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References
9.1 Further Reading
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).
J. D. Watson and F. H. C. Crick, Genetical implications of the structure of deoxyribonucleic acid, Nature (London) 171, 964–967 (1953).
9.2 Books
W. Saenger, Principles of Nucleic Acid Structure, Springer, New York, Berlin, Heidelberg, and Tokyo, 315 (1984).
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).
T.L. James (ed.) Methods in Enzymology. Nuclear Magnetic Resonance and Nucleic Acids, Academic Press, San Diego (1995).
V.N. Soyfer, and V.N. Potaman, Triple-Helical Nucleic Acids, Springer - Verlag New York (1996).
V.A. Bloomfield, D. Crothers, I. Tinoco and J. Hearst, Nucleic Acids: Structures, Properties and Functions, University Science Books (2000).
David L. Nelson, David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd BK & CD edition, W.H. Freeman & Company (2000).
B. Lewin, Genes, 7th edition, Oxford University Press (2000).
Lubert Stryer, Jeremy M. Berg and John L. Tymoczko, Biochemistry, 5th Ed. W.H.Freeman & Co Ltd. (2002).
9.3 DNA Structure
G. Lipari and A. Szabo, Nuclear magnetic resonance relaxation in nucleic acid fragments: models for internal motion, Biochemistry 20, 6250–6256 (1981).
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).
D.J. Patel. A. Pardi and K. Itakura, DNA conformation, dynamics and interactions in solution, Science 216, 581–590 (1982).
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).
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).
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).
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).
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).
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).
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).
K. Gehring, J.L. Leroy and M. Gueron. A tetrameric DNA structure with protonated cytosine-cytosine base pair, Nature 363, 561–565 (1993).
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).
O.Y. Federof, B.R. Reid, and V.P. Chuprina, Sequence dependence of DNA in solution, J. Mol. Biol. 235, 325–330. (1994).
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).
9.4 Parallel Stranded DNA
N. Pattabiraman, Can the double helix be parallel? Biopolymers 25, 1603–1606 (1986).
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).
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).
G. Raghunathan, H.T. Miles and V. Sasisekharan, Parallel nucleic acid helices with Hoogsteen base pairing: Symmetry and structure Biopolymers, 34, 1573–1581 (1994).
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).
9.5 Triple-Helical Nucleic Acids
G. Felsenfield, D.R. Davies, and A. Rich, Formation of a three-stranded polynucleotide molecule. J. Am. Chem. Soc. 79, 2023–2024 (1957).
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).
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).
S.M. Mirkin, and M.D. Frank-Kamenetskii, H-DNA and related structures, Ann. Rev. Biophys. Biomol. Struct. 23, 541–576 (1994).
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).
V.N. Soyfer, and V.N. Potaman, Triple-Helical Nucleic Acids, Springer - Verlag New York (1996).
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).
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).
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).
9.6 Isotope labelling of Nucleic Acids
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).
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).
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).
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).
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).
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Chary, K., Govil, G. (2008). Structure And Dynamics Of Nucleic Acids. In: Chary, K., Govil, G. (eds) NMR in Biological Systems. Focus on Structural Biology, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6680-1_7
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