Abstract
We propose an index of DNA homogeneity (IDH) based on a binary distribution model that quantifies structural and thermodynamic aggregates present in DNA primary structures. Extensive analysis of sequence databases with the IDH uncovers significant constraints on DNA sequence other than those derived from codon usage or protein function. This index clearly distinguishes between organisms of different evolutive origins and places them in disjoint domains of DNA sequence space.
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References
Arques DG, Michel CJ (1990) A model of DNA sequence evolution. Bull Math Biol 52:741–742
Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1–11
Bernardi G (1993) Genome organization and species formation in vertebrates. J Mol Evol 37:331–337
Bilofsky HS, Burks C, Fickett JW, Goad WB, Lewitter FI, Rindone WP, Swindell CD, Tung CS (1986) The GenBank genetic sequence databank. Nucl Acids Res 14:1–4
Breslauer KJ, Frank R, Blöcker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83:3746–3750
Calladine CR (1982) Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol 161:343–352
Chuprina VP, Lipanov AA, Fedoroff OY, Kim SG, Kintanar A, Reid BR (1991) Sequence effects on local DNA topology. Proc Natl Acad Sci USA 88:9087–9091
Conrad M, Ebeling W (1992) M.V. Volkenstein evolutionary thinking and the structure of fitness landscapes. Biosys 27:125–128
Costerton JW, Poffenroth L, Wilt JC, Kordová N (1976) Ultrastructural studies of the nucleids of the pleomorphic forms of 6BC: a comparation with bacteria. Can J Microbiol 22:16–28
Delcourt SG, Blake RD (1991) Stacking energies in DNA. J Biol Chem 266:15160–15169
Dickerson RE (1983) Base sequence and helix structure variations in B and A DNA. J Mol Biol 166:419–441
Dickerson RE (1992) DNA structure from A to Z. Methods Enzymology 211:67–111
Dorit RL, Schoenbach L, Gilbert W (1990) How big is the universe of exons? Science 250:1377–1382
Eickbush TH, Mondrianakis EN (1978) The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids. Cell 13:295–306
Eigen M, McCaskill J, Schuster P (1988) The Molecular quasi-species. Adv Chem Phys 75:149–263
Hess ST, Blake JD, Blake RD (1994) Wide variation in neighbor-dependent substitution rates. J Mol Biol 236:1022–1033
Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Evol 146:1–21
Izatt RM, Christiansen JJ, Rytting H (1971) Site and thermodynamic quantities associated with proton and metal ion interactions with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides. Chem Rev 71:439–481
Jukes TH (1990) Genetic code 1990. Experientia 46:1149–1157
Karlin S, Mocarski ES, Scahchtel, GA (1994) Molecular evolution of Herpesviruses: genomic and protein sequence comparisons. J Virol 68:1886–1902
Kaul R, Tao S, Wenman WM (1992) Interspecies structural diversity among chlamydial genes encoding histone H1. Gene 112:129–132
Marzilli LG, Kistenmacher TJ (1977) Stereoselectivity in the binding of transition-metal chelate complexes to nucleic acid constituent: bonding and nonbonding effects. Acc Chem Res 10:146–152
Medrano L, Cocho G, Miramontes P, Rius JL (1994) The effect of DNA stability on mutation and sequence evolution Evol Theo 10:249–258
Nussinov R (1991) Compositional variations in DNA sequences. Comput Appl Biosci 7:287–293
Osawa S, Muto A, Ohama T, Andachi Y, Tanaka R, Yamao F (1990) Prokaryotic genetic code. Experientia 46:1097–1106
Pabo CO, Sauer RT (1984) Protein-DNA recognition. Ann Rev Biochem 53:293–321
Rein R, Garduño R, Egan JT, Columbano S, Coeckelenbergh Y, Macelroy RD (1977) Elements of a DNA-polypeptide recognition code: electrostatic potential around the doublet helix, and a stereospecific model for purine recognition. Biosystems 9:131–137
Sabeur G, Macaya G, Kadi F, Bernardi G (1993) The isochore patterns of mammalian genomes and their phylogenetic implications. J Mol Evol 37:93–108
Smith AT, Santama N, Dacey S, Edwards M, Bray RC, Thomeley RN, Burke JF (1990) Expression of a synthetic gene for horseradish peroxidase C in Escherichia coli and folding and activation of the recombinant enzyme with Ca2+ and heme. J Biol Chem 256:13335–13343
Trifonov EN (1982) Sequence-dependent variations of B-DNA structure and protein-DNA recognition. In: Symposia on quantitative biology, vol 47. Cold Spring Harbor Laboratory, Cold Spring Harbor NY, pp 271–278
Volkenstein MV (1987) Punctualism, non-adaptationism, neutralism and evolution. Biosys 20:289–304
Wright S (1967) Surfaces of selective value. Proc Natl Acad Sci USA 58:452–458
Yanagi K, Privé GG, Dickerson RE (1991) Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J Mol Biol 217:201–214
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On sabbatical leave from Facultad de Ciencias, UNAM, México
Correspondence to: P. Miramontes
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Miramontes, P., Medrano, L., Cerpa, C. et al. Structural and thermodynamic properties of DNA uncover different evolutionary histories. J Mol Evol 40, 698–704 (1995). https://doi.org/10.1007/BF00160519
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DOI: https://doi.org/10.1007/BF00160519