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At least 127 records · Page 7Linked to original sources
PubMed1999

Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC). poly(dG-dC) and poly(dA). 2poly(dT).

The helix-helix transitions which occur in poly(dG-dC). poly(dG-dC) and in poly (dG-m(5)dC). poly(dG-m(5)dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering like the "alternating B-DNA" put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA). 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA). poly(dT) can actually be observed by fibre X-ray diffraction measurements.

DNA↗
PubMed2005

Energetics of binding the mammalian high mobility group protein HMGA2 to poly(dA-dT)2 and poly(dA)-poly(dT).

The mammalian high mobility group protein A2 (HMGA2) is a chromosomal architectural transcription factor involved in oncogenesis and cell transformation. It has three "AT-hook" DNA binding domains, which specifically bind to the minor groove of AT DNAs. The interaction of HMGA2 with poly(dA-dT)2 and poly(dA)poly(dT) has been investigated using the ethidium displacement assay, isothermal titration calorimetry, and UV melting studies. Each AT hook DNA binding domain was found to bind to 5 bp and each HMGA2 molecule binds to 15 bp. Although an individual AT hook DNA binding domain binds to AT DNAs with moderate affinity, HMGA2 binds with very high affinity to both DNAs in solutions containing 20 mM Na+ at 25 degrees C. The K(a) and binding enthalpy for poly(dA-dT)2 were determined to be, respectively, 1.9x10(14)M(-1) and -29.1(+/-0.5)kcal/mol. The binding reaction is enthalpy-driven with a favorable free energy of -19.5 kcal/mol and unfavorable entropy of -32.5 cal/mol K (-TDeltaS= +9. 7kcal/mol) at a 1M reference state. Interestingly, although HMGA2 binds to poly(dA)poly(dT) with a binding constant of 9.6x10(12) M(-1), the binding reaction is entropy-driven with an unfavorable enthalpy of +0.6 kcal/mol, a free energy of -17.7 kcal/mol and an entropy of +61.4 cal/mol K (-TDeltaS=-18.3 kcal/mol) at the 1 M state. The enthalpy-entropy compensation is similar to that of several minor groove-binding drugs such as netropesin, distamycin A and Hoechst33258 and may be a reflection of dehydration difference of different ligand-DNA complexes. The salt-dependence of the binding constant of HMGA2 with both DNAs showed that electrostatic interaction is a dominant force for the binding reactions. The temperature dependence of binding enthalpy for poly(dA-dT)2 indicates a large heat capacity of binding of -705(+/-113) cal/molK, consistent with an important role of solvent displacement in the linked folding/binding processes in this system.

Amino Acid Sequence↗
PubMedDate not supplied

Poly(amino acid)-b-poly(N,N-diethylacrylamide)-b-poly(amino acid) conjugates of well-defined structure.

Carboxy-terminated oligomers of N,N-diethylacrylamide (DEAAm) with low polydispersity were synthesized by group-transfer polymerization. The oligomers were conjugated with the N terminus of epsilon-N-CBZ-protected poly(lysine) and s-CBZ-protected poly(L-cysteine). The resulting conjugates precipitated in a narrow region of lower critical solution temperatures (LCST) around 29 degrees C. The LCST of poly(lysine)-polyDEAAm-poly(lysine) conjugates was pH-independent and independent of the lengths of poly(lysine) segments. Water-soluble nonstoichiometric conjugate-DNA complexes precipitated above the conjugate's LCST. Covalent complexes of human albumin and poly(cysteine)-polyDEAAm-poly(cysteine) conjugates showed temperature-sensitive behaviour in aqueous solutions.

Acrylamides↗
PubMed2005

Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo- fragment of DNA polymerase I.

The extension of the G-strand of long (700 bp) poly(dG)-poly(dC) by the Klenow exo(-) fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5' ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)-poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)-poly(dG)-poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DNA.

Circular Dichroism↗
PubMed1981

The mechanism of preferential synthesis of poly[r(purine)] in the transcription of poly[d(purine)] . poly[d(pyrimidine)] by T. thermophilus RNA polymerase.

The mechanism of preferential transcription on poly[d(purine)] . poly[d(pyrimidine)] was investigated using RNA polymerase of T. thermophilus HB8. Though the machinery for initiation is lacking, the core enzyme has the latent ability to synthesize poly[r(pyrimidine)] as well as poly[r(purine)]. The holoenzyme can synthesize poly[r(purine)] in the usual manner. Poly[r(pyrimidine)] synthesis by the holoenzyme is, however, forbidden. These results suggest that the sigma factor plays a crucial role in this preferential transcription, and that this preferential transcription may be useful as a model for the sense strand recognition. Various results led us to the hypothesis that the high affinity site for the poly[d(pyrimidine)] strands on the enzyme plays a very important role.

Adenosine Triphosphate↗
PubMed1976

Protonated polynucleotide structures, 20. Interaction between poly(dG)-poly(dC) and poly(rC).1.

