SINGLE-STRANDED OLIGOMERS AND POLYMERS OF CYTIDYLIC AND 2′-DEOXYCYTIDYLIC ACIDS: COMPARATIVE OPTICAL ROTATORY STUDIES

The-use of synthetic polynucleotides as models for RNA and DNA has recently received much attention. Evidence, much of it based upon optical rotatory dispersion (ORD)1 for detection of asymmetric secondary structures, has accumulated for the importance of base-stacking interactions, as well as for hydrogen bonding, in stabilizing RNA in aqueous solution. One of the remaining problems is to examine the effect of the carbohydrate residue upon macromolecular properties, that is, to compare the structure of ribonucleotides to those of the analogous deoxyribonucleotides. At neutral pH, polycytidylic acid (poly-rC) exists as a nonprotonated,2 singlestranded helical structure.3 4 This conformation is very different from the halfprotonated, double-stranded5 helix held together by cytosine-cytosine hydrogen bonds in acid solution. The properties of single-stranded poly-rC can be calculated fairly well from consideration of nearest-neighbor base-stacking interactions.6 Similarly, polydeoxycytidylic acid (poly-dC) undergoes a structural transition during titration, although this polymer differs markedly from poly-rC in its titration curve and hypochromicity,7 and in the stability of its complexes with poly-rI8 and with poly-rG.9 Several studies (utilizing ORD,'0-12 circular dichroism,3' 14 and hypochromism"6' 16) have investigated the forces involved in oligoriboadenylic acids, and have traced the building up of helical structures characteristic of poly A. The present report is concerned with a comparison of the structure and stability of oligocytidylic acids, as well as high-molecular-weight polymers, of both the ribocytidylic and deoxyribocytidylic series. Of these, only the dinucleoside monophosphate cytidyl (3' --' 5') cytidine (r-CpC), at room temperature, has been previously studied.6' 17 Materials.-CMP-5' was purchased from Schwarz BioResearch, dCMP-5' from Pabst, and r-CpC from Calbiochem. Poly-rC, the K+ salt from Miles Chemical Co., had e = 7.18. Preparation and characterization of rC oligomers (chain length 3 to 14) will be reported.18 We are grateful to Dr. M. J. Chamberlin for a sample of poly-dC.8 The dC oligomers, as NH4+ salts of chain length 2-10, were a gift from Dr. H. G. Khorana; they were synthesized chemically."9 Water was redistilled from glass; ethylene glycol was Fisher reagent grade. Solutions and Concentrations.-The solvent for temperature-dependence studies was 0.08 M NaCl, 0.02 M tris-tris hydrochloride, pH 8.5. Far-ultraviolet (<225 mIu) spectra and ORD were run in 0.1 M NaF, adjusted to a suitable pH with HCl or NaOH. Polymer solutions were heated briefly and slow-cooled to ensure formation of the equilibrium conformation.3 All solutions were run through Millipore filters. Concentrations were usually in the range of 0.7 to 1.1 I< 10-4 M cytosine residues, corresponding to a maximum absorbance of 0.4-0.8 for a 1-cm path length. Exceptions to this range occurred during concentration-dependence experiments, and in the ORD scan of poly-dC (Fig. 1, concentration 3.1 X 10-4 M, 2-mm path). The extinction coefficients which were used for determination of oligomer concentrations are listed in Table 1. They were obtained by measurement of the loss of hypochromicity upon transfer of the nucleotides from pH 8.5 aqueous buffer into 90% ethylene alcohol (other buffer com-