Summary
The eukaryotic and prokaryotic databases are scanned for potential nearest-neighbor doublet preferences at the 5′ and 3′ flanks of some oligomers. Here we focus on oligomers containing alternating nucleotides, i.e., UV, UVUV, and UUVV where U≠V. Strong, consistent trends are observed in eukaryotic sequences. A/T alternation oligomers are preferentially flanked by A/T. G/C flanks are disfavored. G/C alternation oligomers are preferentially flanked by G/C. A/T flanks are disfavored. These trends are consistent with those observed previously for homooligomer tracts (Nussinov et al. 1989a,b). G/C tracts are preferentially flanked by G/C. A/T nearest neighbors are disfavored. The reverse holds for A/T tracts. Additional patterns are described here as well. The possible origin of these DNA composition and sequence trends is discussed. These trends are suggested to stem from protein-DNA interaction constraints.
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References
Blaisdell BE (1985) Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eukaryotic nuclear DNA sequences both protein-coding and noncoding. J Mol Evol 21:278–288
Broyles SS, Pettijohn DE (1986) Interaction of theEscherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered helical pitch. J Mol Biol 187:47–60
Drew HR, Travers AA (1985) DNA binding and its relation to nucleosome positioning. J Mol Biol 186:773–790
Drlica K (1987) The nucleoid. In: Neidhard FC (ed)Escherichia coli andSalmonella typhimurium. American Society for Microbiology, Washington DC, pp 91–103
Gupta G, Sarma MH, Sarma RH (1988) On the question of DNA bending: two dimensional NMR studies on d(GTTTTAAAAC)2 in solution. Biochemistry 27:7909–7919
Hagerman PJ (1986) Sequence-directed curvature of DNA. Nature 321:449–450
Katahira M, Sugeta H, Kyogoku Y, Fujii S, Fujisawa R, Tomita K-I (1988) One and two dimensional NMR studies on the conformation of DNA containing the oligo(dA) oligo(dT) tract. Nucleic Acids Res 16:8619–8632
Kohwi-Shigematsu T, Kohwi Y (1985) Poly(dG)-poly(dC) sequences under torsional stress, induce an altered DNA conformation upon neighboring DNA sequences. Cell 43:199–206
Koo HS, Wu HM, Crothers DM (1986) DNA bending at adenine-thymine tracts. Nature 320:501–506
Larsen A, Weintraub H (1982) An altered DNA conformation detected by SI nuclease occurs at specific regions in active chick globin gene. Cell 29:609–622
Marini JC, Levene SD, Crothers DM, England PT (1982) Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci USA 79:7664–7668
McGhee JD, Wood WI, Dolan M, Engel JD, Felsenfeld G (1981) A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell 27:45–55
Nussinov R (1980) Some rules in the ordering of nucleotides in the DNA. Nucleic Acids Res 8:4545–4562
Nussinov R (1981a) Nearest neighbor nucleotide patterns: structural and biological implications. J Biol Chem 256:8458–8462
Nussinov R (1981b) The eukaryotic dinucleotide preference rules and their implications on degenerate codon choice. J Mol Biol 149:125–131
Nussinov R (1984a) Doublet frequencies in evolutionary distinct groups. Nucleic Acids Res 12:1749–1763
Nussinov R (1984b) Strong doublet preferences in nucleotide sequences and DNA geometry. J Mol Evol 20:111–119
Nussinov R, Sarai A, Smythers GW, Jernigan RL (1989a) Distinct patterns in homooligomer tracts sequences context in prokaryotic and eukaryotic DNA. Biochim Biophys Acta 1008:329–338
Nussinov R, Sarai A, Smythers GW, Wang D, Jernigan RL (1989b) Strong patterns in homooligomer tract occurrences in potential regulatory sites in eukaryotic genomes. J Biomol Struct & Dyn 7:707–722
Phillips GJ, Arnold J, Ivarie R (1987) Mono- through hexanucleotide composition of theEscherichia coli genome: a Markov chain analysis. Nucleic Acids Res 15:2611–2626
Sarma MH, Gupta G, Sarma RH (1988) Structure of a bent DNA: two dimensional NMR studies on d(GAAAATTTTC)2. Biochemistry 27:3423–3432
Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191:659–675
Travers A (1987) DNA binding and nucleosome positioning. Trends Biochem Sci 12:108–112
Travers A, Klug A (1987) DNA wrapping and writhing. Nature 327:280–281
Wu HM, Crothers DM (1984) The locus of sequence directed and protein induced DNA bending. Nature 308:509–513
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Nussinov, R. Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences. J Mol Evol 33, 259–266 (1991). https://doi.org/10.1007/BF02100677
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DOI: https://doi.org/10.1007/BF02100677