A study of the interaction between poly(dG)-poly(dC) and poly(rC) demonstrates that, at neutral pH and high ionic strength, there is replacement of the dC strand by poly(rC). At acid pH, formation of a triple-stranded complex which equally may involve the replacement phenomenon is observed. There is no evidence for interaction at neutral pH between poly(dG)-poly(dC) and oligo(rC), while a three-stranded complex is formed at acid pH. These data are consistent with the studies of comparative stabilities of double stranded deoxy or ribo polymers and deoxy-ribo hybrids.

Circular Dichroism↗
PubMed1977

[Study of the antiviral activity of a poly I : poly-C complex with poly-L-lysine in monkeys].

Antiviral activity of poly-I-poly-C complex with poly-L-lysine was studied on macaco rhesus. The complex bifilamentous polyribonucleotide induced active production of serum interferon and provided pronounced protection of the monkeys infected intracutaneously with the variolovaccine virus (10 LD50 for the monkeys in intracutaneous infection). The effectiveness of the protective effect depended on the scheme and route of the drug administration. The highest prophylactic and therapeutic effect was provided by local administration of the complex in a dose of I mg per I kg of the body weight, the incubation period being increased 2--3 times and the period of the skin affections being decreased approximately 2 times. The results of the studies on the effect of poly-I-poly-C complex with poly-L-lysine were evident of definite prophylactic activity of the drug against experimental vernal encephalitis in the monkeys. The animals not treated with the inductor died on the 16th or 17th day after infection because of the paralysis of the trunc and extremities muscles. The clinical evidences of the disease in the animals treated with the drug were not uniform: from complete health to death.

Animals↗
PubMedDate not supplied

[Effect of a poly I-poly C complex with poly-L-lysine on experimental tick-borne encephalitis].

The influence of the poly(I)-poly(C) complex with poly-l-lysine on the development and course of experimental tick-borne encephalitis was studied in Macaca rhesus monkeys. Prophylactic administration of the substance under study, although not preventing the disease, modified its course and facilitated recovery of the animals. Poly(I)-poly(C) and its complex with poly-l-lysine were shown to have no effect on production of infectious virus or its antigen demonstrable by the immunofluorescence procedure in HEp-2 cells chronically infected with tick-borne encephalitis virus.

Animals↗
PubMed2002

Modification of capillary electrophoresis capillaries by poly(hydroxyethyl methacrylate), poly(diethylene glycol monomethacrylate) and poly(triethylene glycol monomethacrylate).

Modification of capillary electrophoresis (CE) capillaries by poly(hydroxyethyl methacrylate) (poly(HEMA), poly(diethylene glycol monomethacrylate) (poly(DEGMA) and poly(triethylene glycol monomethacrylate) (poly(TEGMA), was studied. Methods based on physical adsorption of the modifier and on its chemical binding were compared on the basis of the electroosmotic flow (EOF) reproducibility, the EOF dependence on the pH, the symmetry of the peak of positively charged tyramine, the stability of the coating and the separation of standard and milk proteins in the modified capillaries. Reproducible coatings were obtained by chemical binding of the polymers to the capillary walls and by coating with a solution of a polymer, as also demonstrated by the atomic force microscopy.

Adsorption↗
PubMed1980

Poly (d trp-L Leu), poly (D Phe-L Leu) and poly (D Val-L Val-D Val-L Ala) as model polymers for the elucidation of the gramicidin a conformation.

From infrared observations it is concluded that the conformation of poly (D Trp-L leu), poly (D Leu-L Trp), poly (D Phe-L leu) and poly (D val-L Val-D Val-L Ala) wich are model polymers of Gramicidin A is the same as one species of the antibiotic. Diffraction investigations indicate that poly-(D Phe-L Leu) and poly (D Val-L Val-D Val-L Ala) have a helical conformation which is most probably the pi DL 8 helix.

Gramicidin↗
PubMed2005

Solvent relaxation study of pH-dependent hydration of poly(oxyethylene) shells in polystyrene-block-poly(2-vinylpyridine)-block-poly(oxyethylene) micelles in aqueous solutions.

The hydration of the poly(oxyethylene) shell in polystyrene-block-poly(2-vinylpyridine)-block-poly(oxyethylene) micelles was investigated by monitoring the solvent relaxation response of a solvent-sensitive fluorophore (patman). It has been found that the relaxation occurs on the nanosecond time scale. Results for triblock copolymer micelles have been compared with those obtained for polystyrene-block-poly(2-vinylpyridine) micelles in order to evaluate the effect of the outer polyoxyethylene layer. Considerable pH-dependent changes in the hydration of poly(oxyethylene) units at the poly(2-vinylpyridine)/polyoxyethylene interface were observed. Additionally, the paper shows that the solvent relaxation technique is a suitable tool for studying polymeric nanoparticles and that the measurement of time-dependent half-width of the emission spectrum allows for estimation of the extent of relaxation process observed by a given experimental setup.

