Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 1986 Jun;83(11):3746-50.
doi: 10.1073/pnas.83.11.3746.

Predicting DNA Duplex Stability From the Base Sequence

Free PMC article

Predicting DNA Duplex Stability From the Base Sequence

K J Breslauer et al. Proc Natl Acad Sci U S A. .
Free PMC article

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.

Similar articles

See all similar articles

Cited by 438 articles

See all "Cited by" articles

References

    1. Cold Spring Harb Symp Quant Biol. 1966;31:77-84 - PubMed
    1. Nucleic Acids Res. 1985 Jul 11;13(13):4811-24 - PubMed
    1. Nature. 1971 Apr 9;230(5293):362-7 - PubMed
    1. J Mol Biol. 1973 Feb 5;73(4):483-96 - PubMed
    1. Nat New Biol. 1973 Nov 14;246(150):40-1 - PubMed

Publication types

LinkOut - more resources

Feedback