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Nucleic Acids Research, 2003, Vol. 31, No. 14 4211-4217
© 2003 Oxford University Press

Thermodynamic calculations and statistical correlations for oligo-probes design

O. V. Matveeva*, S. A. Shabalina1, V. A. Nemtsov2, A. D. Tsodikov3, R. F. Gesteland and J. F. Atkins

Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112, USA, 1 National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20814, USA, 2 MGGT, Ul. Lavochkina 23(A), 125502, Moscow, Russia and 3 Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA

*To whom correspondence should be addressed. Tel: +1 801 581 5191; Fax: +1 801 585 3910; Email: olgam{at}howard.genetics.utah.edu

Optimization of probe design for array-based experiments requires improved predictability of oligonucleotide hybridization behavior. Currently, designing oligonucleotides capable of interacting efficiently and specifically with the relevant target is not a routine procedure. Multiple examples demonstrate that oligonucleotides targeting different regions of the same RNA differ in their hybridization ability. The present work shows how thermodynamic evaluations of oligo-target duplex or oligo self-structure stabilities can facilitate probe design. Statistical analysis of large sets of hybridization data reveals that thermodynamic evaluation of oligonucleotide properties can be used to avoid poor RNA binders. Thermodynamic criteria for the selection of 20 and 21mers, which, with high probability, interact efficiently and specifically with their targets, are suggested. The design of longer oligonucleotides can also be facilitated by the same calculations of {Delta}G°T values for oligo-target duplex or oligo self-structure stabilities and similar selection schemes.


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