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PubMed2004

Protection of polynucleotides against nuclease-mediated hydrolysis by complexation with schizophyllan.

Schizophyllan is a beta-(1-->3)-D-glucan existing as a triple helix in water and as a single chain in dimethylsulfoxide (DMSO), respectively. As we already reported, when some homo-polynucleotide (for example, poly(dA) or poly(C)) is added to the schizophyllan/DMSO solution and subsequently DMSO is exchanged for water, the single chain of schizophyllan (s-SPG) forms a complex with the polynucleotide. The present work demonstrates that the polynucleotide bound in the complex is more stable to nuclease-mediated hydrolysis than the polynucleotide itself (i.e., naked polynucleotide), using high-performance liquid chromatography and ultraviolet absorbance technique. A kinetic study for the hydrolysis clarified that the simple Michaelis-Menten relation is held and the maximum velocity for the complex is one-sixth as small as that of the naked polynucleotide. This low hydrolysis rate for the complex suggests that s-SPG is applicable to a carrier for antisense oligonucleotides.

Biocompatible Materials↗
PubMed2001

Spontaneous entrapment of polynucleotides upon electrostatic interaction with ethanol-destabilized cationic liposomes.

This study describes the effect of ethanol and the presence of poly(ethylene) glycol (PEG) lipids on the interaction of nucleotide-based polyelectrolytes with cationic liposomes. It is shown that preformed large unilamellar vesicles (LUVs) containing a cationic lipid and a PEG coating can be induced to entrap polynucleotides such as antisense oligonucleotides and plasmid DNA in the presence of ethanol. The interaction of the cationic liposomes with the polynucleotides leads to the formation of multilamellar liposomes ranging in size from 70 to 120 nm, only slightly bigger than the parent LUVs from which they originated. The degree of lamellarity as well as the size and polydispersity of the liposomes formed increases with increasing polynucleotide-to-lipid ratio. A direct correlation between the entrapment efficiency and the membrane-destabilizing effect of ethanol was observed. Although the morphology of the liposomes is still preserved at the ethanol concentrations used for entrapment (25-40%, v/v), entrapped low-molecular-weight solutes leak rapidly. In addition, lipids can flip-flop across the membrane and exchange rapidly between liposomes. Furthermore, there are indications that the interaction of the polynucleotides with the cationic liposomes in ethanol leads to formation of polynucleotide-cationic lipid domains, which act as adhesion points between liposomes. It is suggested that the spreading of this contact area leads to expulsion of PEG-ceramide and triggers processes that result in the formation of multilamellar systems with internalized polynucleotides. The high entrapment efficiencies achieved at high polyelectrolyte-to-lipid ratios and the small size and neutral character of these novel liposomal systems are of utility for liposomal delivery of macromolecular drugs.

Cations↗
PubMed1985

Covalent binding of benzo[a]pyrenediol epoxides to polynucleotides.

Spectroscopic studies on the trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene- (anti-BPDE-) modified synthetic polynucleotide solutions reveal interesting sequence-dependent stereoselective covalent binding of anti-BPDE to DNA. Absorption spectral results indicate that the G.C polymers are much more reactive than the A.T polymers toward this metabolite and the homopolymer suffers higher modification than its corresponding alternating polynucleotide. The covalently attached anti-BPDE exhibits only a 2-3-nm red shift in the guanine-containing polynucleotide and native DNA solutions as opposed to the 8-nm red shift in poly(G) and none in the A.T polymers. Distinct stereoselectivities are exhibited by poly(dG-dC).poly(dG-dC) vs. poly(dG).poly(dC) as suggested by the oppositely signed CD in the pyrene spectral region. Comparison with the syn-BPDE modified polynucleotides reveals some interesting differences with its anti diastereomer. Significant contributions from the intercalated syn-BPDE are apparent in the modified guanine-containing polynucleotides as indicated by the appearance of 10-nm red-shifted shoulders. In contrast to the strong dependence on polynucleotides for anti-BPDE, the rate of hydrolysis of syn-BPDE appears to be insensitive to their presence in the solution. anti-BPDE modification on the 50 microM hexaamminecobalt-induced Z-form poly(dG-dC).poly(dG-dC) is much less extensive than its corresponding B form, possibly the consequence of both structural and ionic strength factors. The spectral characteristics of anti-BPDE bonded to these two forms are distinctly different, with the Z form resembling more closely those of A.T polymers.(ABSTRACT TRUNCATED AT 250 WORDS)

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMedDate not supplied

[Effect of the protein product of phage f1, gene 5, on heat denaturation of synthetic polynucleotides].

