Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence:...

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.