Summary
A doublet frequency count (set of frequencies of the sixteen possible two-base sequences) can be calculated from the experimentally determined overall sequence of a nucleic acid. In this paper, a statistical methodology is developed for comparing such counts with random, with others of the same type or with doublet proportions found in whole DNAs. The methods are applied to two major categories of sequenced RNAs. It is found that vertebrate ribosomal and transfer RNAs show significant differences from the overall vertebrate DNA pattern, especially in the frequency of the doublet CG. Bacterial rRNA and tRNA, on the other hand, show less dissimilarity from total DNA. In the RNA of the small bacteriophage MS2, the doublet frequencies of the translated regions of the genome resemble those in the hostE. coli, whereas those in the intercistronic regions differ substantially. All these findings are discussed in relation to the origin, evolution and selection of the nucleic acids concerned.
Similar content being viewed by others
References
Berzin, V.M., Gren, E.Y. (1972). Biokhimiya, 37, 874
Billeter, M.A., Dahlberg, J.E., Goodman, H.M., Hindley, J., Weissmann, C. (1969). Nature (Lond.) 224, 1083
Billingsley, P. (1961). Ann. Math. Statist. 32, 12
Bronson, M.J., Squires, C., Yanofsky, C. (1973). Proc. Nat. Acad. Sci. (Wash.) 70, 2335
Brownlee, G.G., Cartwright, E.M., Cowan, N.J., Jarvis, J.M., Milstein, C. (1973). Nature New Biol. 244, 236
Brownlee, G.G., Sanger, F., Barrell, B.G. (1968). J. Mol. Biol. 34, 379
Bullock, E., Elton, R.A. (1972). J. Mol. Evol. 1, 315
Contreras, R., Vandenberghe, A., Min Jou, W., De Wachter, R., Fiers, W. (1971). FEBS Lett. 18, 141
Contreras, R., Vandenberghe, A., Volckaert, G., Min Jou, W., Fiers, W. (1972). FEBS Lett. 24, 339
Contreras, R., Ysebaert, M., Min Jou, W., Fiers, W. (1973). Nature New Biol. 241, 99
Cory, S., Marcker, K.A., Dube, S.K., Clark, B.F.C. (1968). Nature (Lond.) 220, 1039
Dayhoff, M.O. (1972). Atlas of protein sequence and structure 1972. Silver Spring, Md.: National Biomedical Research Foundation
Dhar, R., Zain, S., Weissman, S.M., Pan, J., Subramanian, K. (1974). Proc. Nat. Acad. Sci. (Wash.) 71, 371
Elton, R.A. (1973a). Nature New Biol. 243, 287
Elton, R.A. (1973b). J. Mol. Evol. 2, 263
Elton, R.A. (1973c). J. Mol. Evol. 2, 293
Elton, R.A. (1974). J. Theoret. Biol. 45, 533
Fellner, P., Ehresmann, C., Ebel, J.P. (1970). Nature (Lond.) 225, 26
Ford, P.J., Southern, E.M. (1973). Nature New Biol. 241, 7
Forget, B.G., Weissman, S.M. (1967). Sci. (N.Y.) 158, 1695
Fraser, N.W., Maden, B.E.H., Burdon, R.H. (1973). FEBS Lett. 36, 257
Gilbert, W., Maxam, A. (1973). Proc. Nat. Acad. Sci. (Wash.) 70, 3581
Goel, N.S., Subba Rao, G., Yčas, M., Bremermann, H.J., King, L. (1972). J. Theoret. Biol. 35, 399
Haegeman, G., Fiers, W. (1973). Eur. J. Biochem. 36, 135
Holmquist, R., Jukes, T.H., Pangburn, S. (1973). J. Mol. Biol. 78, 91
Josse, J., Kaiser, A.D., Kornberg, A. (1961). J. Biol. Chem. 236, 864
Keith, G., Picaud, F., Weissenbach, J., Ebel, J.P., Petrissant, G., Dirheimer, G. (1973). FEBS Lett. 31, 345
Kimura, M., Ohta, T. (1973). Nature New Biol. 243, 199
Lebowitz, P., Weissman, S.M., Radding, C.M. (1971). J. Biol. Chem. 246, 5120
Maizels, N.M. (1973). Proc. Nat. Acad. Sci. (Wash.) 70, 3585
Min Jou, W., Haegeman, G., Ysebaert, M., Fiers, W. (1972). Nature (Lond.) 237, 82
Morrison, J.M., Keir, H.M., Subak-Sharpe, J.H., Crawford, L.V. (1967). J. Gen. Virol. 1, 101
Nazar, R.N., Busch, H. (1973). Biochim. Biophys. Acta, 299, 428
Nichols, J.L. (1970). Nature (Lond.) 225, 147
Pechman, K.J., Woese, C.R. (1972). J. Mol. Evol. 1, 230
Robertson, H.D., Barrell, B.G., Weith, H.L., Donelson, J.E. (1973). Nature New Biol. 241, 38
Russell, G.J., McGeoch, D.J., Elton, R.A., Subak-Sharpe, J.H. (1973). J. Mol. Evol. 2, 277
Sanger, F., Donelson, J.E., Coulson, A.R., Kössel, H., Fischer, D. (1973). Proc. Nat. Acad. Sci. (Wash.) 70, 1209
Scherberg, N.H., Weiss, S.B. (1970). Proc. Nat. Acad. Sci. (Wash.) 67, 1164
Shapiro, L., August, J.T. (1965). J. Mol. Biol. 11, 272
Skalka, A., Burgi, E., Hershey, A.D. (1968). J. Mol. Biol. 34, 1
Staehelin, M., Rogg, H., Baguley, B.C., Ginsberg, T., Wehrli, W. (1968). Nature (Lond.) 219, 1363
Steitz, J.A. (1969). Nature (Lond.) 224, 957
Subak-Sharpe, J.H. (1967). Brit. Med. Bull. 23, 161
Subak-Sharpe, J.H. (1969). In: Proceedings of the 8th Canadian Cancer Research Conference, p. 242. London: Pergamon
Subak-Sharpe, J.H., Bürk, R.R., Crawford, L.V., Morrison, J.M., Hay, J., Keir, H.M. (1966). Cold Spr. Harb. Symp. Quant. Biol. 31, 737
Sueoka, N. (1961). Proc. Nat. Acad. Sci. (Wash.) 47, 1141
Swartz, M.N., Trautner, T.A., Kornberg, A. (1962). J. Biol. Chem. 237, 1961
De Wachter, R., Merregaert, J., Vandenberghe, A., Contreras, R., Fiers, W. (1971). Eur. J. Biochem. 22, 400
Weissmann, C., Billeter, M.A., Goodman, H.M., Hindley, J., Weber, H. (1973). Ann. Rev. Biochem. 42, 303
Whittle, P. (1955). J. Roy. Statist. Soc., Ser. B, 17, 235
Yudelevich, A. (1971). J. Mol. Biol. 60, 21
Ziff, E.B., Sedat, J.W., Galibert, F. (1973). Nature New Biol. 241, 34
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Elton, R.A. Doublet frequencies in sequenced nucleic acids. J Mol Evol 4, 323–346 (1975). https://doi.org/10.1007/BF01732535
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF01732535