DNA Structures

Biochemistry 201

Advanced Molecular Biology

January 5, 2000

Doug Brutlag

DNA Structure Handout

DNA Structure Slides

(You must use Acrobat Reader to View Handout)

Internet Resources

Protein Structure Database

Nucleic Acid Structure Database

Molecules R US

RasMol and CHIME Plugin Distribution

Swiss Prot Database Viewer

Swiss Prot Database Viewer Tutorial

Kinemage Distribution

Protein/DNA Kinemages

 

Literature References

  1. Camerini-Otero, R. D. and Hsieh, P. (1993). Parallel DNA triplexes, homologous recombination, and other homology-dependent DNA interactions. Cell 73(2), 217-23.
  2. Crothers, D. M., Haran, T. E. and Nadeau, J. G. (1990). Intrinsically Bent DNA. J. Biol. Chem, 265(May 5), 7093-7096.
  3. Dickerson, R. E. (1992). DNA structure from A to Z. Methods Enzymology 211, 67-111.
  4. Drew, H., McCall, M. J., and Calladine, C. R. (1988). Recent studies of DNA in the crystal. Annu. Rev. Cell. Biol. 4, 1-20.
  5. el Hassan, M. A. and Calladine, C. R. (1995). The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. J Mol Biol, 251(5), 648-664.
  6. el Hassan, M. A. and Calladine, C. R. (1996). Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol, 259(1), 95-103.
  7. el Hassan, M. A. and Calladine, C. R. (1996). Structural mechanics of bent DNA. Endeavour, 20(2), 61-67.
  8. El Hassan, M. A. and Calladine, C. R. (1998). Two distinct modes of protein-induced bending in DNA. J Mol Biol, 282(2), 331-343.
  9. Gabrielian A, Vlahovicek K, Pongor S. (1997). Distribution of sequence-dependent curvature in genomic DNA sequences. FEBS Letters 406(1-2):69-74
  10. Grzeskowiak, K. (1996). Sequence-dependent structural variation in B-DNA. Chem Biol, 3(10), 785-90.
  11. Hagerman, P. J. (1990). Sequence-Directed Curvature of DNA Annu. Rev. Biochemistry 59, 755-781.
  12. Herbert, A., & Rich, A. (1996). The biology of left-handed Z-DNA. J Biol Chem, 271(20), 11595-8.
  13. Hunter, C. A. (1996). Sequence-dependent DNA structure. Bioessays, 18(2), 157-62.
  14. Hunter CA, Lu XJ J. (1997). Construction of double-helical DNA structures based on dinucleotide building blocks. Biomol Struct Dynamics 14(6):747-56.
  15. Johnston, B. H. (1992). Generation and detection of Z-DNA. Methods Enzymol 211, 127-58.
  16. Piper, A. (1998) Light on a dark lady TIBS 23, 121-156.
  17. Rich, A., Nordheim, A. and Wang, A. H. J. (1984). The Chemistry and Biology of Left-Handed Z-DNA. Annual Review of Biochemistry, 53, 791-846.
  18. Rich, A. (1993). DNA comes in many forms. Gene, 135(1-2), 99-109.
  19. Rich, A. (1994). Speculation on the biological roles of left-handed Z-DNA. Ann N Y Acad Sci, 726, 1-16; discussion 16-7.
  20. Rippe, K. and Jovin, T. M. (1992). Parallel-stranded duplex DNA. Methods Enzymol 211, 199-220.
  21. Sen, D. and Gilbert, W. (1992). Guanine quartet structures. Methods Enzymol 211, 191-9.
  22. Stasiak, A. (1992). Three-stranded DNA structure; is this the secret of DNA homologous recognition? Mol Microbiol 6(22), 3267-76.
  23. Travers, A. A. (1990). Why bend DNA? Cell, 60(2), 177-80.
  24. Vologodskii, . V. and Cozzarelli, N. R. (1994). Conformational and thermodynamic properties of supercoiled DNA. Annu Rev Biophys Biomol Struct, 23, 609-43.
  25. Watson, J. D. and Crick, F. H. C. (1953a). Molecular structure of nucleic acids. Nature 171, 737-738.
  26. Watson, J. D. and Crick, F. H. C. (1953b). The structure of DNA. Cold Spring Harbor Symp. Quant. Biol. 18, 123-131.
  27. Wells, R. D. (1988). Minireview: Unusual DNA structures. J. Biol. Chem. 263, 1095-1098.
  28. Wells , R. D. (1996) Molecular Basis of Genetic Instability of Triplet Repeats (*) . J. Biol. Chem. 271, 2875-2878.
  29. Williamson, J. R. (1994). G-quartet structures in telomeric DNA. Annu Rev Biophys Biomol Struct, 23, 703-30.