The Unusual X-Form DNA in Oligodeoxynucleotides: Dependence of Stability on the Base Sequence and Length

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 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.

Circular dichroism and conformational polymorphism of DNA

“…d(TA) 4 provide a remarkable CD spectrum at high concentrations of CsF (63) or in aqueous ethanol (64,65). In the presence of millimolar NaCl concentrations, poly[d(AT)] isomerizes into the A-form at high ethanol concentrations (27) (Figure 6).…”

DNA coiled coils

“…In particular, it has been known for a long time that poly[d(AT)], under certain conditions, forms a duplex with eight base pairs per turn, the D form of DNA (12). The polymorphism of AT-rich DNA is also apparent from melting (13) and NMR studies (14), which suggest additional conformational transitions. In view of this situation, we have studied the crystallization of a longer sequence, the dodecamer d(ATATATATATAT).…”

Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks

“…25 Its solution counterpart probably is the X-form induced in poly(AT) by high concentrations of CsF. 24 The X-form is characterized by a deep negative CD band at 275 nm while the negative CD band at 245 nm is simultaneously diminished, so that the spectra pass through an isodichroic point during the transition which takes place between 3M and 6M CsF. 9,23 The process has fast kinetics,occuring in less than a minute.…”

“…19,20 Poly(AT) isomerizes into the Aform at high ethanol or TFE concentrations, 21 Z-form in concentrated NaCl ϩ millimolar NiCl 2 , 22 and X-form in concentrated CsF. 23 The X-form appears to be a solution counterpart of the D-DNA double helix 24 adopted by poly(AT) in dehydrated fibers. 25 CD spectroscopy is very sensitive to the conformation of DNA (e.g., Ref.…”