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Nucleic Acids Research, 1985, Vol. 13, No. 5 1683-1701
© 1985

Articles

Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts

Andrzej K. Konopka, Johanes Reiter1,*, Manfred Jung2, David A. Zarling+ and Thomas M. Jovin

Abteilung Molekulare Biologie, Max-Planck-Institut für biophysikalische Chemie, D-3400 Göttingen FRG 1Institut für theoretische Chemie und Strahlchemie der Universität A-1090 Wien, Austria 2Abteilung Biochemische Kinetik, Max-Planck-Institut für biophysikalische Chemie D-3400 Göttingen, FRG

Received December 7, 1984. Revised February 4, 1985. Accepted February 4, 1985.

The recent electronmicroscopic and biochemical mapping of Z-DNA sites in {varphi}x174, SV40, pBR322 and PM2 DNAs has been used to determine two sets of criteria for identification of potential Z-DNA sequences in natural DNA genomes. The prediction of potential Z-DNA tracts and corresponding statistical analysis of their occurrence have been made on a sample of 14 DNA genomes.

Alternating purine and pyrimidine tracts longer than 5 base pairs in length and their clusters (quasi alternating fragments) in the 14 genomes studied are under-represented compared to the expectation from corresponding random sequences. The fragments [d(G.C)]n and [d(C.6)]n, (n)3) in general do not occur in circular DNA genomes and are under-represented in the linear DNAs of phages {lambda} and T7, whereas in (linear genomes of adenoviruses they are strongly over-represented. With minor exceptions, potential Z-DNA sites are also under-represented compared to random sequences.

In the 14 genomes studied, predicted Z-DNA tracts occur in non-coding as well as in protein coding regions. The predicted Z-DNA sites in {varphi}x174, SV40, pBR322 and PM2 correspond well with those mapped experimentally. A complete listing together with a compact graphical representation of alternating purine-pyrimidine fragments and their Z-forming potential are presented.

*Present address: Stanford University, Department of Chemistry, Stanford, CA 94305, USA

+Present address: University of California-Berkeley, Naval Biosciences Laboratory, Oakland, CA 94625, USA


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