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Nucleic Acids Research, 1988, Vol. 16, No. 11 5137-5151
© 1988

Articles

Unusual duplex formation in purine rich oligodeoxyribonucleotides

W.David Wilson*, Minh-Hoa Dotrong, Elizabeth T. Zuo and Gerald Zon1,{dagger}

Department of Chemistry and Laboratory for Microbial and Biochemical Sciences, Georgia State University Atlanta, GA 30303-3083, USA 1Molecular Pharmacology Laboratory, Division of Biochemistry and Biophysics, Food and Drug Administration 8800 Rockville Pike, Bethesda, MD 20892, USA

*To whom correspondence should be addressed

Received January 14, 1988. Revised March 17, 1988. Accepted March 17, 1988.

The purine rich oligodeoxyribonucleotides 1C, d(ATGACGGAATA) and 2C, d(ATGAGCGAATA) alone exhibit highly cooperative melting transitions. Analysis of the concentration dependence of melting, and electrophoretic studies indicate that these oligomers can form an unusual purine rich offset double helix. The unusual duplex is predicted to contain four A·T, two G·C, and four G·A mismatch base pairs as well as a single A base stacked on the 3' end of each chain of the helix. Other possible models for the duplex are unlikely because they are predicted to contain many base pairs of low stability. Changing the central sequence to CGG or GGG should destabilize the duplex and this is observed. The unusual duplex of 2C is more stable than the duplex of 1C indicating that the stability of G·A base pairs is quite sensitive to the surrounding sequence. Addition of 1C and 2C to their complementary pyrimidine strands results in normal duplexes of similar stability. We feel that the unusual duplexes are significantly stabilized by the intrinsic stacking tendency of purine bases.

{dagger}Present address: Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA


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