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Nucleic Acids Research, 1988, Vol. 16, No. 8 3559-3572
© 1988

Articles

The TFIIIA recognition fragment d(GGATGGGAG)·d(CTCCCATCC) is B-form in solution

Fareed Adoul-ela, Gabriele Varani, G.Terrance Walker and Ignacio Tinoco, Jr

Department of Chemistry and Laboratory of Chemical Biodynamics, University of California Berkeley, CA 94720, USA

Received December 2, 1987. Revised March 16, 1988. Accepted March 16, 1988.

The deoxyoligonucleotide d(GGATGGGAG)·d(CTCCCATCC) is a portion of the gene recognition sequence of transcription factor IIIA (TFIIIA). The crystal structure of this oligonucleotide was shown to be A-form (Mc Call, M., Brown, T., Hunter, W. N., and Kennard, O. 1986 Nature 322, 661–664). The present study employs NMR, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. NMR COSY experiments indicate 16 of the 18 residues are predominantly south (C2-endo) sugar conformation. NMR NOESY indicates glycosidic angles in the range predicted for B-form DNA as opposed to A-form. Related DNA and RNA self-complementary 18-mer sequences, d(GGATGGGAGCTCCCATCC), with U substituted for T in RNA, were studied by circular dichroism. CD spectra support B-form structures for the DNA 9-mer and the DNA 18-mer, and A-form for the RNA 18-mer. High trifluoroethanol concentrations induce a B- to A-form transition in the DNA oligo-nucleotides. Enzymatic and chemical probes also illustrate significant differences between the DNA and the RNA oligonucleotides. We find no evidence to support an A-form conformation for the TFIIIA recognition sequence d(GGATGGOAG)·d(CTCCCATCC in solution.


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