8.592 - HST.452J (Spring 2026)

Statistical Physics in Biology

Lecture 10

DNA denaturation (melting)

1. Macroscopic properties of DNA; packaging into chromatin (eukaryotes)
2. Discovery of DNA Structure and Function: Watson and Crick, L. Pray, Nature Education 1, 1 (2008)
• Microscopic structure of DNA; the four nucleotides;
• DNA Structure
• Importance of stacking interactions, binding energies
3. Nucleic acid thermodynamics:
• denaturation
• hybridization
• (similarity)
• renaturation (zippering)
4. Melting curves based on UV absorption  (ss versus ds content):
• medium chains,
• long chains;
• general features and theoretical issues
5. The pair-stacking model; (Poland D & Scheraga HA. Theory of Helix-Coil Transitions in Biopolymers . Academic Press, New York, 1970.)
6. Theoretical analysis of homopolymer denaturation (presentation by David Mukamel at ITP)

(Lecture notes)

• UNAFold
• DINAMelt Web Server is an online simulation platform that predicts full equilibrium melting profiles, heat capacity, and melting temperatures ($T_m$) for specified DNA or RNA sequences.
• IDT OligoAnalyzer Tool is a web-based GUI application used to calculate the exact melting temperature ($T_m$), GC content, and thermodynamic properties of specified DNA sequences using customizable salt and primer concentrations.