The influence of phage f1 gene 5 protein on melting of the synthetic polynucleotides has been investigated, using UV-spectroscopy. In our experiments we have varied the proteins concentration. It has been shown, that the protein lowers the melting temperature of the studied polynucleotides (d/A--Tn dAndTn, rAndTn, rAn.r n, dAn.rn). The melting temperatures and the shapes of melting curves of various polynucleotides differ when the same protein concentrations are used. We have shown that the protein binds to the double-stranded polynucleotides, containing ribo-ribo-, deoxyribo-ribo-chains. The difference in melting temperatures and shapes of melting curves was explained using the data about the differences in the secondary structure of these polynucleotides. Only for d/A-Tn renaturation was observed after sample cooling. It may reflect the single-stranded hairpin structure of this polynucleotide.

Bacteriophages↗
PubMedDate not supplied

[Circular dichroism study of the reaction between the protein product of bacteriophage f1 gene 5 and synthetic polynucleotides].

The complexes of gene 5 protein (phage f1) with single-stranded and double-stranded polynucleotides were investigated by circular dichroism (CD). In our experiments the concentration of the protein varied accordingly to polynucleotide. A decrease of the CD amplitude for polynucleotide-protein complexes was shown in all the regions of wavelength studied. The data indicate that the protein is bounded to the polynucleotide. This protein bounds differently to double-stranded polynucleotides containing ribo-ribo, ribo-deoxyribo and deoxyribo-deoxyribo chains. This difference is explained by differences in the form of the secondary structure of polynucleotides, containing ribo-ribo, ribo-deoxyribo and deoxyribo-deoxyribo chains.

Bacteriophages↗
PubMed1993

Differential binding of the enantiomers of chloroquine and quinacrine to polynucleotides: implications for stereoselective metabolism.

Interaction of the antimalarial drugs quinacrine and chloroquine with DNA has been studied extensively in order to understand the origin of their biological activity. These studies have shown that they bind to DNA through an intercalative mode and show little sequence specificity. All previous experiments were carried out using the racemic form of these drugs. We have investigated the binding of the enantiomeric forms of quinacrine and chloroquine to synthetic polynucleotides poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly (dG-dC), and found interesting differences in their binding parameters. Quinacrine enantiomers have a much higher binding affinity for the two polynucleotides compared to those of chloroquine. The negative enantiomers were found to have higher binding affinity than the positive ones. The binding constant for the binding of quinacrine(-) to poly(dG-dC).poly(dG-dC) was found to be about 3 times that of quinacrine(+). The differences in these binding affinities were further confirmed by equilibrium dialysis of the complexes of the polynucleotides with the racemic form of the drugs, which resulted in the enrichment of the dialysate with the positive enantiomer. CD spectra of the enantiomers and their polynucleotide complexes are reported. Changes in the fluorescence properties of quinacrine in the presence of the two polynucleotides are also described. Biological implications of these findings are discussed.

Chloroquine↗
PubMed2006

Fuzzy polynucleotide spaces and metrics.

The study of genetic sequences is of great importance in biology and medicine. Mathematics is playing an important role in the study of genetic sequences and, generally, in bioinformatics. In this paper, we extend the work concerning the Fuzzy Polynucleotide Space (FPS) introduced in Torres, A., Nieto, J.J., 2003. The fuzzy polynucleotide Space: Basic properties. Bioinformatics 19(5); 587-592 and Nieto, J.J., Torres, A., Vazquez-Trasande, M.M. 2003. A metric space to study differences between polynucleotides. Appl. Math. Lett. 27:1289-1294: by studying distances between nucleotides and some complete genomes using several metrics. We also present new results concerning the notions of similarity, difference and equality between polynucleotides. The results are encouraging since they demonstrate how the notions of distance and similarity between polynucleotides in the FPS can be employed in the analysis of genetic material.

Algorithms↗
PubMed2003

Affinity chromatography of DNA on nonporous copolymerized particles of styrene and glycidyl methacrylate with immobilized polynucleotide.

