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Nucleic Acids Research, 2000, Vol. 28, No. 23 4679-4688
© 2000 Oxford University Press

A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs

David M. Prescott* and Sarah J. Dizick

University of Colorado, Department of Molecular, Cellular and Developmental Biology, Boulder, CO 80309-0347, USA

The 50 non-coding bases immediately internal to the telomeric repeats in the two 5' ends of macronuclear DNA molecules of a group of hypotrichous ciliates are anomalous in composition, consisting of 61% purines and 39% pyrimidines, A>T (ratio of 44:32), and G>C (ratio of 17:7). These ratio imbalances violate parity rule 2, according to which A should equal T and G should equal C within a DNA strand and therefore pyrimidines should equal purines. The purine-rich and base ratio imbalances are in marked contrast to the rest of the non-coding parts of the molecules, which have the theoretically expected purine content of 50%, with A = T and G = C. The ORFs contain an average of 52% purines as a result of bias in codon usage. The 50 bases that flank the 5' ends of macronuclear sequences in micronuclear DNA (12 cases) consist of ~50% purines. Thus, the 50 bases in the 5' ends of macronuclear sequences in micronuclear DNA are islands of purine richness in which A>T and G>C. These islands may serve as signals for the excision of macronuclear molecules during macronuclear development. We have found no published reports of coding or non-coding native DNA with such anomalous base composition.

* To whom correspondence should be addressed. Tel: +1 303 492 8381; Fax: +1 303 492 7744; Email: prescotd{at}spot.colorado.edu


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