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Nucleic Acids Research, 1980, Vol. 8, No. 1 169-182
© 1980

Articles

Loopstructures in synthetic oligodeoxynucleotides

Cornelis A.G. Haasnoot, Jeroen H.J. den Hartog, Jan F.M. de Rooij, Jacques H. van Boom and Cornelis Altona

Gorlaeus Laboratories, State University P.O. Box 9502, 2300 RA Leiden, The Netherlands

Received October 17, 1979. A comparative nuclear magnetic resonance study of the hydrogen-bonded imino protons in a series of synthetic DNA fragments is presented. The fragments ATCCTA(Tn]TAGGAT are in principle capable of forming either a self-complementary hairpin loop structure [monomer form] or an interior loop structure [dimeric form). It has been shown2, that for n=l only the dimer structure 1s present in aqueous solution, whereas the exclusive existence of the hairpin loop structure is indicated for n=3, 4 & 5. Surprisingly, for n=2 two different structures appear to be present in solution. Concentration studies show that both monomers and dimers exist side by side in this case. Hairpins as well as interior loops form extra "melting sites" in addition to the wellknown fraying phenomenon at the terminus of the double helix.


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