Author: John Woods Dubendorff
Publisher:
ISBN:
Category : DNA polymerases
Languages : en
Pages : 262
Book Description
The Interaction of Base-analog Subsituted Lambda PR̳ Promoters with E. Coli RNA Polymerase
Author: John Woods Dubendorff
Publisher:
ISBN:
Category : DNA polymerases
Languages : en
Pages : 262
Book Description
Publisher:
ISBN:
Category : DNA polymerases
Languages : en
Pages : 262
Book Description
The Interaction of E. Coli RNA Polymerase with Lambda Phage PR Promoter
Author: Won-Chul Suh
Publisher:
ISBN:
Category :
Languages : en
Pages : 430
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 430
Book Description
The Interaction of Escherichia Coli RNA Polymerase with Phage [lambda] Promoters
Author: Jung-Hye Roe
Publisher:
ISBN:
Category : Bacteriophage lambda
Languages : en
Pages : 422
Book Description
Publisher:
ISBN:
Category : Bacteriophage lambda
Languages : en
Pages : 422
Book Description
Interaction of E.coli RNA Polymerase with Phage [lambda] Promoters
Author: Elizabeth Margaret Owens
Publisher:
ISBN:
Category : Bacteriophage
Languages : en
Pages : 172
Book Description
Publisher:
ISBN:
Category : Bacteriophage
Languages : en
Pages : 172
Book Description
Kinetic Investigation of the Molecular Processes Involved in the Mechanism of Open Complex Formation Between E. Coli RNA Polymerase and the [lambda]Pr Promoter
Author: Wayne Kontur
Publisher:
ISBN:
Category :
Languages : en
Pages : 200
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 200
Book Description
Studies on the Interaction of E. Coli RNA Polymerase with Lactose Promoter DNA
Author: Donald Duane Lorimer
Publisher:
ISBN:
Category : DNA.
Languages : en
Pages : 260
Book Description
Publisher:
ISBN:
Category : DNA.
Languages : en
Pages : 260
Book Description
Kinetics and Mechanism of Open Complex Formation, Stabilization, and Initiation by E. Coli RNA Polymerase at [lambda]PR and T7A1 Promoters
Author: Hao-Che Wang
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
Book Description
The flow of genetic information in cells starts with transcription by the enzyme RNA polymerase (RNAP) of DNA information to synthesize a wide variety of structural and functional RNAs which collectively participate in most cellular processes. Transcription is therefore a highly regulated step in gene expression. Research discussed here focuses on transcription initiation, the earliest phase of transcription, and on questions of how differences in promoter DNA sequences and length affect initiation thermodynamics and kinetics. During transcription initiation, RNAP binds to and unwinds the transcription start site region of promoter DNA, opening 13 bp to form an open complex (OC). Chapter 2 reports a detailed kinetic-mechanistic comparison of OC formation for the model λPR and T7A1 promoters, and Chapter 3 does the same for OC dissociation kinetics and mechanisms. For OC formation, kinetics of 2-amino purine (-4) fluorescence, Cy3 (-100) - Cy5 (+14) FRET, and single-dye PIFE were determined and compared with filter binding kinetics of formation of long-lived promoter complexes. A range of temperatures and of glycine betaine concentrations was examined. From these comparisons, we conclude that early steps in the mechanism of OC formation are similar for the two promoters while later steps including DNA opening differ significantly. Our data are consistent with previous reports that opening of the T7A1 bubble occurs in two adjacent kinetic steps vs. one step for λPR. After the DNA opening transition state, the kinetics and mechanisms of OC formation at these two promoters become similar again. In Chapter 3, we investigated the roles of clamp closing and of allosteric effects of discriminator and upstream interactions on downstream elements in stabilizing E. coli RNA polymerase- λPR promoter open complexes (OC). Our approach is to determine dissociation rate constants for the stable OC (kd) and for the unstable I2 intermediate OC (k-2) at λPR and T7A1 promoters and promoter variants with exchanged discriminators, core promoters or UP elements by filter binding assays. Values of kd are also determined for downstream-truncated promoters (at +12, +6) and for a jaw deletion RNAP variant. Analysis yields free energy changes 8́6G3^o for the conversion of unstable I2 to a stable OC, and the large contribution to 8́6G3^o for all promoters, from clamp closing on the promoter from +6 upstream, as well as the significant contributions to 8́6G3^o for promoters with the λPR discriminator from downstream interactions with the Îø lobe and Îø' jaw that are allosterically controlled by interactions of the discriminator with ϳ1.2 and the Îø gate loop. Lastly, in chapter 4, we further test how promoters with different OC stability affect the escaping of the RNAP from promoter. Preliminary results indicate the OC lifetime mainly alters the rate for converting the OC into initial complex (IC) for NTP incorporations. Taken together, our studies provide a more complete understanding of how promoter sequence and length influences different phases of transcription initiation.
