Interaction of DNA with anti-cancer drugs: copper-thiosemicarbazide system

The interaction of copper-thiosemicarbazide complexes with DNA was investigated using ultraviolet and infrared spectroscopy. Evidence for the interaction of the complexes with nucleic acid bases and with the phosphate group is presented.

Interaction of metal ions with nucleic acids and related compounds. II. Studies on Au(III)-nucleic acid system

The nature of interaction of Au(III) with nucleic acids was studied by using methods such as uv and ir spectrophotometry, viscometry, pH titrations, and melting-temperature measurements. Au(III) is found to interact slowly with nucleic acids over a period of several hours. The uv spectra of native calf-thymus DNA 9pH 5.6 acetate buffer containing (0.01M NaCIO4) showed a shift in λ max to high wavelengths and an increase in optical density at 260 nm. There was a fourfold decrease in viscosity (expressed as ηsp/c). The reaction was faster at pH 4.0 and also with denatured DNA (pH 5.6) and whole yeast RNA (pH 5.6). The order of preference of Au(III) (as deduced from the time of completion of reaction) for the nucleic acids in RNA > denatured DNA > DNA. The reaction was found to be completely reversible with respect KCN. Infrared spectra of DNA-Au(III) complexes showed binding to both the phosphate and bases of DNA. The same conclusions were also arrived at by melting-temperature studies of Au(III)-DNA system. pH titrations showed liberation of two hydroxylions at r = 0.12 [r = moles of HAuCl4 added per mole of DNA-(P)] and one hydrogen ion at r = 0.5. The probable binding sites could be N(1)/N(7) of adenine, N(7) and/or C(6)O of guanine, N(3) of cytosine and N(3) of thymine. DNAs differing in their (G = C)-contents [Clostridium perfingens DNA(G = C, 29%), salmon sperm DNA (G + C, 42%) and Micrococcus lysodeikticus DNA(G + C, 29%), salmon sperm DNA (G = C, 72%)] behaved differently toward Au(III). The hyperchromicity observed for DNAs differing in (G + C)-content and cyanide reversal titrations indicate selectivity toward ( A + T)-rich DNA at lw values of r. Chemical analysis and job's continuous variation studies indicated the existence of possible complexes above and below r = 1. The results indicate that Au(III) ions probably bind to hte phosphate group in the initial stages of the reaction, particularly at low values of r, and participation of the base interaction also increases. Cross-linking of the two strands by Au(III) may take place, but a complete collapse of the doulbe helix is not envisaged. It is probable that tilting of the bases or rotaiton of the bases around the glucosidic bond, resulting in a significant distrotion of the double helix, might take place due to binding of Au(III) to DNA.

Kinetic studies on the interaction of gold(III) with nucleic acids. I. Native DNA-Au(III) system-spectrophotometric studies

Kinetics of the interaction of Au(III) with native calf thymus DNA has been studied spectrophotometrically to determine the kinetic parameters and to examine their dependency on the concentrations of DNA and Au(III), temperature, ionic strength and pH. The reaction is of the first order with respect to both the nucleotide unit of DNA and Au(III) in the stoichiometry of 2∶1 respectively. The rate constants vary with the initial ratio of DNA to Au(III) and is attributed to the effect of free chloride ions and the existence of a number of reaction sites with slight difference in the rate constants. The activation energies of this interaction have been found to be 14–16 kcal/mol. From the effect of ionic strength the reaction is found to occur between a positive and a negative ion in the rate-limiting step. The logarithm of rate constants are the linear function of pH and the slopes are dependent on ther-values. A plausible mechanism has been proposed which involves a primary dissociation of the major existing species (AuCl2(OH)2)−, to give (AuCl2)+ which then reacts with a site in the nucleotide unit of DNA in the rate-liminting step followed by a rapid binding to another site on the complementary strand of the DNA double helix. There exist a number of binding sites with slight difference in reactivity.

Use of α- and β-subunit specific antibodies in studying interaction of hCG with Leydig cell receptors