Journal Article↗
PubMed2006

Electrochemically modulated permeability of poly(aniline) and composite poly(aniline)-poly(styrenesulfonate) membranes.

The influence of oxidation state on the permeability of several probe molecules through conducting polymer membranes comprising composites of poly(aniline) and poly(styrenesulfonate) was examined in aqueous solution. Pure poly(aniline) membranes displayed a characteristic increase in permeability between reduced and half-oxidized states for neutrally charged phenol and negatively charged 4-hydroxybenzenesulfonate. In contrast, positively charged pyridine experienced decreased permeability through the membrane when poly(aniline) was switched from the reduced to the half-oxidized state. This behavior can be explained by a combination of oxidation-induced film swelling and the anion-exchange character of the positively charged membrane. The membrane composition was modified to include a fixed negative charge by the addition of poly(styrenesulfonate) during synthesis. The incorporation of this negatively charged component introduced cation-exchange character to the film and substantially reduced membrane permeability to 4-hydroxybenzenesulfonate in both oxidation states. In addition, increasing the fraction of poly(styrenesulfonate) in the membrane served to decrease film permeability for all species because of a densification of the membrane. This work demonstrates how both film composition and oxidation state can be used to tune the permeability of conducting polymer membranes.

Journal Article↗
PubMed2006

Synthesis and characterization of poly(ethylene glycol)-poly(D,L-lactide-co-glycolide) poly(ethylene glycol) tri-block co-polymers modified with collagen: a model surface suitable for cell interaction.

This study focused on the synthesis and characterization of poly(ethylene glycol)-poly(D,L-lactide-co-glycolide)-poly(ethylene glycol) tri-block co-polymer (PEG-PDLLG-PEG), and its modification with type-I collagen. To this aim, a PEG-PDLLG-PEG tri-block co-polymer was synthesized in two steps by reacting poly(ethylene glycol)bis(carboxymethyl)ether with thionyl chloride to obtain an acyl-halide-terminated poly(ethylene glycol) and subsequently coupling this compound to hydroxyl-terminated poly(D,L-lactide-co-glycolide) (PDLLG). The new carboxyl endgroups of PEG-PDLLG-PEG were subsequently reacted with N-hydroxysuccinimide (NHS) in the presence of the hetero-bifunctional cross-linking agent dicyclohexylcarbodiimide (DCC) in order to activate the co-polymer for coupling with collagen. PEG-PDLLG-PEG and its activated form PEG-PDLLG-NHS were characterized by Fourier transform infrared (FT-IR) and 1H-NMR spectroscopy. Molecular weights of the polymeric products were determined by SEC. Type-I collagen in phosphate buffer was reacted with PEG-PDLLG-NHS. The resultant product, PEG-PDLLG-Col, was characterized by FT-IR. This biopolymer was used for preparation of a suitable surface for cell growth experiment. To measure the degree of cell proliferation, the films prepared with PDLLG, PEG-PDLLG-NHS and PEG-PDLLG-Col were seeded with L929 mouse fibroblasts. Cell growth was followed by SEM photography and quantitated by the neutral red uptake assay. It was shown that the attachment of collagen significantly increased the number of cells on the co-polymers.

Animals↗
PubMed1994

Non-covalent interaction between poly(ADP-ribose) and cellular proteins: an application of a poly(ADP-ribose)-western blotting method to detect poly(ADP-ribose) binding on protein-blotted filter.

We describe a sensitive method for the detection of interactions between poly(ADP-ribose) and proteins. Proteins were blotted onto nitrocellulose filters and incubated with 32P-labeled poly(ADP-ribose). Purified core histones and poly(ADP-ribose) polymerase were found to bind poly(ADP-ribose) polymer. Blots of HeLa cell protein extracts revealed a 48 kDa protein and several others of smaller than 35 kDa likewise bound the polymers even at high salt concentrations. Those proteins, along with a 69 kDa protein, also showed resistance to competitor DNA. Polymer binding of aforesaid HeLa extract proteins was restricted to polymers above 20 residues in length. Thus poly(ADP-ribose)-protein affinities were polymer-length dependent.

Base Sequence↗
PubMed1982

Synthesis and physicochemical properties of two analogs of poly(dA): poly(2-aminopurine-9-beta-D-deoxyribonucleotide) and poly 2-amino-deoxyadenylic acid.

Polymerization of chemically synthesized dn2h6ATP and dn2ATP by deoxynucleotidyl transferase from calf thymus furnished poly(dn2h6A) and poly(dn2A) respectively. The synthetic polynucleotides were characterized by spectroscopic, ultracentrifugation and enzymatic methods. In polynucleotide-polynucleotide interaction, poly(dn2h6A) and poly(dn2A) behaved like analogs of poly(dnA).

Animals↗