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
Book Description
The flow of genetic information in cells starts with transcription by the enzyme RNA polymerase (RNAP) of DNA information to synthesize a wide variety of structural and functional RNAs which collectively participate in most cellular processes. Transcription is therefore a highly regulated step in gene expression. Research discussed here focuses on transcription initiation, the earliest phase of transcription, and on questions of how differences in promoter DNA sequences and length affect initiation thermodynamics and kinetics. During transcription initiation, RNAP binds to and unwinds the transcription start site region of promoter DNA, opening 13 bp to form an open complex (OC). Chapter 2 reports a detailed kinetic-mechanistic comparison of OC formation for the model λPR and T7A1 promoters, and Chapter 3 does the same for OC dissociation kinetics and mechanisms. For OC formation, kinetics of 2-amino purine (-4) fluorescence, Cy3 (-100) - Cy5 (+14) FRET, and single-dye PIFE were determined and compared with filter binding kinetics of formation of long-lived promoter complexes. A range of temperatures and of glycine betaine concentrations was examined. From these comparisons, we conclude that early steps in the mechanism of OC formation are similar for the two promoters while later steps including DNA opening differ significantly. Our data are consistent with previous reports that opening of the T7A1 bubble occurs in two adjacent kinetic steps vs. one step for λPR. After the DNA opening transition state, the kinetics and mechanisms of OC formation at these two promoters become similar again. In Chapter 3, we investigated the roles of clamp closing and of allosteric effects of discriminator and upstream interactions on downstream elements in stabilizing E. coli RNA polymerase- λPR promoter open complexes (OC). Our approach is to determine dissociation rate constants for the stable OC (kd) and for the unstable I2 intermediate OC (k-2) at λPR and T7A1 promoters and promoter variants with exchanged discriminators, core promoters or UP elements by filter binding assays. Values of kd are also determined for downstream-truncated promoters (at +12, +6) and for a jaw deletion RNAP variant. Analysis yields free energy changes 8́6G3^o for the conversion of unstable I2 to a stable OC, and the large contribution to 8́6G3^o for all promoters, from clamp closing on the promoter from +6 upstream, as well as the significant contributions to 8́6G3^o for promoters with the λPR discriminator from downstream interactions with the Îø lobe and Îø' jaw that are allosterically controlled by interactions of the discriminator with ϳ1.2 and the Îø gate loop. Lastly, in chapter 4, we further test how promoters with different OC stability affect the escaping of the RNAP from promoter. Preliminary results indicate the OC lifetime mainly alters the rate for converting the OC into initial complex (IC) for NTP incorporations. Taken together, our studies provide a more complete understanding of how promoter sequence and length influences different phases of transcription initiation.
Cumulated Index Medicus
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 998
Book Description
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 998
Book Description
Dissertation Abstracts International
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 626
Book Description
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 626
Book Description
Proceedings of the Robert A. Welch Foundation Conferences on Chemical Research
Author:
Publisher:
ISBN:
Category : Chemistry
Languages : en
Pages :
Book Description
Publisher:
ISBN:
Category : Chemistry
Languages : en
Pages :
Book Description