Open AccessRNA secondary structures of the bacteriophage φ6 packaging regions
Author(s) -
Markus Pirttimaa,
Dennis H. Bamford
Publication year - 2000
Publication title -
rna
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.037
H-Index - 171
eISSN - 1469-9001
pISSN - 1355-8382
DOI - 10.1017/s1355838200992598
Subject(s) - biology , rna , bacteriophage , computational biology , genetics , rna polymerase , nucleic acid structure , protein secondary structure , nucleic acid secondary structure , polymerase , dna , gene , biochemistry , escherichia coli
Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.