RNA (Secondary Structure)

1. Structure and function of RNA
2. The 'RNA world' hypothesis
3. Structural levels:
   • primary, secondary, tertiary;
   • Structural elements (stem, loop, bulge, …)
   • experimental methods
4. Representations without psuedoknots
5. 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".
6. Recursive (Hartree) calculation of partition function
7. Counting secondary structures. [Chandrasekhar. "Stochastic Problems in Physics and Astronomy." Reviews of Modern Physics 15, no. 1 (1943): 1–89.]
8. The melting of a hairpin

• The RNA world website
• The Zuker group's web-page
• The Vienna RNA package

(Detailed Lecture Notes (PDF))