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

• Published in: Nucleic acids research 1985, Vol.13 (5), p.1683-1701
• Main Authors: Konopka, A.K, Reiter, J, Jung, M, Zarling, D.A, Jovin, T.M
• Format: Article
• Language: English
• Subjects: algorithms; bacteriophages; chromosome mapping; clustered alternating fragment; DNA conformation; genome; mitochondrial DNA; nucleotide sequences; plasmids; purine nucleotides; pyrimidine nucleotides; quasi-alternating fragment; simian polyomavirus; statistical analysis; sv40; uniform alternating fragment; viruses; Z-DNA
• ISSN: 0305-1048; 1362-4962

The recent electron microscopic and biochemical mapping of Z-DNA sites in phiX174, 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.G)]n (n greater than or equal to 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 phiX174, 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.