what is the primary difference between RNA and DNA
2’ OH in RNA (makes it ribose) and secondarily we have uridine instead of thymidine
what form does RNA take?
A-form, sugar pucker more energetically favorable (3’ endo)
T/F. RNA:RNA duplexes are much more stable than DNA:DNA duplexes
True, which is why you often see folded RNA but not folded DNA
why is 2’OH group destabilizing?
can be activated as a nucleophile under alkaline conditions or by RNAses
RNA secondary structure
commonly stem loops, other 3D elements
RNA tertiary structures
long range interactions - like pseudoknots, triple base interactions, ribose zippers, A platforms, tetraloop interactions
phylogenetic covariation analysis
align RNAs from members of family to look for concerted changes, often consistent with Watson-Crick basepairing rules
what are three edges of bases that can form H-bonds
Hoogsteen, watson-crick, sugar
T/F. Metal ions are sometimes necessary for RNA folding.
False, metal ions are required for RNA folding. Metal ions neutralize the electrostatic repulsion between phosphate groups and allow for stacking/folding
what is most common hydrated cation used for RNA folding
Mg2+
