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Original Article

Long range and symmetry considerations in the DNA

Pages 69-79 | Received 16 Apr 1991, Published online: 11 Jul 2009

References

  • Breslauer K. J., Frank R., Blocker H., Marky L. A. Predicting DNA duplex stability from base sequence. Proc. Natl. Acad. Sci. 1986; 83: 3746–3750
  • Calladine C. R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 1982; 161: 343–352
  • Dickerson R. E. Base sequence and helix variation in B and A DNA. J. Mol. Biol. 1983; 166: 419–441
  • Drew H. R., Dickerson R. E. Structure of a B-DNA dodecamer III. Geometry of hydration. J. Mol. Biol. 1981; 151: 535–556
  • Gotoh O., Tagashira Y. Stabilities of nearest neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 1981a; 20: 1033–1042
  • Gotoh O., Tagashira Y. Locations of frequently opening regions on natural DNAs and their relations to functional loci. Biopolymers 1981b; 20: 1043–1058
  • Hagerman P. J. Sequence-directed curvature of DNA. Nature 1986; 321: 449–450
  • Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine-thymine tracts. Nature 1986; 320: 502–506
  • Kohwi-Shigematsu T., Kohwi Y. Poly (dG)-poly (dC) sequences, under torsional stress induce an altered DNA conformation upon neighboring DNA sequences. Cell 1985; 43: 199–206
  • Larsen A., Weintraub H. An Altered DNA conformation detected by 51 nuclease occurs at specific regions in active chick globin chromatin. Cell 1982; 29: 609–622
  • McClarin J. A., Frederick C. A., Wang B-C., Green P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution. Science 1986; 234: 1526–1541
  • McGhee J. D., Wood W., Donlan M., Engel J. D., Felsenfield G. A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell 1981; 27: 45–55
  • Nussinov R. Some rules in the ordering of the nucleotides in the DNA. Nucl. Acids Res. 1980; 8: 4545–4562
  • Nussinov R. Promoter helical variation at the E. coli polymerase interaction sites. J. Biol. Chem. 1984; 259: 6798–6805
  • Nussinov R. Large helical conformational deviation from ideal B-DNA and prokaryotic regulatory sites. J. Theor. Biol. 1985; 115: 179–189
  • Nussinov R. The ordering of the nucleotides in the DNA: Computational problems in molecular biology. Computers in Biology and Medicine 1989; 19: 269–281
  • Nussinov R. Sequence signals in eukaryotic upstream regions. CRC Critical Reviews in Biochemistry and Molecular Biology 1990a; 25: 185–224
  • Nussinov R. General nearest neighbor preferences in G/C oligomers interrupted by A/T: Correlation with DNA structure. J. Biomolec. Str. and Dyn. 1990b; 8: 399–412
  • Nussinov R. The ordering of nucleotides in the DNA: strong pyrimidine-purine patterns and homoligomer tracts. J. Theor. Biol. 1991a; 149: 21–42
  • Nussinov R. Distinct patterns in the dinucleotides nearest neighbors to G/C and A/T oligomers in eukaryotic sequences. J. Mol. Evol. 1991b, In press
  • Nussinov R., Lennon G. G. Structural features are as important as sequence homologies in Drosophila heat shock gene upstream regions. J. Mol. Evol. 1984; 20: 106–110
  • Nussinov R., Shapiro B., Lipkin K. E., Maizel J. V. DNAase I hyper-sensitive sites may be correlated with genomic regions of large structural variations. J. Mol. Biol. 1984; 177: 591–608
  • Olson W. K., Srinivasan A. R. The translation of DNA primary base sequence into three dimensional structure. Comp. Appl. in the BioSciences 1988; 4: 133–142
  • Phillips G. J., Arnold J., Ivarie R. Mono-through hexanucleotide composition of the Escherichia coli genome: A markov chain analysis. Nucl. Acids Res. 1985; 2611–2626
  • Sarai A., Mazur J., Nussinov R., Jernigan R. L. Origin of DNA helical structure and its sequence-dependence. Biochemistry 1988a; 27: 8498–8502
  • Sarai A., Mazur J., Nussinov R., Jernigan R. L. Sequence dependence of DNA conformations: means and fluctations. Structure and Expression Vol. 3: DNA Bending and Curvature, W. K. Olson, M. H. Sarma, R. Sarma, M. Sundaralingam. Adenine Press, New York 1988b; 213–223
  • Sarai A., Mazur J., Nussinov R., Jernigan R. L. Sequence dependence of DNA conformational flexibility. Biochemistry 1989; 28: 7842–7849
  • Srinivasan A. R., Torres R., Clark W., Olson W. K. Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. J. Biomolec. Str. and Dyn. 1987; 5: 459
  • Tinoco I., Jr., Borer P. N., Dengler B., Levine M. D., Uhlenbeck O. C., Crothers D. M., Gralla J. Improved estimation of secondary structure in ribonucleic acids. Nature New Biol. 1973; 246: 40–41
  • Turner D. H., Sugimoto N., Freier S. M. RNA structure prediction. Ann. Rev. Biophys. Chem. 1988; 17: 167–192
  • Wada A., Suyama A. Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog. Biophys. Molec. Biol. 1986a; 47: 113–157
  • Wada A., Suyama A. Homogeneous double helix stability in individual genes. Proc. Fourth Conversation in Biomolec. Stereodynamics, R. H. Sarma, M. K. Sarma. Adenine Press, New York 1986b; 255–269

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