Thermodynamic profiles of the DNA binding of benzophenanthridines sanguinarine and ethidium: A comparative study with sequence specific polynucleotides

Energetics of the binding of two known classical DNA intercalating molecules, ethidium and sanguinarine with four sequence specific polynucleotides, poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT), and poly(dA).poly(dT) have been compared under identical conditions. The binding of both the molecules was characterized by strong stabilization of the polynucleotides against thermal strand separation in optical melting as well as differential scanning calorimetry studies. Isothermal titration calorimetry results revealed that the binding of both sanguinarine and ethidium to poly(dG-dC).poly(dG-dC), poly(dA-dT).poly(dA-dT), and poly(dG).poly(dC) was exothermic and favoured by negative enthalpy changes. On the other hand, the binding of both molecules to poly(dA).poly(dT) was endothermic and entropy driven. The binding affinity values obtained from isothermal titration calorimetry data was in close proximity to that derived from thermal melting data. The heat capacity changes obtained from temperature dependence of the enthalpy change gave negative values in the range (?0.4 to 1.25) kJ · mol^?1 · K^?1 for the binding of ethidium and sanguinarine to these polynucleotides. The variations in the values indicate important differences in the formation of the complexes. New insights into the energetics and specificity aspects of interaction of these molecules to DNA have emerged from these studies.     

Some aspects of the DNA hypochromic effect theory

The expressions for the polymer absorption band hypochromism and oscillator strength are studied in frames of the first-order perturbation theory. The physically justified approximations for a polymer hypochromism calculation are indicated. The uniform interpretation of the effect origin is given independently on the approximation used. In frames of the perturbation theory the DNA hypochromism formula is obtained, from which the known experimental dependences of hypochromism on chain length and polymer helicity degree follows directly. The analytic expression of the DNA hypochromism dependence on AT pairs content is obtained. It is established that in most cases for natural DNA the nucleotide sequence does not influence in practice the value of the hypochromic effect.     

Calorimetric and thermal analysis studies on the binding of phenothiazinium dye thionine with DNA polynucleotides

Binding of the phenothaizinium dye thionine with four sequence specific deoxyribopolynucleotides, poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT), and poly(dA).poly(dT) has been investigated by means of thermal helix melting, isothermal titration calorimetry, and differential scanning calorimetry experiments. The binding affinity values evaluated from isothermal titration calorimetry suggests that thionine exhibits the highest binding affinity to poly(dG-dC).poly(dG-dC). The binding to poly(dG-dC).poly(dG-dC), poly(dA-dT).poly(dA-dT), and poly(dG).poly(dC) is exothermic and favoured by negative enthalpy changes while binding to poly(dA).poly(dT) is endothermic and anomalous. The values of heat capacity changes of the interaction are negative and in the range (?0.4 to ?0.5) kJ · K^?1 · mol^?1. The binding is characterized by strong stabilization of the polynucleotides against thermal strand separation. The binding affinity values derived from thermal melting data are in excellent agreement with those obtained from isothermal titration calorimetry data. Insights into the energetic aspects and guanine–cytosine selectivity of the DNA interaction of thionine have been obtained from these studies.     

Energy of planar autoassociation of xanthine and spatial structure of poly(riboxanthylic acid)

First- and second-order perturbation theory in a polarization approximation was employed to calculate interaction energies of planar xanthine–xanthine pairs in stable configurations. Electrostatic energy was obtained in the atomic-dipole approximation. The results provided a basis for formulation of a four-stranded model of poly(xanthylic acid) that allows two hydrogen bonds per base. The model accounts satisfactorily for the unusual thermal stability and the observed pH transition of the polymer. The latter is due to the gradual dissociation of the N₃ protons accompanying by disrupture of the weak N₃? H ··· O₆ hydrogen bonds. However, the structure is only moderately weakened since the configuration of the coplanar bases remains stabilized by four N₁? H ··· O₂ hydrogen bonds.     