Antisera (a/s) raised to individual α- and β-subunits of human chorionic gonadotropin (hCG) have been characterized for specificity using immunoaffinity procedures and used to study the disposition of the two subunits when intact hCG is complexed with luteinizing hormone (LH) receptor of the Leydig cells. Three kinds of experiments were done. (a) The ability of the preformed hormone-antibody (H-Ab) complex to bind to receptor and stimulate a response; (b) the ability of the a/s to dissociate hCG from its complex with the receptor and thereby terminate response; and (c) the ability of the premixed antibody and receptor to compete for binding of labeled hCG. Although the subunit specific a/s used here were equipotent in binding hCG (capacity to bind and Ka being very similar), their behavior once the receptor preparation or Leydig cell is introduced into the system was drastically different. The β-subunit antibody relative to the α-subunit antibody, appeared to be poorly effective in preventing hCG from either binding to the receptor or inhibiting the continuation of response. The results suggest that hCG upon interaction with the receptor loses the determinants specific to the β-region more rapidly compared to those specific to the α-region suggesting thereby that the initial interaction of hCG with the receptor should be occurring through sites in the β-subunit. Although the α-subunit portion of the hCG molecule is available for binding to the antibody for a relatively longer time, the biological response of the cell seems very sensitive to such binding with the antibody as it invariably results in loss of response. In the Leydig cell system, the ability of the a/s to bind hCG that is already complexed to the receptor appears to be dependent upon the time of addition of the antibody to the incubation medium. The antisera were totally ineffective in inhibiting steroidogenic response to hCG if added 60 min after addition of hCG. This would suggest that the hormone-receptor complex once formed perhaps continues to change its orientation with the result that with time relatively less and less of antigenic determinants become available for antibody binding.

Interaction of Gibberellic Acid and Indole-3-acetic Acid in the Growth of Excised Cuscuta Shoot Tips in Vitro1

Gibberellic acid (GA3) induced a marked elongation of 2.5-centimeter shoot tips of Cuscuta chinensis Lamk. cultured in vitro. In terms of the absolute amount of elongation, this growth may be the largest reported for an isolated plant system. The response to hormone was dependent on an exogenous carbohydrate supply. The hormone-stimulated growth was due to both cell division and cell elongation. The growth response progressively decreased if GA3 was given at increasingly later times after culturing, but the decreased growth response could be restored by the application of indole-3-acetic acid (IAA) to the apex. Explants deprived of GA3 gradually lost their ability to transport IAA basipetally, but this ability was also restored by auxin application. The observations are explained on the basis that: (a) the growth of Cuscuta shoot tip in vitro requires, at least, both an auxin and a gibberellin; and (b) in the absence of gibberellin the cultured shoot tip explants lose the ability to produce and/or transport auxin.

Studies on interaction of colloidal Ag nanoparticles with Bovine Serum Albumin (BSA)

Biofunctionalization of noble metal nanoparticles like Ag, Au is essential to obtain biocompatibility for specific biomedical applications. Silver nanciparticles are being increasingly used in bio-sensing applications owing to excellent optoelectronic properties. Among the serum albumins, the most abundant proteins in plasma, a wide range of physiological functions of Bovine Serum Albumin (BSA) has made it a model system for biofunctionalization. In absence of adequate prior reports, this study aims to investigate the interaction between silver nanoparticles and BSA. The interaction of BSA [0.05-0.85% concentrations] with Ag nanoparticles [50 ppm concentration] in aqueous dispersion was Studied through UV-vis spectral changes, morphological and surface structural changes. At pH 7, which is More than the isoelectric point of BSA, a decrease in absorbance at plasmon peak of uninteracted nanciparticles (425 mn) was noted till 0.45% BSA, beyond that a blue shift towards 410 urn was observed. The blue shift may be attributed to enhanced electron density on the particle surfaces. Increasing pH to 12 enhanced the blue shift further to 400 rim. The conformational changes in BSA at alkaline pH ranges and consequent hydrophobic interactions also played an important role. The equilibrium adsorption data fitted better to Freundlich isotherm compared to Langmuir Curve. The X-ray diffraction study revealed complete coverage of Ag nanoparticles by BSA. The scanning electron microscopic study of the interacted nanoparticles was also carried Out to decipher morphological changes. This study established that tailoring the concentration of BSA and pH of the interaction it was possible to reduce aggregation of nanoparticles. Biofunctionalized Ag nanoparticles with reduced aggregation will be more amenable towards bio-sensing applications. (C) 2009 Elsevier B.V. All rights reserved.

Interaction of Sesbania Mosaic Virus Movement Protein with VPg and P10: Implication to Specificity of Genome Recognition

Sesbania mosaic virus (SeMV) is a single strand positive-sense RNA plant virus that belongs to the genus Sobemovirus. The mechanism of cell-to-cell movement in sobemoviruses has not been well studied. With a view to identify the viral encoded ancillary proteins of SeMV that may assist in cell-to-cell movement of the virus, all the proteins encoded by SeMV genome were cloned into yeast Matchmaker system 3 and interaction studies were performed. Two proteins namely, viral protein genome linked (VPg) and a 10-kDa protein (P10) c v gft encoded by OFR 2a, were identified as possible interacting partners in addition to the viral coat protein (CP). Further characterization of these interactions revealed that the movement protein (MP) recognizes cognate RNA through interaction with VPg, which is covalently linked to the 59 end of the RNA. Analysis of the deletion mutants delineated the domains of MP involved in the interaction with VPg and P10. This study implicates for the first time that VPg might play an important role in specific recognition of viral genome by MP in SeMV and shed light on the possible role of P10 in the viral movement.

