Genomes and DNA conformation

Biological Chemistry

Volumn 378, Issue 12, 1997, Pages 1397-1404

  Amano, Naoki ^a,b   Ohfuku, Yuko ^a,b,c   Suzuki, Masashi ^a,d  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

^c NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

Autocorrelation; DNA conformation; DNA protein interaction; Genome analysis; Transcription

Indexed keywords

DINUCLEOTIDE; DNA FRAGMENT; PURINE; PYRIMIDINE;

AMINO ACID SEQUENCE; DNA CONFORMATION; DNA SEQUENCE; FOURIER ANALYSIS; GENE; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW;

DNA; GENOME; NUCLEIC ACID CONFORMATION; PURINES; PYRIMIDINES;

EID: 0031438454     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (30)

1. Babcock, M.S., Pednault, E.P.D., and Olson, W.K. (1994). Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237, 125-156.
2. Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., and Sutton, G.G. et al. (1996). Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
3. Burland, V., Plunkett III, G., Sofia, H.J., Daniels, D.L., and Blattner, F.R. (1995). Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res. 23, 2105-2119.
4. Calladine, C.R. (1982). Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161, 343-352.
5. Dickerson, R.E. (1983). Base sequence and helix structure variation in B-and A-DNA. J. Mol. Biol. 166, 419-441.
6. Dickerson, R.E., Bansal, M., Calladine, C.R., Diekmann, S., Hunter, W.N., Kennard, O. et al. (1989). Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205, 787-791.
7. EL Hassan, M.A., and Calladine, C.R. (1995). A new local calculation scheme for the assessment of the kinematics of dinucleotide steps. J. Mol. Bio. 251, 648-664.
8. 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, 95-103.
9. Fickett, J.W. (1982). Recognition of protein coding regions in DNA sequences. Nucleic Acids Research. 10, 5303-5318.
10. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R. et al. (1995). Whole-Genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269, 496-512.
11. Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
12. Gatlin, L.L. (1966). The information content of DNA. J. Theoret. Biol. 10, 281-300.
13. Goffeau, A., Aert, R., Agostini-Carbone, M.L., Ahmed, A., Aigle, M., Alberghina, L. et al. (1997). The yeast genome directory. Nature 387 (suppl.), 1-105.
14. Guigó, R., and Fickett, J.W. (1995). Distinctive sequence features in protein coding genic non-coding, and intergenic human DNA. J. Mol. Bio. 253, 51-60.
15. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y. et al. (1996). Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA. Res. 3, 109-136.
16. Karlin, S., Ghandour, G., Ost, F., Tavare, S., and Korn, L.J. (1983). New approaches for computer analysis of nucleic acid sequences. Proc. Natl. Acad. Sci. USA 80, 5660-5664.
17. Lowman, H., and Bina, M. (1990). Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA. Biopolymers 30, 861-876.
18. Nussinov, R. (1984). Strong doublet preferences in nucleotide sequences and DNA geometry. J. Mol. Evol. 20, 111-119.
19. Satchwell, S.C., Drew, H.R., and Travers, A.A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675.
20. Shepherd, J.C.W. (1981). Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl. Acad. Sci. USA 78, 1596-1600.
21. Staden, R. (1984). Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. Nucl. Acids Res. 12, 551-567.
22. Suzuki, M., and Yagi, N. (1995). Stereochemical basis of DNA bending by transcription factors. Nucl. Acids Res. 23, 2083-2091.
23. Suzuki, M., Allen, M.D., Yagi, N., and Finch, J. (1996a). Analysis of co-crystal structures to identify the stereochemical determinants of the orientation of TBP on the TATA box. Nucl. Acids Res. 24, 2767-2773.
24. Suzuki, M., Yagi, N., and Finch, J.T. (1996b). Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS Letters 379, 148-152.
25. Suzuki, M., Yagi, N., and Gerstein, M. (1995). DNArecognition and superstructure formation by helix-turn-helix proteins. Protein Engineering 8, 329-338.
26. Trifonov, E.N., and Sussman, J.L. (1980). The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816-3820.
27. Widom, J. (1996). Short-range order in two eukaryotic genomes: relation to chromosome structure. J. Mol. Biol. 259, 579-588.
28. Yagil, G. (1994). The frequency of Oligopurine. Oligopyrimidine and other two-base tracts in Yeast Chromosome III. Yeast 10, 603-611.
29. Yano, T., and Hasegawa, M. (1974). Entropy increase of amino acid sequence in protein. J. Mol. Evol. 4, 179-187.
30. Young, M.A., Ravishanker, G., Breridge, D.L., and Berman, H.M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.