Nonporous particles of microsize were prepared by the dispersion polymerization of styrene and glycidyl methacrylate and chemically modified to introduce amino groups on the surface by grafting with either hexamethylenediamine or N-methyl-1,3-propanediamine. Aminated particles were then coupled with phosphorylated single-stranded polynucleotides at the 5'-end through covalent linkages. The affinity columns packed with these prepared polynucleotide-immobilized particles effectively retained single-stranded DNA, which could base-pair with the immobilized sequence. Bound DNAs could be eluted to yield a sharp peak by using an aqueous solution of 0.4M NaOH. The nonspecific adsorption due to the electrostatic interaction between the polynucleotide and the residual amino groups on the particle surface via the amination with hexamethylenediamine was significant and could only be reduced by using a high salt (NaCl) concentration. A higher salt concentration in the elution solution could result in a portion of complementary polynucleotide eluted in the nonretained fraction. However, the nonspecific adsorption of polynucleotides was insignificant in the column packed with DNA-immobilized particles prepared via amination using N-methyl-1,3-propanediamine. The column was effective for microanalysis of sequence-specific DNA.

Base Sequence↗
PubMed1999

The effect of the chain length of polynucleotides on their binding with platinum complexes.

The effect of the length of polynucleotides on their binding with platinum complexes was studied. The highest reaction rate was observed in the reaction with guanosine-containing polynucleotides, whereas cytidine- and adenosine-containing polynucleotides were much less efficient. The monoaqua-forms of the platinum complexes exhibited the highest reactivity in the interaction with polynucleotides in solution. The mechanism implies the formation of the monodentate complex at the first stage which is transformed into the corresponding bidentate complex of chelate type at the second stage. Increase in the length of the polynucleotide chain was shown to enhance its interaction with the platinum complexes.

Adenine↗
PubMed1986

The rho-115 mutation in transcription termination factor rho affects its primary polynucleotide binding site.

We have investigated the effect of the rho-115 mutation on the catalytic properties of the Escherichia coli termination protein, rho. Comparison of the primary and secondary polynucleotide binding sites activities reveals dramatic differences between the mutant and wild-type molecules. Wild-type rho must bind single-stranded polynucleotides to activate its nucleotide triphosphatase (NTPase) activity, and either poly(C), or poly(dC) plus oligo(C), will suffice. In contrast, attempted activation of the rho-115 NTPase with poly(C) in the presence of poly(dC) showed the latter to be a potent inhibitor. Inclusion of small oligonucleotides such as oligo(C) in the activation assay does not inhibit the poly(C)-induced NTPase reaction of either wild-type rho or rho-115. This would indicate, in the two polynucleotide binding site model for rho proposed by Richardson (Richardson, J.P. (1982) J. Biol. Chem. 251, 5760-5766), that the mutation in rho-115 affects the primary polynucleotide binding site. Transcription termination in vitro at the rho-dependent site trp t' showed dramatically reduced termination with rho-115 protein compared to wild-type rho. In the presence of rho-115, the transcript is longer and termination occurs over a narrower range of nucleotides than with wild-type rho. This suggests that the primary polynucleotide binding site is important not only for efficient termination of transcription but may also be involved in determining the terminal end point of the transcript itself.

Binding Sites↗
PubMedDate not supplied

[Compact form of synthetic polynucleotides. Relationship between secondary structure and circular dichroism spectra].

The formation of compact particles from synthetic double- and triplestranded polynucleotides in water-salt solutions, containing poly(ethylene glycol) (PEG) has been investigated. CD spectra of compact particles are characterized by intense bands (positive or negative) in the region of 270 nm, compact particles being divided into two families--psi- and psi+--according to the CD band sign. The amplitude of the CD band at 270 nm increases with the increase of CPEG. Heating of a solution, containing compact particles, results in a disappearance of the CD band, the "melting" of compact particles as revealed by the CD method occuring prior to the melting of the secondary structure of the corresponding polynucleotide. It is concluded that intense CD bands, which are characteristic of the compact form of synthetic polynucleotides, arise (similar to the case of DNA or dsRNA) from regular arrangement of polynucleotide chains in compact particles. The question, concerning the relation between parameters of the secondary structure of polynucleotides and their belonging either to psi- or to psi+ family is discussed. The factors, which could account for the appearance of intense bands in CD spectra of compact particles are also considered.