Sensitive determination of nucleotides and polynucleotides based on the fluorescence quenching of the Tb3+-Tiron complex

 A sensitive method using fluorescence quenching for the determination of nucleotides (ATP, ADP, AMP, CTP, UTP) and polynucleotides[poly(A), poly(I), poly(U)] is proposed. It is based on the ability of nucleotides and polynucleotides to inhibit the formation of a strongly fluorescent complex of Tb³⁺ ion with Tiron. The possibilities of spectrofluorimetric measurements of these systems were studied under optimal conditions (pH 6.9 in hexamethylene tetramine-HCl buffer, 1.2×10^-6 mol/L of Tb³⁺, 4.0×10^-6 mol/L of Tiron, λ_ex=317 nm, λ_em=546 nm). The results showed that the Tb³⁺-Tiron complex could be used as a fluorescence test for the phosphate moieties of nucleotides and polynucleotides. The detection limits are 0.3, 1.2, 3.7, 0.2, 0.3, 1.1, 0.6 and 0.9 ng/mL for ATP, ADP, AMP, CTP, UTP, poly(A), poly(I), and poly(U), respectively. The relative standard deviations (6 replicates) are within 4.0% in the middle of the linear range. The fluorescence quenching mechanism of these systems is also discussed. Received: 16 July 1996 / Revised: 13 November 1996 / Accepted: 13 November 1996     

Study of thermal decomposition of poly-(vinyl chloride)-type polymers with the use of model substances-V: Pyrolysis of cis-5-chloro-3-heptene and cis- and trans-5-acetoxy-3-heptene in the phase

The gas phase pyrolyses of cis-5-chloro-3-heptene (in the range 267–337°) and cis- and trans-5-acetoxy-3-heptene (300–378°) are homogeneous unimolecular first-order reactions with rate constants given respectively by: log k = (12·03 = 0·13) - (36·2 ± 0·4)/2·303 RT and (12·80 ± 0·11) - (43·0 ± 0·3)/2·303 RT. (Frequency factors in sec^?1 units, activation energies in kcal mol^?1.) No significant differences were found between the rates of decomposition of cis and trans isomers of 5-acetoxy-3-heptene. From the decomposition of these models of poly(vinyl chloride) and poly(vinyl acetate), some conclusions about the role of internal unsaturated groups in the thermal decomposition of both polymers were drawn. The possibility that groups with cis internal double bonds are the most labile structures in a poly(vinyl) chloride macromolecule is discussed.     

Determination of side‐chain‐rotamer and side‐chain and backbone virtual‐bond‐stretching potentials of mean force from AM1 energy surfaces of terminally‐blocked amino‐acid residues,for coarse‐grained simulations of protein structure and folding. I. The method

In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simulations of protein structure and dynamics. In this article, we describe the methodology for determining the corresponding potentials of mean force (PMF's) from the energy surfaces of terminally‐blocked amino‐acid residues calculated with the AM1 quantum‐mechanical semiempirical method. The approach is based on minimization of the AM1 energy for fixed values of the angles λ for rotation of the peptide groups about the C^α ··· C^α virtual bonds, and for fixed values of the side‐chain dihedral angles χ, which formed a multidimensional grid. A harmonic‐approximation approach was developed to extrapolate from the energy at a given grid point to other points of the conformational space to compute the respective contributions to the PMF. To test the applicability of the harmonic approximation, the rotamer PMF's of alanine and valine obtained with this approach have been compared with those obtained by using a Metropolis Monte Carlo method. The PMF surfaces computed with the harmonic approximation are more rugged and have more pronounced minima than the MC‐calculated surfaces but the harmonic‐approximation‐and MC‐calculated PMF values are linearly correlated. The potentials derived with the harmonic approximation are, therefore, appropriate for UNRES for which the weights (scaling factors) of the energy terms are determined by force‐field optimization for foldability. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Conformational studies of double-helical polynucleotides by the method of pair-wise potential functions

Double-helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A-T))·poly(d(T-A))·poly(dG)·poly(dC), and poly(d(G-C))·poly(d(C-G)) are analyzed by the atom–atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β-D -deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3–5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (? = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ? ?24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A–B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A–B transition.     

Rapid Location of the Preferred Interaction Sites between Small Polar Molecules and Macromolecules. II. Binding of Water to a Model Segment of B-DNA

The procedure developed in Part I of this series is applied to the homopolymeric sequences poly(dA) · poly(dT) and poly(dG) · poly(dC) on the double helical structure of B-DNA. Some aspects of the base sequence influence on the polymer's attraction for water molecule are described. The results are used to discuss the general hydration features of those systems in relation to recent experimental studies of DNA single crystals.     

