi, 71–104 (1991).Google Scholar
  10. S.G. Kim, L.J. Lin and B.R. Reid, Determination of nucleic acid backbone conformation by 1 H NMR, Biochemistry 31, 3564–3574 (1992).CrossRefGoogle Scholar
  11. K. Gehring, J.L. Leroy and M. Gueron. A tetrameric DNA structure with protonated cytosine-cytosine base pair, Nature 363, 561–565 (1993).CrossRefGoogle Scholar
  12. R. Nibedita, R.A. Kumar, A. Majumdar, R.V. Hosur, G. Govil, K. Majumder and V.S. Chauhan, Solution structure of GCAAT recognition motif by 2D NMR, spectral simulation, molecular modelling, and distance geometry calculations, Biochemistry 32, 9053–9064 (1993).CrossRefGoogle Scholar
  13. O.Y. Federof, B.R. Reid, and V.P. Chuprina, Sequence dependence of DNA in solution, J. Mol. Biol. 235, 325–330. (1994).CrossRefGoogle Scholar
  14. S.R. Bhaumik and K.V.R. Chary, Molecular dynamics and mechanics calculations on a DNA duplex with A + -C, G-T and T-C mispairs, J. Bio. Struct. Dynamics 3, 199–206 (2002).Google Scholar

9.4 Parallel Stranded DNA

  1. N. Pattabiraman, Can the double helix be parallel? Biopolymers 25, 1603–1606 (1986).CrossRefGoogle Scholar
  2. J.H. van de Sande, N.B. Ramsing, M.W. Germann, W. Elhorst, B.W. Kalisch, V.E. Kitzing, R.T. Pon, R.C. Clegg and T.M. Jovin, Parallel stranded DNA Science 241, 551–557 (1988).CrossRefGoogle Scholar
  3. C. Otto, K. Rippe, K. Thomas, N.B. Ramsing and T.M. Jovin, The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick, Biochemistry 30, 3062–3069 (1991).CrossRefGoogle Scholar
  4. G. Raghunathan, H.T. Miles and V. Sasisekharan, Parallel nucleic acid helices with Hoogsteen base pairing: Symmetry and structure Biopolymers, 34, 1573–1581 (1994).CrossRefGoogle Scholar
  5. V. Rani Parvathy, S.R. Bhaumik, K.V.R. Chary., G. Govil, K. Liu, B.H. Frank and H.T. Miles, NMR structure of a parallel-stranded DNA duplex at atomic resolution, Nucleic Acids Res. 30, 1500–1511 (2002).CrossRefGoogle Scholar

9.5 Triple-Helical Nucleic Acids

  1. G. Felsenfield, D.R. Davies, and A. Rich, Formation of a three-stranded polynucleotide molecule. J. Am. Chem. Soc. 79, 2023–2024 (1957).CrossRefGoogle Scholar
  2. J.S. Lee, D.A. Johnson, and A.R. Morgan, Complexes formed by (pyrimidine)n. (purine)n DNAs on lowering the pH are three-stranded, Nucleic Acids Res., 6, 3073–3091 (1979).CrossRefGoogle Scholar
  3. N.B. Ramsing, K. Rippe, and T.M. Jovin, Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides, Biochemistry, 28, 9528–9535 (1989).CrossRefGoogle Scholar
  4. S.M. Mirkin, and M.D. Frank-Kamenetskii, H-DNA and related structures, Ann. Rev. Biophys. Biomol. Struct. 23, 541–576 (1994).CrossRefGoogle Scholar
  5. S.R. Bhaumik, K.V.R. Chary, G. Govil, K. Liu, and H.T. Miles, NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH, Nucleic Acids Res. 23, 4116–4121 (1995).CrossRefGoogle Scholar
  6. V.N. Soyfer, and V.N. Potaman, Triple-Helical Nucleic Acids, Springer - Verlag New York (1996).Google Scholar
  7. S.R. Bhaumik, K.V.R. Chary, G. Govil, K. Liu, and H.T. Miles, Homopurine and Homopyrimidine strands complementary in parallel orientation form an antiparallel duplex at neutral pH with A-C, G{\-T and T-C mismatched base pair}, Biopolymers 41, 773–785 (1997).CrossRefGoogle Scholar
  8. S.R. Bhaumik, K.V.R. Chary, G. Govil, Molecular mechanics calculations on a triple stranded DNA involving C + .G-T and T.A + -C mismatched base triples, J. Biomol. Structure and Dynamics 16, 527–534 (1998).Google Scholar
  9. S.R. Bhaumik, K.V.R. Chary, G. Govil, L. Keliang, and H.T. Miles, A novel palindromic triple stranded structure formed by homopyrimidine dodecamer d-CTTCTCCTCTTC and homopurine hexamer d-GAAGAG, Nucleic Acids Res. 26, 2981–2988 (1998).CrossRefGoogle Scholar

9.6 Isotope labelling of Nucleic Acids

  1. D.P. Zimmer, and D.M. Crothers, NMR of enzymatically synthesized uniformly 13C/15 N-labeled DNA oligonucleotides, Proc. Natl. Acad. Sci., USA 92, 3091–3095 (1995).CrossRefGoogle Scholar
  2. D.E. Smith, J. Su, and F.M. Jucker, Efficient enzymatic synthesis of 13C, 15 N-labeled DNA for NMR studies, J. Biomol. NMR 10, 245–253 (1997).CrossRefGoogle Scholar
  3. J.E. Masse, P. Bortmann, T. Dieckmann, and J. Feigon, Simple, efficient protocol for enzymatic synthesis of uniformly 13C, 15 N-labeled DNA for heteronuclear NMR studies, Nucleic Acids Res. 26, 2618–2624 (1998).Google Scholar
  4. G. Mer, and W.J. Chazin, Enzymatic synthesis of region-specific isotope-labeled DNA oligomers for NMR analysis, J. Am. Chem. Soc. 120, 607–608 (1998).CrossRefGoogle Scholar
  5. R. Sunita, B.J Rao and K.V.R. Chary, A novel approach for uniform 13>C and 15 N labeling of DNA for NMR studies, Biochem. Biophys. Res. Com. 290, 928–932 (2002).CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London Limited 2008

Authors and Affiliations

  • K.V.R. Chary
    • 1
  • Girjesh Govil
    • 1
  1. 1.Tata Institute of Fundamental ResearchMumbaiIndia

Personalised recommendations