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  Home > JCE Print > Journal of Chemical Education > Issues > 2000  > November  >
In the Laboratory
Thermodynamics of DNA Duplex Formation: A Biophysical Chemistry Laboratory Experiment
Kathleen P. Howard
Department of Chemistry, Swarthmore College, Swarthmore, PA 19081
Cover
November 2000
Vol. 77 No. 11
p. 1469
Abstract
The goal of this biophysical experiment is to measure thermodynamic properties of a short DNA duplex by melting the ordered native structure (duplex) into the disordered, denatured state (single strands) while monitoring the transition using ultraviolet spectrophotometry. The DNA samples we used were two complementary synthetic DNA oligomers, dCA7G and dCT7G. The absorbance of four separate DNA samples with different concentrations (10-75 mM for each single strand) is measured at 260 nm as the temperature is increased from 10 to 70 °C. As the ordered regions of stacked base pairs in the DNA duplex are disrupted, the UV absorbance increases. The profile of UV absorbance versus temperature is called a melting curve and the midpoint of the transition is defined as the melting temperature, Tm. The dependence of Tm on strand concentration can be analyzed to yield quantitative thermodynamic data (DH°, DS°, DG°).
Supplement
A student handout and detailed set of instructor notes for setting up this experiment are available.
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*  Citation
 Howard, Kathleen P. J. Chem. Educ. 2000 77 1469.
*  Keywords
 Biophysical Chemistry; Laboratory Instruction; Nucleic Acids / DNA / RNA; Thermodynamics; UV-Vis Spectroscopy
*  History
 Created:
Last Updated:		 October 6, 2000
August 31, 2005
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