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Nucleic Acids Research, 1989, Vol. 17, No. 6 2223-2231
© 1989

MOLECULAR BIOLOGY

Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC)

Ichiro Hirao, Yoshifumi Nishimura1, Tetsushi Naraoka, Kimutsuna Watanabe+, Yoji Arata1 and Kin-ichiro Miura

Department of Industrial Chemistry, Faculty of Engineering University of Tokyo Hong, Tokyo 113, Japan 1Faculty of Pharmaceutical Science, University of Tokyo Hongo, Tokyo 113, Japan

Received December 9, 1988. Revised February 20, 1988. Accepted February 20, 1989.

Short single-stranded DNA fragments carrying a GCGAAAGC sequence were found to move unexpectedly faster than other fragments of the same length in electrophoresis on a polyacrylamide gel containing a denaturing agent. The fragments were noted to have a stable structure even in 7M urea solution, but the stability cannot be explained simply on the basis of base pair formation alone. Physical characterization of the GCGAAAGC fragment indicated that it takes a hairpin-like structure in spite of the short chain length with only two G-C base pairs, comprised of GCG and AAAGC subsegments, each possessing a helical configuration independent of the others. Some biological implications of this unusual structure are discussed.

+Present address: Department of Life Chemistry, Tokyo Institute of Technology, Nagatsuta, Yokohama 227, Japan


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