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Nucleic Acids Research, 1988, Vol. 16, No. 22 10643-10655
© 1988

CHEMISTRY

Immunochemical detection of multiple conformations within a 36 base pair oligonucleotide

David Sanford, Karen J. Kotkow and B.David Stollar*

Department of Biochemistry, Tufts University Health Sciences Campus Boston, MA 02111, USA

*To whom correspondence should be addressed

Received July 22, 1988. Revised October 4, 1988. Accepted October 4, 1988.

A 36 base pair chimeric oligonucleotide containing a central core of DNA duplex flanked by RNA/DNA hybrid at each end was synthesized. These distinct regions of the oligonucleotide adopt different conformations which were detected with antibody probes. Enzyme linked immunosorbent assays (ELISA) and a gel electrophoresis retardation assay were used to demonstrate the binding of antibodies which recognize B-DNA, Z-DNA and RNA/DNA hybrid. The DNA duplex core of this oligonucleotide adopts the B-conformation in 0.14 M NaCl. In high salt solution (4 M NaCl) the DNA core adopts the Z-conformation. The RNA/DNA hybrid at the ends of the oligomer adopt a conformation which is distinct from both B-DNA and A-RNA.


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