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Nucleic Acids Research, 1995, Vol. 23, No. 12 2287-2291
© 1995

COMPUTATIONAL BIOLOGY

SSCP primer design based on single-strand DNA structure predicted by a DNA folding program

David A. Nielsen*,, Alexey Novoradovsky1 and David Goldman2

Sections of Molecular Genetics USA 1Human Neurogenetics USA 2Laboratory of Neurogenetics NIAAA, NIH, Bethesda, MD 20892-0001, USA

* To whom correspondence should be addressed

Received January 20, 1995. Revised April 22, 1995. Accepted April 22, 1995.

To predict alterations in single-strand DNA mobility in non-denaturing electrophoretlc gels, Zuker's RNA folding program was modified. Energy files utilized by the LRNA RNA folding algorithm were modified to emulate folding of single-strand DNA. Energy files were modified to disallow G•T base pairing. Stacking energies were corrected for DNA thermodynamics. Constraints on loop nucleotide sequences were removed. The LRNA RNA folding algorithm using the DNA fold energy files was applied to predict folding of PCR generated single-strand DNA molecules from polymorphic human ALDH2 and TPH alleles. The DNA-Fold version 1.0 program was used to design primers to create and abolish SSCP mobility shifts. Primers were made that add a 5' tag sequence or alter complementarity to an internal sequence. Differences in DNA secondary structure were assessed by SSCP analysis and compared to single-strand DNA secondary structure predictions. Results demonstrate that alterations in single-strand DNA conformation may be predicted using DNA-Fold 1.0.


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