[Virulence comparison of genetic engineering virus containing different length poly(C) tract of foot-and-mouth disease virus].

OBJECTIVE: Study the association of the length of poly(C) tract with virulence of foot-and-mouth disease virus. METHODS: The recombinant plasmids pGEM-XJ/AKT/69 containing the full-length cDNA of FMDV were linearized by Nhe I /Not I and transcribed by T7 RNA polymerase. The in vitro transcripts were transfected into BHK-21 cells using Lipofectamine 2000 reagent. Then, the genetic engineering virus was rescued from BHK-21 cells. The poly(C) tracts were sequenced at different passages of rescued virus, and the pathogenicities were evaluated with 3-day-old mice and BHK-21 cells by detection of LD50 and TCID50. RESULTS: After six passages in BHK-21 cells, cytopathic effect was observed by microscopy. The rescued virus was rejuvenated once in unweaned mice, and then came back to cell passage. We found that the poly(C) tract of rescued virus was shortened when the virus was passaged twice in BHK-21 cells. Although the data of LD50 in mice and TCID50 in BHK-21 cells showed that the virulence and infectivity of genetic engineering viruses were lower than its parental virus, no significant difference was observed between the genetic engineering viruses with the different length poly(C) tract. CONCLUSION: The length of poly(C) tract ranged from 12 to 17 nucleotides did not cause significant influence on the virulence and infectivity of genetic engineering virus.

Nucleo-copolymers: oligonucleotide-based amphiphilic diblock copolymers.

For the first time, poly(butadiene) has been covalently linked to an oligonucleotide sequence and the resulting nucleo-copolymer exhibits amphiphilic properties in dilute aqueous solution, self-assembling into nanometer-sized vesicular structures.

Comparison of ribonucleic acid homopolymer ionization energies and charge injection barriers.

Thin films of guanosine and uridine ribonucleic acid (RNA) homopolymers (poly rG, poly rU) were grown in high vacuum in several steps on highly oriented pyrolytic graphite (HOPG) using electrospray deposition. Between deposition steps, the sample surface was characterized with X-ray and ultraviolet photoemission spectroscopy (XPS, UPS). The resulting spectra series allowed the determination of the orbital alignment at the HOPG interface, as well as the ionization energies of the homopolymer thin films. Comparison with earlier results on cytidine and adenosine RNA homopolymers (poly rC, poly rA) indicates significant ionization energy and charge injection barrier differences between purines and pyrimidines.

Ionization energy and electronic structure of polycytidine.

Ribonucleic acid (RNA) polycytidine (poly rC) homopolymer thin films were prepared on highly oriented pyrolytic graphite (HOPG) substrates. The films were grown from aqueous solution directly in a vacuum in multiple steps with use of an electrospray (ES) deposition system. Before poly rC deposition and after each deposition step the sample was characterized with X-ray and ultraviolet photoemission spectroscopy (XPS, UPS). Evaluation of the UP-spectra sequence allowed the determination of ionization energy and highest occupied molecular orbital (HOMO) electronic structure, as well as the charge injection barriers between HOPG and poly rC. Comparison with earlier results on polyadenosine (poly rA) indicates significant differences between ionization energies (poly rC: 8.1 eV; poly rA: 6.8 eV) and orbital alignment at the graphite interface. The larger ionization energy of poly rC results in a larger hole injection barrier and a smaller electron injection barrier relative to the HOPG Fermi level.

Studies on precellular evolution: the encapsulation of polyribonucleotides by liposomes.

Liposomes are 5 to 50 micron vesicles with an internal aqueous environment, whose amphiphilic lipidic components self-assemble into systems with at least one double-layered membrane. Liposomes have been suggested as possible models of precellular systems formed in the early Archean Earth from lipids of non-enzymatic origin. Since it is generally accepted that RNA molecules preceded double-stranded DNA molecules as genetic material, we have studied the encapsulation of polyribonucleotides within liposomes made from dipalmitoyl phosphatidylcholine, and from egg yolk phosphatidylcholine to which cholesterol was added in some cases. The liposomes were prepared under anoxic conditions following the reverse phase evaporation method described by Szoka and Papahadjopoulos. Quantitative determinations show that approximately 50% of the available lipids form liposomes, and that up to 5% of the polyribonucleotides can be entrapped by them. We have also studied the encapsulation of polyribonucleotides in the presence of 1) urea and cyanamide, two non-electrolytes that have been used as prebiotic condensing agents, and 2) of Zn++ and Pb++, two cations employed in the non-enzymatic template-directed synthesis of polyribonucleotides from activated nucleotides.