Circular Dichroism↗
PubMedDate not supplied

[Unwinding effect of F1 gene 5 protein on double-stranded polynucleotides and DNA].

The effect of gene 5 protein from bacteriophage f1 on melting of double-stranded polynucleotides and DNAs has been investigated using the UV-spectroscopy method. A dependence of the melting temperature of polynucleotide (DNA)-gene 5 protein complexes upon the polynucleotide (DNA) GC-pair content has been detected. Using experimental data and examining some model systems we came to the supposition that the lowering of melting temperature of polynucleotide (DNA) induced by this protein is probably stipulated by intercalation of the protein tyrosyl residues into one of the chains of polynucleotide (DNA) double helix.

Coliphages↗
PubMedDate not supplied

[Comparative study of slow 1H to 3H exchange in synthetic polynucleotides of A- and B-type conformations].

The rate of 1H leads to 3H exchange between water and C(8)H-groups of purinic residues in synthetic polynucleotides in wide temperature range measured. At temperatures below their Tm the rate of the exchange is shown to be lower as compared with that in corresponding mononucleotides. In the case of polynucleotides of A-conformation (poly(A).poly(U), poly(A).2poly(U) and poly(dA).2poly(dT), and poly(G).poly(C) the exchange is retarded by a factor of 5.7--7.5, whereas in the case of those of B-conformation (poly(dA).poly(dT), poly(dA--dT).poly(dA--dT) and poly(dG).poly(dC)) the exchange is retarded only by a factor of 2.3--2.5. Assuming the ylide mechanism of exchange the retardation is interpreted as a consequence of sterical hidrance in polynucleotides helical structure, which hampers contacts between purinic C(8)H-groups and OH-ions of solvent. Analysis of atomic arrangement around C(8)H-group and interatomic distances calculated on the basis of published atomic coordinates support our general conclusion that the sterical hindrance is more significant in the A-form as compared with that in the B-form. Elucidated correlation between the degree of the retardation in purine-containing polynucleotides and their conformation in solution allows to estimatf the type of conformation of polynucleotide with unknown structure on account of the slow 1H leads to 3H exchange data.

Hydrogen↗
PubMedDate not supplied

[The selectivity of the mutagenic action of DNA and other polynucleotides].

A paper summarises the results of author's and his collaborators studies on the mutagenic action of DNA and other natural and synthetic polynucleotides. These results were published with rare exception in Russian and Ukrainian scientific journals. Analogous results obtained by other authors of several countries are also discussed. It was proved that unlike conventional physical and chemical mutagens, polynucleotides selectively induce visible and lethal mutations preferentially in certain genes, different in case of treatment with different polynucleotides. Polynucleotides often induce mutation in several non-allelic genes in a single germ cell of the host (multimutational effect). Polynucleotides do not induce gross chromosome aberration.

Animals↗
PubMed1983

Binding of RecA protein to single-stranded nucleic acids: spectroscopic studies using fluorescent polynucleotides.

Binding of the recA gene product from Escherichia coli to single-stranded polynucleotides has been investigated using poly(dA) that have been modified by chloroacetaldehyde to yield fluorescent 1,N6-ethenoadenine (epsilon A) bases. A strong enhancement of the fluorescent quantum yield of poly(d epsilon A) is induced upon RecA protein binding. A 4-fold increase is observed in the absence of ATP or ATP gamma S and a 7-fold increase in the presence of either nucleoside triphosphate. RecA protein can bind to poly(d epsilon A) in the absence of both Mg2+ ions and ATP (or ATP gamma S) but Mg2+ ions are required to observe RecA protein binding in the presence of ATP (or ATP gamma S) at pH 7.5. ATP binding to the RecA-poly(d epsilon A) complex induces a dissociation of RecA from the polynucleotide followed by re-binding of [RecA-ATP-Mg2+] ternary complex. Whereas ATP-induced dissociation of RecA-poly(d epsilon A) complexes is a fast process, the subsequent binding reaction of [RecA-ATP-Mg2+] is slow. A model is proposed whereby [RecA-ATP-Mg2+] binding to poly(d epsilon A) involves slow nucleation and elongation processes along the polynucleotide backbone. The nucleation reaction is shown to involve at least a trimer or a tetramer. Polymerization of the [RecA-ATP-Mg2+] ternary complex stops when the polynucleotide is entirely covered with 6 +/- 1 nucleotides per RecA monomer. ATP hydrolysis then induces a release of RecA-ADP complexes from the polynucleotide template.

