Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination.
Passage of E. coli RNA polymerase through an intrinsic transcription terminator, which encodes an RNA hairpin followed by a stretch of uridine residues, results in quick dissociation of the elongation complex. We show that folding of the hairpin disrupts the three upstream base pairs of the 8 bp RNA:DNA hybrid, a major stability determinant in the complex. Shortening the weak rU:dA hybrid from 8 nt to 5 nt causes dissociation of the complex. During termination, the hairpin does not directly compete for base pairing with the 8 bp hybrid. Thus, melting of the hybrid seems to result from spatial restrictions in RNA polymerase that couple the hairpin formation with the disruption of the hybrid immediately downstream from the stem. Our results suggest that a similar mechanism disrupts elongation complexes of yeast RNA polymerase II in vitro.
Komissarova
Natalia
N
NCI Center for Cancer Research, Frederick Cancer Research and Development Center, Frederick, MD 21702, USA. natkom@mail.ncifcrf.gov
Becker
Jodi
J
Solter
Stephanie
S
Kireeva
Maria
M
Kashlev
Mikhail
M
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism*; D009693:Nucleic Acid Hybridization; D011196:Potassium Permanganate / Q000494:pharmacology; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism*; D013997:Time Factors; D014158:Transcription, Genetic
D009692:Nucleic Acid Heteroduplexes; D011196:Potassium Permanganate; D012313:RNA; D004247:DNA; D012319:RNA Polymerase II