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A computer aided thermodynamic approach for predicting the formation of Z‐DNA in naturally occurring sequences.
Author(s) -
Ho P.S.,
Ellison M.J.,
Quigley G.J.,
Rich A.
Publication year - 1986
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/j.1460-2075.1986.tb04558.x
Subject(s) - dna , dna supercoil , information retrieval , biology , computational biology , computer science , combinatorics , genetics , mathematics , dna replication
The ease with which a particular DNA segment adopts the left‐handed Z‐conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z‐hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z‐DNA formation. Incorporated into Z‐hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z‐forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z‐forming potential of sequences with different base compositions and different sequence lengths. Using Z‐hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus‐2. The results are compared with those previously obtained by others from experiments designed to locate Z‐DNA forming regions in these sequences using probes which show specificity for the left‐handed DNA conformation.