Interaction of nucleic acids with carbon nanotubes and dendrimers

Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

Sequence specific interaction of Mycobacterium smegmatis topoisomerase I with duplex DNA

We have identified strong topoisomerase sites (STS) for Mycobacteruim smegmatis topoisomerase I in double-stranded DNA context using electrophoretic mobility shift assay of enzyme-DNA covalent complexes; Mg2+, an essential component for DNA relaxation activity of the enzyme, is not required for binding to DNA, The enzyme makes single-stranded nicks, with transient covalent interaction at the 5'-end of the broken DNA strand, a characteristic akin to prokaryotic topoisomerases. More importantly, the enzyme binds to duplex DNA having a preferred site with high affinity, a. property similar to the eukaryotic type I topoisomerases, The preferred cleavage site is mapped on a 65 bp duplex DNA and found to be CG/TCTT. Thus, the enzyme resembles other prokaryotic type I topoisomerases in mechanistics of the reaction, but is similar to eukaryotic enzymes in DNA recognition properties.

A model for the interaction of trifluoroethanol with peptides and proteins

The structural stabilizing property of 2,2,2-trifluoroethanol (TFE) in peptides has been widely demonstrated, More recently, TFE has been shown to enhance secondary structure content in globular proteins, and to influence quaternary interactions in protein multimers. The molecular mechanisms by which TFE exerts its Influence on peptide and protein structures remain poorly understood. The present analysis integrates the known physical properties of TFE with a variety of experimental observations on the interaction of TFE with peptides and proteins and on the properties of fluorocarbons. Two features of TFE, namely the hydrophobicity of the trifluoromethyl group and the hydrogen bonding character (strong donor and poor acceptor), emerge as the most important factors for rationalising the observed effects of TFE. A model is proposed for TFE interaction with peptides which involves an initial replacement of the hydration shell by fluoroalcohol molecules, a process driven by apolar interactions and favourable entropy of dehydration. Subsequent bifurcated hydrogen-bond formation with peptide carbonyl groups, which leave intramolecular interactions unaffected, promotes secondary structure formation.

Studies on interaction of Paenibacillus polymyxa with iron ore minerals in relation to beneficiation

Interaction between Paenibacillus polymyxa with minerals such as hematite, corundum, quartz and kaolinite brought about significant surface chemical changes on all the minerals. Quartz and kaolinite were rendered more hydrophobic, while hematite and corundum, became more hydrophilic after biotreatment. The predominance of bacterial polysaccharides on interacted hematite and corundum and of proteins on quartz and kaolinite was responsible for the above surface-chemical changes. Bio-pretreatment of the above iron ore mineral mixtures resulted in the selective separation of silica and alumina from iron oxide, through bioflotation and bioflocculation. The utility of bioprocessing in the beneficiation of iron ores is demonstrated.

Solution of a System of Generalized Abel Integral Equations Using Fractional Calculus

A method is presented for obtaining useful closed form solution of a system of generalized Abel integral equations by using the ideas of fractional integral operators and their applications. This system appears in solving certain mixed boundary value problems arising in the classical theory of elasticity.

Interaction of Co, Mn, Mg and AI with d(GCGTACGC): a spectroscopic study

Spectroscopic study on the interactions of trace elements Co, Mn, Mg and Al with d(GCGTACGC) indicated the following: Al and Mg did not alter T-m values. Mn enhanced T-m at lower concentration and decreased it at higher concentrations. Interestingly Co at higher concentration elevated the T-m. These studies also showed lower concentrations of Mn displaced EtBr, whereas Al could displace it at higher ionic strength. Mg and Co displaced EtBr fluorescence at moderate concentrations. The binding constant values and CD spectra clearly indicated strong binding of these elements to DNA.

A comparative Raman study of the interaction of electron donor and acceptor molecules with graphene prepared by different methods

Interaction of tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) with few-layer graphene samples prepared by the exfoliation of graphite oxide (EG), conversion of nanodiamond (DG) and arc-evaporation of graphite in hydrogen (HG) has been investigated by Raman spectroscopy to understand the role of the graphene surface. The position and full-width at half maximum of the Raman G-band are affected on interaction with TTF and TCNE and the effect is highest with EG and least with HG. The effect of TTF and TCNE on the 2D-band is also maximum with EG. The magnitude of interaction between the donor/acceptor molecules varies in the same order as the surface areas of the graphenes. (C) 2009 Published by Elsevier B. V.