Conformation and molecular and ionic transformations of polycytidylic acid immobilized in multilayer Langmuir and polyelectrolyte films

Multilayer films of complexes of polycytidylic acid with dioctadecyldimetylammonium were obtained by the Langmuir-Blodgett method (LB films), and complexes of poly(C) with polycations (poly-L-lysisne, polyethyleneimine, polyallylamine) were obtained by the method of alternate adsorption (polyionic assembly) from solutions of oppositely charged polyelectrolytes on the solid carrier (SA films). It was shown that poly(C) exists in SA films in a single-stranded state irrespective of whether in the starting solution it occurred in the single-stranded nonprotonated or double-stranded protonated conformation. Conversely, in the LB film poly(C) preferred to be in a double protonated conformation. UV-spectra of water-insoluble LB and SA films at different pH values of surrounding water medium were investigated. Proton titration curves of poly(C) immobilized in LB films were obtained. The analysis of the shape of titration curves showed that the molecular-ionic transformation of poly(C) in LB films is accompanied by both the conformational transition of the polynucleotide and the molecular rearrangement in the whole film. Poly(C) was found to transform from the double- to single-stranded state and vice versa in the "deprotonation-protonation" cycle of LB film due to cooperative release/binding of hydrogen ions by cytosine bases. In contrast, poly(C) "protonation-deprotonation" in SA films occurred without conformational transitions of the polynucleotide. As opposed to poly(C) in solution a rather big hysteresis of forward and back titration curves was found for both types of multilayer films, indicating molecular rearrangements in films. The reason for the structural transformations of poly(C) upon fabrication of LB or SA films and the mechanism of molecular ionic transformations of poly(C) in films are discussed in terms of a simple model of ion exchange. An assumption about the nature of structural transformations of LB and SA films during their protonation-deprotonation is put forward.     

Hydrogen-ion binding of polycytidylic acid immobilized between Langmuir layers of dimethyldioctadecylammonium (DODA) in thin multilayer films

The report describes the study of hydrogen-ion binding of Langmuir-Blodgett films contained with polycytidylic acid. A variety of multilayer films are analyzed and their UV absorption spectra are recorded. Poly (C) molecules established between dimethyldioctadecylammonium (DODA) layers are shown to exist in double stranded and semiprotonated form, independent of the pH value of the solution from which the films were made. A large hysteresis was found between forward and back proton titration of poly(C) immobilized in the LB films. This hysteresis points to a marked transference of both types of molecules during the film titration. This behavior also depends upon the types of molecules from which the films were made.     

Structure of the single-stranded polyribonucleotide polycytidylic acid.

The Fourier transformation was obtained from the experimental diffuse X-ray scattering curve of adult human oxyhaemoglobin in an aqueous solution. The correlation function of the form of the molecule was calculated from known coordinates of horse haemoglobin atoms. The distribution function of inhomogeneities was deduced from the above Fourier transformation and the correlation function. This distribution function of inhomogeneities is described by a series of maxima providing evidence for a short and long-range order extending up to 5 nm which is close to the maximum dimension of the haemoglobin molecule.     

pH-Dependent Raman spectra and thermal melting profiles for polycytidylic acid

The Raman spectrum of polycytidylic acid was investigated in the pH range of 6.6–4.1. The thermal melting temperatures and the nature of the thermal melting profiles change in this range as monitored by the three Raman band envelopes, which include the 780-, 805-cm^?1 bands, the 1190-, 1285-cm^?1 bands, and the 1527-cm^?1 band. By coupling these data with the theory of Raman scattering intensity and quantitative pH profiles for cytidine, it is shown that the band envelopes studied exhibit specific, yet different information regarding the thermal melting process. The band envelopes at 1170–1310 and 1527 cm^?1, which are a sensitive function of both the extent of protonation and base stacking (hypochromic), reveal T_m values which agree with values derived from uv melting profiles. The 760–830-cm^?1 envelope, which is not directly sensitive to cytosine residue protonation, but includes information associated with base stacking (the 780-cm^?1 band) and the nature of the phosphodiester backbone (the frequency-dependent 805-cm^?1 component), exhibits T_m values which deviate from the values obtained from the other bands. The observed differences are pH-dependent and correlate well with the extent of deprotonation that takes place in the denaturation process. Details of the spectrum of neutral and protonated poly(C) from pH 7 to 4.1 are discussed and related to the nature of the thermal denaturation process.     

