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PubMed · 3459152

Predicting DNA duplex stability from the base sequence.

K J Breslauer·R Frank·H Blöcker·L A Marky
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Abstract

We report the complete thermodynamic library of all 10 Watson-Crick DNA nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 DNA oligomers and 9 DNA polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequence. We illustrate our method of calculation by using the nearest-neighbor data to predict transition enthalpies and free energies for a series of DNA oligomers. These predicted values are in excellent agreement with the corresponding values determined experimentally. This agreement demonstrates that a DNA duplex structure thermodynamically can be considered to be the sum of its nearest-neighbor interactions. Armed with this knowledge and the nearest-neighbor thermodynamic data reported here, scientists now will be able to predict the stability (delta G degree) and the melting behavior (delta H degree) of any DNA duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as predicting the stability of a probe-gene complex; selecting optimal conditions for a hybridization experiment; deciding on the minimum length of a probe; predicting the influence of a specific transversion or transition on the stability of an affected DNA region; and predicting the relative stabilities of local domains within a DNA duplex.

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Base CompositionBase SequenceDNANucleic Acid ConformationNucleic Acid DenaturationOligodeoxyribonucleotidesThermodynamicsJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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K J Breslauer, R Frank, H Blöcker, L A Marky. 1986. Predicting DNA duplex stability from the base sequence.. https://doi.org/10.1073/pnas.83.11.3746

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