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

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...

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Bibliographic Details
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
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Summary: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.
ISSN:0305-1048
1362-4962