The unusual X-form DNA in oligodeoxynucleotides: dependence of stability on the base sequence and length.
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 pyrimidinepurine 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)8 is shown to be the second most predisposed oligodeoxynucleotide in the (dT-dA)n 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)n sequence. Consequently, the (dT-dA)n 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.
Kypr
J
J
Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
Chládková
J
J
Arnold
L
L
Sági
J
J
Szemzö
A
A
Vorlícková
M
M
D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D013329:Structure-Activity Relationship; D013696:Temperature
D009838:Oligodeoxyribonucleotides; D011687:Purines; D011743:Pyrimidines; D004247:DNA; C030986:pyrimidine; C030985:purine