DNA loops and semicatenated DNA junctions

Background  

Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized.     

DAMAGE TO URACIL- AND ADENINE-CONTAINING BASES, NUCLEOSIDES, NUCLEOTIDES AND POLYNUCLEOTIDES: QUANTUM YIELDS ON IRRADIATION AT 193 AND 254 NM

Abstract Photoreactions, such as base release and decomposition of the base moiety, induced by either 20 ns laser pulses at 193 nm or continuous 254 nm irradiation, were studied for a series of uracil and adenine derivatives in neutral aqueous solution. The quantum yield of chromophore loss (φ) depends significantly on the nature of the nucleic acid constituent and the saturating gas (Ar, N₂O or O₂). In the case of polynucleotides the destruction of nucleotides was measured by high-performance liquid chromatography after hydrolysis; the quantum yields (φ) are comparable to those of chromophore loss or larger. The φ_cl and aφ_dn of 0.04–0.1 for poly(U) and poly(dU), obtained for both wavelengths of irradiation, are due to processes originating from the lowest excited singlet state, i.e. formation of photohydrates and photodimers, and a second part from photoionization using λ_irr= 193 nm. Irradiation at 193 nm effectively splits pyrimidine dimers and thus reverts them into monomers. The quantum yield for release of undamaged bases (φ_br) from nucleosides, nucleotides and polynucleotides upon irradiation at 254 nm is typically φ_br= (0.1–1) × 10^?4 Breakage of the N-glycosidic bond is significantly more efficient for λ_irr=193 nm, e.g. φ_br= 1.1 × 10^?3, 0.8 × 10^?3, 4.3 × 10^?3 and 0.5 × 10^?3 for poly(A), poly(dA), poly(U) and poly(dU) in Ar-saturated solution, respectively. Enhanced φ values for λ_irr= 193 nm, essentially for adenine and its derivatives, are caused by photo-processes that are initiated by photoionization.     

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly?A, poly?G, poly?C, poly?U), double-stranded DNA polynucleotides (poly?dAdT-poly?dAdT, poly?dGdC-poly?dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly?dAdT-poly?dAdT, at variance to preferred binding of Im and Py to only major groove of poly?dGdC-poly?dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.     

EMISSION SPECTRA FROM SYNTHETIC POLYNUCLEOTIDES AND DEOXYRIBONUCLEIC ACID IN AQUEOUS SOLUTIONS†

A study has been made of the emission spectra at 77°K from poly A, poly U, poly C, their complexes, and from native and heat-denatured DNA in buffered aqueous solutions containing 0·25 per cent glucose: no emission was observed from these polynucleotides at room temperature. The spectra differed from those obtained in the polyalcoholic glasses used by other workers. The principal differences between the emission spectra of poly A and adenosine at pH 7 in a water-glucose mixture were: (a) a decrease in both P/F and the overall intensity in poly A; (b) absence of the structure normally found in adenosine phosphorescence; and (c) appearance of a new short-lived component in the phosphorescence decay. Further changes in the emission characteristics (e.g. the increase of P/F, the proportional increase of the short-lived component in the phosphorescence decay) from poly A were observed at pH 5. These can not be explained solely by protonization of adenosine residues, but rather appear to depend upon exciton interactions of the most intense π–π* transition in double-stranded poly A. and perturbation of the lowest-lying emitting band. When poly A or poly C is complexed with poly U or poly I the luminescence intensity decreases in two-strand complexes and is completely quenched in poly (A + 2U), poly (A+2I) and poly (C⁺+I); no emission was observed from either, single-strand poly I or poly U. Identical emission patterns were obtained from native and heat-denatured samples of DNA. The comparison of polynucleotide emission spectra in the water-glucose medium with those obtained from polyalcoholic glasses leads to the conclusion that the emission spectra depend most critically upon the relative proportions of base-solvent and base-base interactions in each environment: the possible importance of proton tunneling and/or triplet-triplet transfer mechanisms is briefly discussed.     

