- Structure and function of RNA
- The ‘RNA world’ hypothesis
- Structural levels:
- primary, secondary, tertiary;
- Structural elements (stem, loop, bulge, …)
- experimental methods
- Representations without psuedoknots
- Algorithms for finding optimal secondary structure: Nussinov, R., and A.B. Jacobson. “Fast algorithm for predicting the secondary structure of single-stranded RNA.” PNAS 77, no. 11(1980): 6309-6313. “Research by Michael Zuker”.
- Recursive (Hartree) calculation of partition function
- Counting secondary structures. [Chandrasekhar. “Stochastic Problems in Physics and Astronomy.” Reviews of Modern Physics 15, no. 1 (1943): 1–89.]
- The melting of a hairpin
Lecture Notes
RNA (Secondary Structure)
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2011
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