The Unusual X-Form DNA in Oligodeoxynucleotides: Dependence of Stability on the Base Sequence and Length |
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| Authors: | Jaroslav Kypr Jana Chládková Luboš Arnold János Sági Attila Szemzö Michaela Vorlíčková |
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| Affiliation: | 1. Institute of Biophysics, Czech Academy of Sciences , CZ-61265 , Brno , Czech Republic;2. Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , CZ-16610 , Prague , Czech Republic;3. Central Research Institute for Chemistry, Hungarian Academy of Sciences , PO Box 17, H-1525 , Budapest , Hungary |
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| Abstract: | Abstract X-form is an unusual double helix of DNA adopted by poly(dA-dT) or (dT-dA)4 at high concentrations of CsF. On the other hand, poly(dA).poly(dT), (dA-dT)4 and most other DNAs do not adopt this conformer. Here we demonstrate that the X-form is strongly destabilized by GC pairs or even minute perturbations of the alternating pyrimidine- purine sequence. For example, the 30-mer d(TATAAT)5, containing five tandem repeats of the Pribnow box, fails to isomerize into the X-form. After (dT-dA)4, the 16-mer (dT- dA)g is shown to be the second most predisposed oligodeoxynucleotide in the (dT-dA)., series to isomerize into the X-form while the duplex lengths corresponding to n=3,5,6,7,9,12 and 20 make the X-form unstable even in the strictly alternating (dT-dA)., sequence. Consequently, the (dT-dA)., duplex length is also a crucial factor of the X-form stability on the oligodeoxynucleotide level. We discuss a possibility that the X-form is a solution counterpart of the D-form adopted in dehydrated poly(dA-dT) fibers because properties of these two conformers are remarkably similar in many respects. |
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