Identification of bent DNA and ARS fragments in the genome of Choristoneura fumiferana nuclear polyhedrosis virus

Abstract

We identified four CfMNPV DNA fragments with autonomously replicating sequences ( ARS) functional in Saccharomyces cerevisiae. A 0.9-kb fragment which, mapped to 54.5 to 55.3 map units within EcoRI HI of the CfMNPV genome, showed the strongest ARS activity of the four. Sequence analysis of this 0.9-kb DNA segment revealed an A + T-rich region separated from a G + C-rich region by 320 bp. Although no sequence matched exactly the ARS core-consensus sequence, 13 near-matches differing by only one or two nucleotides from the core-consensus sequence, were identified. Ten near-matches were clustered within a 105-bp A + T-rich region, and were arranged as inverted repeats. A section of bent DNA structure was predicted within this region. The bent DNA, which showed temperature-dependent retardation during polyacrylamide gel electrophoresis, was unique as its sequence was arranged as a symmetrical ‘tilde’ (~) structure. The second (1.0 kb) and third (1.6 kb) ARS-bearing fragments mapped within EcoRI-E and -B fragments which contain homologous repeat sequences. The fourth (1.5 kb) fragment had the weakest ARS activity and mapped to the EcoRI-D or -B regions of the genome.