Synthesis of biocompatible and biodegradable block copolymers of polyvinyl alcohol‐block‐poly(ε‐caprolactone) using metal‐free living cationic polymerization

Applications of metal‐free living cationic polymerization of vinyl ethers using HCl · Et₂O are reported. Product of poly(vinyl ether)s possessing functional end groups such as hydroxyethyl groups with predicted molecular weights was used as a macroinitiator in activated monomer cationic polymerization of ε‐caprolactone (CL) with HCl · Et₂O as a ring‐opening polymerization. This combination method is a metal‐free polymerization using HCl · Et₂O. The formation of poly(isobutyl vinyl ether)‐b‐poly(ε‐caprolactone) (PIBVE‐b‐PCL) and poly(tert‐butyl vinyl ether)‐b‐poly(ε‐caprolactone) (PTBVE‐b‐PCL) from two vinyl ethers and CL was successful. Therefore, we synthesized novel amphiphilic, biocompatible, and biodegradable block copolymers comprised polyvinyl alcohol and PCL, namely PVA‐b‐PCL by transformation of acid hydrolysis of tert‐butoxy moiety of PTBVE in PTBVE‐b‐PCL. The synthesized copolymers showed well‐defined structure and narrow molecular weight distribution. The structure of resulting block copolymers was confirmed by ¹H NMR, size exclusion chromatography, and differential scanning calorimetry. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5169–5179, 2009     

EFFECT OF BASE SEQUENCE ON THE ULTRAVIOLET IRRADIATION PRODUCTS OF DOUBLE-STRANDED POLYNUCLEOTIDES CONTAINING BROMOURACIL AND ADENINE

Abstract —The effects of ultraviolet irradiation of double-stranded synthetic polynucleotides containing BrU and A have been investigated. Homopolymer pairs and alternating copolymers composed of either ribo- or deoxyribo-nucleotides were prepared and were irradiated with either 313 nm or ˜ 285 nm light. Strand separation and a modest amount of strand breakage followed irradiation of the homopolymer pairs. Changes in the ultraviolet absorption spectra of the polymers during irradiation reflected the sum of hyperchromic increases caused by progressive strand separation and loss of absorbance caused by photoproduct formation. Extensive debromination occurred. An RNase digest of irradiated poly(rA)–poly¹⁴C(rBrU), analysed by column chromatography, showed components similar to those found previously upon irradiation of single-stranded poly(rBrU). Little photoproduct was released by RNase digestion as mononucleotides. The major photoproduct was in the dinucleotide fraction, and may be 5,5'-diuracil. Base sequence had a profound effect on the sensitivity of the polynucleotides. Irradiation of alternating copolymers with doses of light comparable to those that produced major photochemical changes in the homopolymer pairs brought about little if any change in the copolymers of alternating base sequence.     

Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition

The binding properties of two anthracene derivatives with calf thymus DNA (CT DNA), poly(dA-dT), and poly(dG) x poly(dC) are reported. One contained bulky, cyclic cationic substituents at the 9 and 10 positions, and the other carried acylic, branched, cationic substituents. Binding of the probes to the DNA was examined by calorimetry, spectroscopy and helix melting studies. The cyclic derivative indicated exothermic binding, strong hypochromism, bathochromism, positive induced circular dichroism (CD, 300-400 nm), significant unwinding of the helix, large increases in the helix melting temperature, strong but negative linear dichroism (LD, 300-400 nm) and considerable stabilization of the helix. In contrast, the acyclic analog indicated thermoneutral binding, smaller hypochromism, no bathochromism, very weak induced CD, and no change in the helix melting temperature with any of the DNA polymers. A sharp distinction between the binding properties of the two probes is indicated, and both have intrinsic binding constants of approximately 10(6) M(-1) for the three polymers. However, when the ionic strength of the medium was lowered (10 mM NaCl), the absorption as well as CD spectral changes associated with the binding of the acyclic derivative corresponded with those of the cyclic derivative. The acyclic derivative showed large preference (10-fold) for poly(dG) x poly(dC) over poly(dA-dT), whereas the cyclic analog showed no preference. The characteristic spectroscopic signatures of the two distinct binding modes of these probes will be helpful in deciphering the interaction of other anthracene derivatives with DNA.     

