TY - JOUR
T1 - Analysis of open complex formation during RNA polymerase II transcription initiation using heteroduplex templates and potassium permanganate probing
AU - Holstege, Frank C.P.
AU - Timmers, H. Th Marc
N1 - Funding Information:
We thank D. Tantin and M. Carey (University of California, Los Angeles) for help in the initial phase of the preparation of heteroduplex DNA fragments. We also are grateful to B. Moss (National Institutes of Health) and H. Stunnenberg (University of Nijmegen) for discussions. We thank P. C. van der Vliet for continued support and U. Fiedler and J. A. van der Knaap for critically reading the manuscript. Financial support was provided to H.Th.M.T. by the Royal Netherlands Academy of Arts and Sciences. This work was also supported in part by the Netherlands Foundation for Chemical Research (SON).
PY - 1997/7
Y1 - 1997/7
N2 - Open complex formation precedes initiation of transcription by RNA polymerases. In the analysis of transcription initiation from eukaryotic class II promoters, we have used promoter DNA structures that represent intermediates in open complex formation. We describe the preparation and isolation of heteroduplex promoter fragments. Probes containing these DNA structures have a general application in the study of proteins binding to junctions of double- and single-stranded DNA. Such proteins play important roles not only in the regulation of RNA synthesis but also in processes like repair, replication, and recombination of DNA. In addition, a protocol is provided for a rapid and quantitative assay for open complexes and transcription bubbles using potassium permanganate as a chemical probe for single-stranded regions in DNA.
AB - Open complex formation precedes initiation of transcription by RNA polymerases. In the analysis of transcription initiation from eukaryotic class II promoters, we have used promoter DNA structures that represent intermediates in open complex formation. We describe the preparation and isolation of heteroduplex promoter fragments. Probes containing these DNA structures have a general application in the study of proteins binding to junctions of double- and single-stranded DNA. Such proteins play important roles not only in the regulation of RNA synthesis but also in processes like repair, replication, and recombination of DNA. In addition, a protocol is provided for a rapid and quantitative assay for open complexes and transcription bubbles using potassium permanganate as a chemical probe for single-stranded regions in DNA.
UR - https://www.scopus.com/pages/publications/0031194867
U2 - 10.1006/meth.1997.0472
DO - 10.1006/meth.1997.0472
M3 - Article
C2 - 9237164
AN - SCOPUS:0031194867
SN - 1046-2023
VL - 12
SP - 203
EP - 211
JO - Methods
JF - Methods
IS - 3
ER -