[Conformation and molecular and ionic transformations of polycytidylic acid immobilized in multilayer Langmuir and polyelectrolyte films]. / Konformatsionnoe sostoianie i osobennosti molekuliarno-ionnogo prevrashcheniia politsitidilovoi kisloty, immobilizovannoi v mul'tisloinykh lengmiurovskikh i poliélektrolitnoi plenkakh.

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.

Influence of preparation method on polynucleotide conformation and pharmacological activity of lipoplex.

Conformations of polyinosinic acid [poly(I)] and polycytidylic acid [poly(C)] in liposomes (lipoplex) were investigated by both circular dichroism (CD) spectroscopy and fluorescence resonance energy transfer (FRET) measurements, and compared with those in aqueous solution. The results indicate that poly(I) and poly(C) take double-stranded structure in aqueous solution at pH 6.5-7.5 in the presence of NaCl at higher concentration than 50mM. Although lipoplex was prepared without NaCl to avoid aggregation of lipoplex particles, poly(I) and poly(C) were double-stranded in pre-mixed poly(I)/poly(C) lipoplex (pre-mixed LIC), prepared by adding a mixed solution of poly(I) and poly(C) to the cationic liposomes. However, poly(I) and poly(C) did not take double-stranded structure in separately mixed LIC, prepared by separate addition of poly(I) solution and poly(C) solution to the cationic liposomes. The physicochemical properties (particle diameter and zeta potential) of pre-mixed LIC and separately mixed LIC were not different, but the anti-proliferative effect of pre-mixed LIC on human epidermoid carcinoma A431 cells was about eight times greater than that of separately mixed LIC. Our results indicate that polynucleotide conformation in lipoplex is markedly influenced by the preparation method, and the polynucleotide conformation in lipoplex has a substantial effect on pharmacological activity.

Double-stranded RNA homopolymer poly(rC).poly(rG) for a new pH-sensitive drug carrier.

Double-stranded RNA homopolymer poly(rC).poly(rG) has been used as a new pH-sensitive drug carrier. The poly(rC).poly(rG) had proton buffering capacity around pH 6, owing to protonation of cytosine, as determined by acid-base titration. By circular dichroism measurement, the protonation caused conformational change of the RNA. The poly(rC).poly(rG) and doxorubicin (Dox), as an anticancer drug, formed the complexes which released the drugs at endosomal pH. The resulting complex exhibited higher anticancer activity than the Dox alone. These results result suggest that the poly(rC).poly(rG) is a promising biopolymer for a new class of pH-sensitive drug carriers.

Poly(ethylene oxide) facilitates the characterization of an affinity between strongly basic proteins with DNA by affinity capillary electrophoresis.

In order to study kin17 protein-DNA affinity, we have developed a fast and reproducible capillary electrophoresis (CE) analysis of a strongly basic protein: kin17 protein, using a nonpermanent coating based on poly(ethylene oxide) (PEO) to avoid adsorption of kin17. The coating procedure was optimized to provide a residual and stable electroosmotic flow (EOF = 5 x 10(-5) cm(2)/V x s), exhibiting RSD of 0.3% and excellent long-term stability. Good intraday and interday reproducibility of kin17 migration times (0.8 and 0.3% relative standard deviation (RSD), respectively) enabled us to consider that the recovery percentage obtained for kin17 protein was satisfactory (79%). The potential of this PEO-based coating procedure was evaluated for affinity CE method in order to study the affinity of kin17 protein for two single-stranded DNA (ssDNA) models: polydeoxyadenylic acid and polydeoxycytidilic acid (pdA and pdC). Binding constants (1.5 x 10(7) +/- 17% and 1.7 x 10(7) + 25%M(-1)) were evaluated assuming a 1:1 affinity between kin17 and pdA or pdC, respectively.

Structural properties of poly C-scleroglucan complexes.

Successive changes of solvent conditions can be used to dissociate and reassociate the triple-helical structure of (1,3)-beta-D-glucans. Ultramicroscopic techniques have revealed a blend of circular and other structures following renaturation. When this solvent exchange process is carried out in the presence of certain polynucleotides, the process creates a novel macromolecular complex. Here, we use size exclusion chromatography (SEC) to study such (1,3)-beta-D-glucan-polynucleotide complexes. Online multi-angle laser-light scattering (MALLS) and refractive index (RI) detectors allowed determination of molecular weight and radius of gyration of the molecules. An ultraviolet (UV) detector allowed specific detection of the polynucleotide. The poly-cytidylic acid (poly C) shifted to coelution with the linear fraction of the scleroglucan following the renaturation of poly C-scleroglucan blends, indicating that poly C is incorporated in linear, but not in circular, structures of scleroglucan. This conclusion was consistent with AFM topographs that revealed a decreased fraction of circular structures upon addition of poly C during the renaturation process. The combined information about radius of gyration (R(g)) and molecular weight (M(w)) allowed us to conclude that the poly C-scleroglucan complexes are more dense and have a higher persistence length than linear scleroglucan triple helixes. The experimentally determined mass per unit length was used as a basis for elucidating possible molecular arrangements within the poly C-scleroglucan complex.

