Oligonucleotide studies. IV. Proton magnetic resonance spectra of three dinucleotides, ApGp, CpGp, and UpGp, in D2O

Physical consequences of chemical modification: circular dichroism of the kethoxalated oligoribonucleotides

Alterations in CD spectra are found in G-containing oligoribonucleotides after modification with kethoxal (beta-ethoxy--alpha-ketobutyraldehyde). Stacking interactions in kethoxalated oligomers are followed by temperature dependence of their CD amplitudes. It is shown that for oligomers with nucleosides in anti-conformation adduct formation destroys the stacking interaction with 3'-neighbour but not with a 5'-neighbour. For nucleosides in non-standard conformation (i.e. syn-conformation of guanine in GpGpCp) the physical alteractions may be seen in those cases, when the substituting group affects the initial conformation or the interplane base contacts via, for instance, blocking NH(2)-group of guanine in GpUp. The results demonstrated that even a single monomer modification in a polymer chain could not be considered as a local event having no influence on the three-dimensional structure. The degree of conformational disorders depends both on the conformation of single nucleotides in the stack and on the nature of the nearest neighbours of the modified base.

Oligonucleotide studies. Optical rotatory dispersion of five homodinucleotides

1. The optical rotatory dispersion (ORD) of five homodinucleotides, ApAp(3'), CpCp(3'), GpGp(3'), IpIp(3') and UpUp(3') (where A, C, G, I and U represent adenosine, cytidine, guanosine, inosine and uridine respectively, and p to the left of a nucleoside symbol indicates a 5'-phosphate and to the right it indicates a 3'-phosphate), were measured as a function of pH, ionic strength and Mg(2+) concentration. 2. The ORD titrations of ApAp(3') and CpCp(3'), which were made by measuring the ORD curves at closely spaced pH intervals, exhibit a maximum at approx. pH5.0 and 5.7 for ApAp(3') and CpCp(3') respectively in the profile of the magnitude of the first Cotton effect versus pH. The results indicate that the conformational rigidity of these dinucleotides depends on the ionization state of a 3'-terminal phosphate group. 3. ApAp(3') was shown to exist as an approximately 1:1 equilibrium mixture of the two major ionic species represented by Ap((-1))Ap((-1)) and Ap((-1))Ap((-2)) at pH6.16, whereas at pH7.5 it exists exclusively as a form of Ap((-1))Ap((-2)). 4. To ascertain the effects of the presence of a terminal phosphate group and of the ionization of the secondary phosphate on the conformation of adenylate dimer, we measured the ORD of ApA, ApAp(3')CH(3) and ApAp(2'). The rotatory power of the first Cotton effect in the above series of dinucleotides decreased at 20 degrees in the order ApA> ApAp(3')CH(3) approximately ApAp(3')((-1))> ApAp(2') at pH7> ApAp(3') at pH7. 5. The pH-rotation profiles were also obtained for ApAp(2'), CpCp(2') and UpUp(3'), but no corresponding maximum was observed. Although simple nearest-neighbour calculations based on the ORD data of IpIp(3') and 5'-IMP account for the observed ORD spectrum of polyinosinic acid at low salt concentration, there were large discrepancies between calculated and experimental results of the polyguanylic acid ORD even at low ionic strength. 6. The extent to which the amplitude of the Cotton effects of IpIp(3') increases with salt concentration, especially by the addition of Mg(2+), was much greater than that observed for ApAp(3'). The implication of such salt effects on the ORD is considered.