The CTD peptide was phosphorylated in a timedependent manner with similar efficiency by both wild type and KR XPD complexes. Wild type and KR XPD complexes were incubated in the presence of homogenous recombinant TBP, TFIIB, TFIIE, TFIIF, and highly purified RNA polymerase II, linearized DNA template containing the adenovirus major late promoter, and ribonucleotides.Interestingly, correctly initiated transcripts were produced in the presence of either wild type and KR XPD complex. This was specifically due to TFIIH activity in both wild type and KR mutant preparations since omission of any basal factor from the reaction mixture did not yield appreciable transcript levels. The level of transcription supported by KR mutant TFIIH varied between different preparations within a fold range as compared with wild type and precluded detection of a statistically significant difference in transcription activity between wild type and KR preparations.To characterize further the possible effect of the KR mutation in the XPD subunit of TFIIH on transcription, we looked at early Targetmol’s Cefadroxil stages of transcription initiation.RNA products shorter than nucleotides accumulate with time, due to multiple rounds of abortive synthesis and initiation by the same RNA polymerase II complex. If subtle differences, such as the dynamic transition from closed to open conformation, exist in the presence of mutant TFIIH, they may become apparent from analysis of small RNA products.Importantly, however, no significant difference is observed in the formation of tri and dinucleotides and nucleotide transcripts in the presence of either wild type or mutant TFIIH.Open regions from to are efficiently detected in the presence of both wild type after production of a nucleotide transcript.Indicated are the positions of thymidine residues with respect to the transcriptional start site as determined with a G A ladder. After incubation, plasmid DNA was isolated, linearized, and subjected to agarose gel electrophoresis.Ethidium bromide staining indicated that equal amounts of DNA were recovered from each reaction shows that some radiolabel is incorporated in the damaged plasmid incubated with UV WCE alone compared with the nondamaged control, whereas increasing amounts of wild type TFIIH are able to stimulate DNA repair synthesis.Surprisingly, different preparations of TFIIH containing KR XPD were also able to stimulate DNA synthesis specifically in the plasmid containing AAF damage, although to a lower level as compared with wild type samples, and other similar experiments, we estimate that the mutant complex stimulates incorporation of nucleotides to about of the wild type level.These findings suggested that the KR XPD mutation might not completely impair the NER function of TFIIH.Therefore, we analyzed in more detail the formation of NER reaction intermediates.B, stimulation of RNA polymerase II transcription by wild type and KR complex is specifically due to TFIIH activity.Transcription reactions contained TFIIH and all basal transcription factors and RNA polymerase II. C, time course analysis of the formation of short RNA products.Basal transcription factors, wild type or KR mutant TFIIH, and RNA polymerase II were incubated with template DNA to allow the formation of preinitiation complexes.Subsequently, ATP was added to allow transient initial opening of the promoter region.