The unusual X-form DNA in oligodeoxynucleotides: dependence of stability on the base sequence and length

• Published in: Journal of biomolecular structure & dynamics Vol. 13; no. 6; p. 999
• Main Authors: Kypr, J, Chládková, J, Arnold, L, Sági, J, Szemzö, A, Vorlícková, M
• Format: Journal Article
• Language: English
• Published: England 01.06.1996
• Subjects: Base Sequence; Circular Dichroism; DNA - chemistry; Models, Molecular; Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry; Purines - chemistry; Pyrimidines - chemistry; Structure-Activity Relationship; Temperature
• ISSN: 0739-1102
• DOI: 10.1080/07391102.1996.10508914

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.