title: A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment.
abstract: Transcription errors by T7 RNA polymerase (RNAP) may occur as the result of a mechanism in which the template base two positions downstream of the 3' end of the RNA (the TSn+1 base) is utilized during two consecutive nucleotide-addition cycles. In the first cycle, misalignment of the template strand leads to incorporation of a nucleotide that is complementary to the TSn+1 base. In the second cycle, the template is realigned and the mismatched primer is efficiently extended, resulting in a substitution error. Proper organization of the transcription bubble is required for maintaining the correct register of the DNA template, as the presence of a complementary nontemplate strand opposite the TSn+1 base suppresses template misalignment. Our findings for T7 RNAP are in contrast to related DNA polymerases of the Pol I type, which fail to extend mismatches efficiently and generate predominantly deletion errors as a result of template-strand misalignment.
authors.affiliation: Department of Microbiology and Immunology, The State University of New York Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA.
authors.forename: Richard T
authors.initials: RT
authors.lastname: Pomerantz
authors.forename: Dmitry
authors.initials: D
authors.lastname: Temiakov
authors.forename: Michael
authors.initials: M
authors.lastname: Anikin
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: William T
authors.initials: WT
authors.lastname: McAllister
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D004260:DNA Repair; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D016368:Frameshift Mutation; D017353:Gene Deletion; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011487:Protein Conformation; D013997:Time Factors; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases; D004259:DNA-Directed DNA Polymerase