RNA Structure and Transcription

structure of RNA

synthesized as a single strand, so forms secondary structures with itself, more common to have non Watson-Crick pairings, structure determined all by sequence, function determined all by structure, hard to predict tertiary structure

RNA folding driven by

sequence, metal ion identity and concentration - not adding metal ion can mean structure won’t form, RNA binding proteins, want to hide hydrophobic surfaces from water (base stacking)

Mg in RNA folding and catalysis

around 10 mM naturally, neutralizes charges and stabilizes RNA by making multidentate contacts, often is an active metal ion, can stabilize phosphotransfer reaction transition states

prediction and determination of secondary structure

RNA fold program, AlphaFold 3 is getting better, hard to model due to lack of data, SHAPE for determination, acylation that target accessible 2’-OH (usually label flexible regions, non W:C regions), acylation inhibits primer extensions in PCR, making a map

transcription steps

from DNA to RNA, similar to replication (initiation, elongation, termination)

initiation of transcription

not all DNA is transcribed equally, depends on need, promotors needed to start, recruit transcription factors (activators, repressors, enhancers, silencers)

replication vs. transcription

new RNA strand leaves template, usually shorter segments, can be concurrently copied, accuracy of transcription is less important

RNA polymerase and initiation in prokaryotes

only Pol-I, a factor sigma recognizes -35 and -10 regions, then binds RNA polymerase, repressors block transcription by binding to the target regions

types of eukaryotic RNA polymerase

Pol-I - all rRNA except 5S
Pol-II - miRNA, siRNA, lncRNA, all mRNA
Pol-III - have types specific to RNA types. tRNA

types of RNA polymerase termination

intrinsic - sequencing specific, U-tract causes a pause in transcription, allowing a hairpin to form, this disrupts EC and causes dissociation
extrinsic - Rho binding sequence, open state of Rho is an open washer, clamps around RNA and pulls on it, stopping transcription