Counter-clockwise rotation starting at 0º gives negative dihedral angles from -1º through

90º ending at -180º (the same dihedral angle  as +180º).

TLS Online TPP Program

#Id: 6298

#Unit 3. Fundamental Processes

The transition from the closed to the open complex involves structural changes in the enzyme and the opening of the DNA double helix to reveal the template and nontemplate strands. This “melting” occurs between positions –11 and +2, with respect to the transcription start site.

TLS Online TPP Program

#Id: 6299

#Unit 3. Fundamental Processes

In the case of the bacterial enzyme bearing s70, this transition, often called isomerization, does not require energy derived from ATP hydrolysis and is instead the result of a spontaneous conformational change in the DNA– enzyme complex to a more energetically favorable form.

TLS Online TPP Program

#Id: 6300

#Unit 3. Fundamental Processes

TLS Online TPP Program

#Id: 6301

#Unit 3. Fundamental Processes

The closed complex is converted into an open complex of 1.3 turns of the double helix in a series of steps by first “melting” a short region of DNA around the -10 region, giving an unstable intermediate open complex within the sequence bound by the enzyme.  Two bases in the non-template strand of the –10 element (A11 and T7) flip out from their base-stacking interactions and instead insert into pockets within the s protein where they make more favorable interactions. By stabilizing the single-stranded form of the –10 element, these interactions drive melting of the promoter region.

TLS Online TPP Program

#Id: 6302

#Unit 3. Fundamental Processes

During abortive Transcription, RNA Polymerase Remains Stationary and Pulls Downstream DNA into Itself RNA polymerase produces and releases short RNA transcripts of 10 nucleotides (abortive synthesis) before escaping the promoter, 

 

During abortive Transcription, RNA Polymerase Remains Stationary and Pulls Downstream DNA into Itself

RNA polymerase produces and releases short RNA transcripts of 10 nucleotides (abortive synthesis) before escaping the promoter, entering the elongation phase, and synthesizing the proper transcript. It has long been unclear how the enzyme’s active site translocates along the DNA template during initial abortive cycles of transcription. Three general models were proposed:- “transient excursion”, “Inchworming”, “Scrunching”

 

TLS Online TPP Program

#Id: 6303

#Unit 3. Fundamental Processes

RNA polymerase can initiate a new RNA chain de novo on a DNA template and thus does not need a primer