Predicting DNA duplex stability from the base sequence

K. J. Breslauer, R. Frank, H. Blocker, L. A. Marky

Research output: Contribution to journalArticlepeer-review

1606 Scopus citations


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 caclculation by using the nearest-neighbor data to predict transition enthalphies 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 (ΔG°) and the melting behavior (ΔH°) of any DNA duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as (i) predicting the stability of a probe-gene complex; (ii) selecting optimal conditions of a hybridization experiment; (iii) deciding on the minimum length of a probe; (iv) predicting the influence of a specific transversion or transition on the stability of an affected DNA region, and (v) predicting the relative stabilities of local domains within a DNA duplex.

Original languageEnglish (US)
Pages (from-to)3746-3750
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number11
StatePublished - 1986
Externally publishedYes

ASJC Scopus subject areas

  • General


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