Faster rates with less catalyst in template-directed reactions.

We have recently shown that the polycytidylic acid-directed polymerization of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) is amenable to kinetic study and that rate determinations as a function of 2-MeImpG concentration can reveal much mechanistic detail (Kanavarioti et al. 1993). Here we report kinetic data which show that, once the reaction has been initiated by the formation of dimers, the elongation of dimers to form longer oligomers is accelerated by decreasing polycytidylate (poly(C)) concentration from 0.05 to 0.002 M. This result is consistent with the previously proposed mechanism. The increase in the observed pseudo-first order rate constant for formation of the trimer, k3', and the corresponding constant for formation of oligomers longer than the trimer, ki' (ki' is independent of oligomer length for i > or = 4), with decreasing template concentration for a given monomer concentration is attributed to an increase in template occupancy as template concentration is reduced.

Computer simulation in template-directed oligonucleotide synthesis.

A computer simulation (KINSIM) modeling up to 33 competing reactions was used in order to investigate the product distribution in a template-directed oligonucleotide synthesis as a function of time and concentration of the reactants. The study is focused on the poly(C)-directed elongation reaction of an oligoguanylate (a 7-mer is chosen) with guanosine 5'-monophosphate-2-methyl-imidazolide (2-MeImpG), the activated monomer. It is known that the elongation of oligoguanylates to form oligomeric products such as 8-mer, 9-mer, 10-mer, etc., is in competition with (1) the dimerization and further oligomerization reaction of 2-MeImpG that leads to the formation of dimers and short oligomers, and (2) the hydrolysis of 2-MeImpG that forms inactive guanosine 5'-monophosphate, 5'-GMP. Experimentally determined rate constants for the above three processes at 37 degrees C and pH 7.95 were used in the simulation; the initial concentrations of 2-MeImpG, [M]o, and of the oligoguanylate primer, [7-mer]o, were varied, and KINSIM calculated the distribution of products as a function of time until equilibration was reached, i.e., when all the activated monomer has been consumed. In order to sort out how strongly the elongation reaction may be affected by the competing hydrolysis and dimerization, we also simulated the idealized situation in which these competing reactions do not occur.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide.

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Association of double-stranded DNA fragments into multistranded DNA structures.

We have previously observed that double-stranded DNA fragments containing a tract of the tandemly repeated sequence poly(CA). poly(TG) can associate in vitro to form stable complexes of low electrophoretic mobility, which are recognized with high specificity by proteins HMG1 and HMG2. The formation of such complexes has since been observed to depend on interactions of DNA with polypropylene surfaces, with the suggestion that the formation of low mobility complexes might be the result of strand dissociation followed by misaligned reassociation of the repetitive sequences. The data presented here show that at high ionic strength the interactions of DNA with polypropylene are sufficiently strong for DNA to remain bound to the polypropylene surface, which suggests that DNA might also be involved in interactions with hydrophobic molecules in vivo. Under such conditions, low-mobility complexes are found only in the material adsorbed to the polypropylene surface, and all DNA fragments are able to form low-mobility structures, whether or not they contain repetitive sequences. Preventing the separation of strands by ligating hairpin loop oligonucleotides at both ends of the fragments does not prevent the formation of low-mobility complexes. Our results suggest two different pathways for the formation of complexes. In the first, dissociation is followed by misaligned reassociation of repetitive sequences, yielding duplexes with single-stranded end regions that associate to form multimeric complexes. In the second, repetitive as well as nonrepetitive DNA molecules bound to polypropylene adopt a conformation with locally unwound regions, which allows interactions between neighboring duplexes adsorbed on the surface, resulting in the formation of low-mobility complexes.

Purification of a novel ribonuclease from dried fruiting bodies of the edible wild mushroom Thelephora ganbajun.

A ribonuclease, with a molecular mass of 30 kDa and a potent inhibitory activity toward HIV-1 reverse transcriptase (IC50=300 nM), was isolated from dried fruiting bodies of the edible wild mushroom Thelephora ganbajun. The ribonuclease exhibited a unique polyhomoribonucleotide specificity, with the highest activity toward poly(U), about 50% and 25% as much activity toward poly(A) and poly(C), respectively, and minimal activity toward poly(G). Unlike other mushroom RNases, the ribonuclease was adsorbed on DEAE-cellulose and Q-Sepharose, and unadsorbed on CM-cellulose. A temperature of 40 degrees C and a pH of 6-7 were required for maximal activity of the enzyme. The enzyme was characterized by an N-terminal sequence without any homology to known proteins.