Adenosine Triphosphate↗
PubMed2006

Minor groove binding of Co(III)meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to various duplex and triplex polynucleotides.

The binding site and the geometry of Co(III)meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (CoTMPyP) complexed with double helical poly(dA).poly(dT) and poly(dG).poly(dC), and with triple helical poly(dA).[poly(dT)](2) and poly(dC).poly(dG).poly(dC)(+) were investigated by circular and linear dichroism (CD and LD). The appearance of monomeric positive CD at a low [porphyrin]/[DNA] ratio and bisignate CD at a high ratio of the CoTMPyP-poly(dA).poly(dT) complex is almost identical with its triplex counterpart. Similarity in the CD spectra was also observed for the CoTMPyP-poly(dG).poly(dC) and -poly(dC).poly(dG).poly(dC)(+) complex. This observation indicates that both monomeric binding and stacking of CoTMPyP to these polynucleotides occur at the minor groove. However, different binding geometry of CoTMPyP, when bind to AT- and GC-rich polynucleotide, was observed by LD spectrum. The difference in the binding geometry may be attributed to the difference in the interaction between polynucleotides and CoTMPyP: in the GC polynucleotide case, amine group protrude into the minor groove while it is not present in the AT polynucleotide.

Binding Sites↗
PubMedDate not supplied

An efficient binding chemistry for glass polynucleotide microarrays.

A variety of methods have been described for making synthetic polynucleotide microarrays. These include in situ synthesis directly on the array surface, for example, by photolithography or ink-jet printing technologies, and the application of presynthesized polynucleotides that are derivatized with various nucleophiles or electrophiles. In the latter case, a variety of surface chemistries have been developed, and several are available commercially. These chemistries must be compatible with nanoliter-scale volumes of polynucleotide reagents, which contact the array over a small portion of their surface. We reasoned that a three-dimensional polymer coating could potentially offer greater surface contact and higher binding efficiency. Here we describe a polyethylenimine-based coating chemistry that provides exceptional binding and hybridization characteristics. In our preferred process, size-fractionated polyethylenimine polymers are cross-linked onto an aminopropylsilanated glass surface in the presence of cyanuric chloride. The resulting three-dimensional coating binds polynucleotides through a mixture of covalent and noncovalent interactions as evidenced by comparisons between 5'-aminoalkyl modified and unmodified polynucleotides. Binding and hybridization comparisons are presented including analogous two-dimensional electrophilic and electrostatic chemistries.

Algorithms↗
PubMed1987

Binding of IKe gene 5 protein to polynucleotides. Fluorescence binding experiments of IKe gene 5 protein and mutual cooperativity of IKe and M13 gene 5 proteins.

Fluorescence studies of the binding of IKe gene 5 protein to various polynucleotides were performed to obtain insight into the question as to what extent the binding characteristics of the gene 5 proteins of the IKe and M13 phages resemble and/or differ from each other. The fluorescence of IKe gene 5 protein is quenched 60% upon binding to most polynucleotides. At moderate salt concentrations, i.e., below 1 M salt, the binding stoichiometry is 4.0 +/- 0.5 nucleotides per IKe gene 5 protein monomer. The affinity of the protein for homopolynucleotides depends strongly on sugar and base type; in order of increasing affinities we find poly(rC) less than poly(dA) less than poly(rA) less than poly(dI) less than poly(rU) less than poly(dU) less than poly(dT). For most polynucleotides studied, the affinity depends linearly on the salt concentration: [d log (Kint omega)]/(d log [M+]) = -3. The binding is highly cooperative. The cooperativity parameter omega, as deduced from protein titration curves, is 300 +/- 150 and appears independent of the type of polynucleotide studied. Estimation of this binding parameter from salt titrations of gene 5 protein-polynucleotide complexes results in systematically higher values. A comparison of the binding data of the IKe and M13 gene 5 proteins shows that the fluorescence quenching, stoichiometry, order of binding affinities, and cooperativity in the binding are similar for both proteins. From this it is concluded that at least the DNA binding grooves of both proteins must show a close resemblance.(ABSTRACT TRUNCATED AT 250 WORDS)

Coliphages↗