Structural polymorphism of oligo(dC) with mixed alpha,beta-anomeric backbone

Oligonucleotides with mixed alpha,beta-anomeric backbone have been proposed recently for the recognition of random DNA sequence via new tripler motif (Doronina and Behr, Chern. Sec. Reviews 26, 63-71 (1997)). In the present w ork we examined alpha- and beta- anomers of cytidine as possible candidates to recognize AT and TA base pairs of the double stranded DNA. The binding properties of beta-oligo(dC) were studied on a series of synthetic oligodeo xynucleotides by UV absorbtion spectroscopy, measurements of bound EtBr flu orescence polarization, circular dichroism (CD) and non-denaturing gel elec trophoresis. The UV thermal denaturation, polarization studies and CD exper iments with three stranded oligonucleotide 5'-C((dC(alpha)) (dC(beta)))(5)- L(dAT)(5)-L-(dAT)(5) (L = triethyleneglycol linker) and other oligonucleoti de models showed that the formation of semiprotonated oligocytidilic comple xes takes place at low temperatures and neutral pH, rather than folding of the clip into intramolecular tripler. The low-temperature transition was ob served in denaturation profiles of any oligonucleotide containing beta- or mixed alpha,beta- cytidine stretches at the concentration of 1 mu M. Self-a ssociation of alpha,beta-oligo(dC) was additionally confirmed by the appear ance of two CD bands (at 290 and 265 nm) characteristic of CC+ base pairs. Despite the effective ability of alpha,beta-oligo(dC) to form self-associat es, we succeeded in targeting 30-bp AT containing random DNA duplex by a 30 -nt alpha,beta-oligocytidilate as evidenced by non-denaturing gel electroph oresis. A complete binding of the duplex was observed at a 5-fold excess of the third strand at 15 degrees C. Along with the formation of the three-st randed complex, self-association of mixed backbone oligo(dC) strands occurr ed.