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ERIC Number: EJ838181
Record Type: Journal
Publication Date: 2009-May
Pages: 7
Abstractor: As Provided
ISSN: ISSN-0021-9584
Thermodynamics of Oligonucleotide Duplex Melting
Schreiber-Gosche, Sherrie; Edwards, Robert A.
Journal of Chemical Education, v86 n5 p644-650 May 2009
Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply rigorous thermodynamic analysis to an important biochemical problem. Because the stacking of base pairs on top of one another is a significant factor in the energetics of oligonucleotide melting, several investigators have applied van't Hoff analysis to melting temperature data using a nearest-neighbor model and have obtained entropies and enthalpies for the stacking of bases. The present article explains how the equilibrium constant for the dissociation of strands from double-stranded oligonucleotides can be expressed in terms of the total strand concentration and thus how the total strand concentration influences the melting temperature. It also presents a simplified analysis based on the entropies and enthalpies of stacking that is manually tractable so that students can work examples to help them understand the thermodynamics of oligonucleotide melting. (Contains 4 tables and 2 figures.)
Division of Chemical Education of the American Chemical Society. Subscription Department, P.O. Box 1267, Bellmawr, NJ 08099-1267. Tel: 800-691-9846; Tel: 856-931-5825; Fax: 856-931-4115; e-mail:; Web site:
Publication Type: Journal Articles; Reports - Descriptive
Education Level: N/A
Audience: Teachers
Language: English
Sponsor: N/A
Authoring Institution: N/A