Hydration of amino acid side chains: dependence on secondary structure.

Energy calculations have been used to study the hydration sites around the polar groups of serine, threonine and tyrosine side chains. These hydration sites depend not only on the hybridization of the polar group but also on the local secondary structure, the chi 1 side chain torsion angle and the position of the hydroxyl hydrogen atom. For tyrosine side chains, two solvent sites are found approximately in the plane of the ring. Even for serine and threonine side chains only two minimum energy sites are found in general of which one is in an expected position within hydrogen bonding of the hydroxyl hydrogen atom (unless this is blocked from interaction with solvent molecules by, for example, Oi-4 or Oi-3. The position of the second of these sites depends not only on the position of the hydroxyl oxygen but also on neighbouring main chain atoms to which it can also hydrogen bond. There is good agreement with the solvent distributions obtained from crystallographic data.     

Structural transitions in polycytidylic acid: proton buffer capacity data

The pH-dependences of proton buffer capacity of poly(C) were computed on the basis of the literature data. In these curves there were observed four peaks: two narrow and two wide ones. The first narrow peak reflects the process of cooperative formation of double helices, which is induced by protonation of the N3 atom of nucleotide bases. The first wide peak is assigned to noncooperative process of poly(C) double helices protonation at the N3 nitrogen atom. It is proposed that the second wide peak corresponds to noncooperative protonation of the neutral cytosine bases at the oxygen atom. This reaction causes cooperative dissociation of the poly(C) double helices. The second narrow peak reflects the dissociation process.     

Purification and properties of a ribonuclease in human urine that hydrolyses polycytidylic acid.

Human urine RNase was purified about 2000-fold. The preparation is free from phosphatase, phosphodiesterase and DNase activities. On electrophoresis through polyacrylamide gel at pH 8.3, it migrates toward the anode and stains with periodic acid-Schiff reagent, suggesting that it is acidic and glycoprotein in nature. Its isoelectric point is at pH 4.1. It has a molecular weight of about 21,500. It is thermostable at pH 4.2 and thermolabile at pH 8.5. It has a pH optimum at 6.5. It exhibits highest preference for cytidine 3'-phosphate linkages. Its activity on poly (C) is endonucleolytic. It cleaves poly (C) via intramolecular transphosphorylation. It has no action on cytidine 2': 3'-cyclic phosphate or uridine 2':3'-cyclic phosphate. Its rate of hydrolysis of poly (U) is less than 2% of that of poly C). Poly (A) and poly (G) are totally inert to its action. Its action on poly (C) is inhibited by poly (G), poly (A) and poly (U). It differs from bovine pancreatic Rnase A in its physical, chemical and catalytic properties. It is, however, similar to human serum and pancreatic RNase in all its properties, suggesting that pancreas is its likely source.     

Protonated polynucleotides. VII. Thermal transitions between different complexes of polyinosinic acid and polycytidylic acid in an acid medium

The interaction between poly (I) and poly (C) in acid medium has been studied by potentiometric titration, mixing curves and thermal denaturation. Phase diagramms as a function of ionic strength, pH, and temperature have been established. From these data it is shown that the acid titration of the complex poly (I) · poly (C) passes through a triple-stranded intermediate poly (I) · poly (C) · poly (C⁺) to yield finally the protonated double-helical complex poly (I) · poly (C⁺). The mixing curves indicate the sole presence of the three-stranded complex in the intermediate zone. On the basis of the pK's the coexistence between the three-stranded complex with the neighboring double-stranded structure is demonstrated in a narrow rang of pH and ionic strength. The geometry of the base arrangements, their conformation and the sense of the strands are discussed in the light of the data presented. A Hoogsteen-type pairing between the bases for poly (I) · poly (C⁺) is favored, although the reverse Hoogsteen pair cannot be excluded.