Synthesis of poly(vinyl alcohol) containing asymmetric nucleic acid base derivatives as grafted pendants

The preparations of new model polymers of polynucleotides with linear poly(vinyl alcohol) (PVA) backbones and an optically active nucleic acid base derivative as a pending side chain are described. (±)-, (+)-, and (?)-2-(thymin-1-yl)propionic acid were grafted onto PVA through ester bonds by direct coupling with dicyclohexylcarbodiimide (DCC) in the presence of highly active catalyst 4-pyrrolidinopyridine (PPY) to give optically active graft polymers. The corresponding monomer and dimer models have been prepared.     

Oxyalkylene polymers with alkylsulfonylmethyl side chains: Gas barrier properties

Gas barrier properties of alkylsulfonylmethyl-substituted poly(oxyalkylene)s are discussed. Oxygen permeability coefficients of three methylsulfonylmethyl-substituted poly(oxyalkylene)s, poly[oxy(methylsulfonylmethyl)ethylene] (MSE), poly[oxy(methylsulfonylmethyl)ethylene-co-oxyethylene] (MSEE), and poly[oxy-2,2-bis (methylsulfonylmethyl)trimethylene oxide] (MST) were measured. MSEE, which has the most flexible backbone of the three polymers, had an oxygen permeability coefficient at 30°C of 0.0036 × 10⁻¹³ cm³(STP)·cm/cm²·s·Pa higher than that of MSE, 0.0014 × 10⁻¹³ cm³(STP)·cm/cm²·s·Pa, because the former polymer's T_g was near room temperature. MST with two polar groups per repeat unit and the highest T_g showed the highest oxygen permeability, 0.013 × 10⁻¹³ cm³(STP) · cm/cm²·s·Pa, among the three polymers, probably because steric hindrance between the side chains made the chain packing inefficient. As the side chain length of poly[oxy(alkylsulfonylmethyl)ethylene] increased, T_g and density decreased and the oxygen permeability coefficients increased. The oxygen permeability coefficient of MSE at high humidity (84% relative humidity) was seven times higher than when it was dry because absorbed water lowered its T_g. At 100% relative humidity MSE equilibrated to a T_g of 15°C after 2 weeks. A 50/50 blend of MSE/MST had oxygen barrier properties better than the individual polymers (O₂ permeability coefficient is 0.0007 × 10⁻¹³ cm³(STP)·cm/cm² ·s·Pa), lower than most commercial high barrier polymers. At 100% relative humidity, it equilibrated to a T_g of 42°C, well above room temperature. These are polymer systems with high gas barrier properties under both dry and wet conditions. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36 : 75–83, 1998     

The synthesis of poly(phenylacetylene)s with bulky chiral silyl groups and the thermal stability of their helical conformation

The polymerization of (−)‐p‐[(tert‐butylmethylphenyl)silyl]phenylacetylene (t‐BuMePhSi*PA) and (+)‐p‐[{methyl(α‐naphthyl)phenyl}silyl]phenylacetylene (MeNpPhSi*PA) with the [(nbd)RhCl]₂ Et₃N catalyst yielded polymers with very high molecular weights over 2 × 10⁶ in high yields. The optical rotations of the formed poly(t‐BuMePhSi*PA) and poly(MeNpPhSi*PA) were as high as −356 and −150° (c = 0.11 g/dL in CHCl₃), respectively. The circular dichroism (CD) spectrum of poly(t‐BuMePhSi*PA) in CHCl₃ exhibited very large molar ellipticities ([θ]) in the UV region: [θ]_max = 9.2 × 10⁴ ° · cm² · dmol⁻¹ at 330 nm and −8.0 × 10⁴ ° · cm² · dmol⁻¹ at 370 nm. The [θ]_max values of poly(MeNpPhSi*PA) were also fairly large: [θ]_max = 7.1 × 10⁴ ° · cm² · dmol⁻¹ at 330 nm and −5.3 × 10⁴ ° · cm² · dmol⁻¹ at 370 nm. The optical rotations of poly(t‐BuMePhSi*PA) and poly(MeNpPhSi*PA), measured in tetrahydrofuran, chloroform, and toluene solutions, were hardly dependent on temperature in the range 22–65 °C. The CD effects of these polymers hardly changed in the temperature range 28–80 °C, either. These results indicate that the helical structures of these polymers are thermally appreciably stable. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 71–77, 2001