Search results for "Nucleic Acid Denaturation"
showing 10 items of 22 documents
Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives
2018
Abstract Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-deriv…
Kinetic evidence for interaction of TMPyP4 with two different G-quadruplex conformations of human telomeric DNA
2018
Background: Stabilization of G-quadruplex helices by small ligands has attracted growing attention because they inhibit the activity of the enzyme telomerase, which is overexpressed in> 80% cancer cells. TMPyP4, one of the most studied G-quadruplex ligands, is used as a model to show that the ligands can exhibit different binding features with different conformations of a human telomeric specific sequence. Methods: UV–Vis, FRET melting Assay, Isothermal Titration Calorimetry, Time-resolved Fluorescence lifetime, T-Jump and Molecular Dynamics. Results: TMPyP4 yields two different complexes with two Tel22 telomeric conformations in the presence of Na+ or K+. T-Jump kinetic experiments show th…
Mutation screening for the prothrombin variant G20210A by melting point analysis with the Light Cycler system: atypical results, detection of the var…
2005
In the differential diagnosis of thrombophilic disorders genotyping of prothrombin and factor V are nowadays performed as a routine analysis. In the following we describe the unusual results of the mutation screening using melting point analysis for two patients and the consecutive detection of the mutation C20209T by sequencing the corresponding gene fragments. The molecular result is discussed with special respect to the medical history, ethnic background and clinical findings of both patients.
The interaction of native calf thymus DNA with FeIII-dipyrido[3,2-a:2’,3’-c]phenazine
2008
The mono and bis dipyrido[3,2-a:2',3'-c]phenazine (dppz) adducts of iron(III) chloride, i.e. [Fe(dppz)]Cl(3) and [Fe(dppz)(2)]Cl(3), have been synthesized and characterized. The interaction of the Fe(III)dppz hydrolyzed aquo complex with native calf thymus DNA has been monitored as a function of the metal complex-DNA molar ratio, by variable temperature UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results obtained in solution at various ionic strength values give support for a tight intercalative binding of the Fe(III)dppz cation with DNA. In particular, the appearance of induced CD bands, caused by the addition of Fe(III)dppz, indicate the exi…
The interaction of native DNA with iron(III)- N ,N'-ethylene-bis(salicylideneiminato)-chloride.
2004
Abstract The interaction between native calf thymus deoxyribonucleic acid (DNA) and Fe III - N , N ′ -ethylene-bis (salicylideneiminato)-chloride, Fe(Salen)Cl, was investigated in aqueous solutions by UV–visible (UV–vis) absorption, circular dichroism (CD), thermal denaturation and viscosity measurements. The results obtained from CD, UV–vis and viscosity measurements exclude DNA intercalation and can be interpreted in terms of an electrostatic binding between the Fe(Salen) + cation and the phosphate groups of DNA. The trend of the UV–vis absorption band of the Fe(Salen)Cl complex at different ratios [DNA phosphate ]/[Fe(Salen)Cl] and the large increase of the melting temperature of DNA in …
The interaction of native DNA with Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine
2007
The interaction of native calf thymus DNA with the Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine (ZnL(2+) and CuL(2+)), in 1 mM Tris-HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results support for an intercalative interaction of both ZnL(2+) and CuL(2+) with DNA, showing CuL(2+) an affinity of approximately 10 times higher than ZnL(2+). In particular, the values of the binding constant, determined by UV spectrophotometric titration, equal to 7.3x10(4) and 1.3x10(6)M(-1), for ZnL(2+) and CuL…
Role of Disorder on the Dynamics of a Nonlinear Model for DNA Thermal Denaturation
1992
The dynamics of thermal denaturation of DNA is a good example in which nonlinearity coexits with disorder. The amplitude of the motions is so high that bonds break and the base sequence is inhomogeneous since it contains the genetic code. Using a simple nonlinear model, we study the role of local inhomogeneities or of extended disorder on the dynamics of the localized excitations and on the denaturation rate by numerical simulations at constrained temperature. Approximate analytical results are obtained for the trapping of the breatherlike excitations by isolated defects and the statistical mechanics of the disordered molecule.
Characterization of Different Deoxyribonucleases in Human Lymphocytes
1975
Abstract Deoxyribonucleases, Disc Electrophoresis, Lymphocytes Four groups of deoxyribonuclease activities from human lymphocytes have been characterized by deoxyribonuclease assay in DNA-containing polyacrylamide gels following their separation by disc-electrophoresis. All activities hydrolyse DNA endonucleolytically. One neutral deoxyribo nuclease found in the cytoplasmic fraction prefers native or UV-irradiated DNA over denatured DNA as substrate and is a 5′-monoester former. Two groups of acid deoxyribonuclease activities are detectable in the nuclear fraction. Both are 3′-monoester formers. One is as well active with denatured DNA as with native DNA, the other one shows the same activ…
Base composition of DNA from glomalean fungi: high amounts of methylated cytosine.
1997
Glomales (Zygomycetes) are obligate fungal symbionts of roots of land plants and form arbuscular mycorrhiza. Sporal DNA of 10 isolates belonging to nine species was purified and the base composition was determined by RP-HPLC. Base composition fell in a narrow range between 30 and 35% G + C. A high amount of methylated cytosine (mC) accounting for 2-4% of the total nucleotides was found in all taxa. The DNA melting profile was defined for Scutellospora castanea. It corresponded to 32% G + C, and the shape of the denaturation curve suggested a heterogeneity in the GC content within the fungal genome. Knowledge of GC contents and variations between taxa are essential for evaluating nuclear DNA…
Inverted and mirror repeats in model nucleotide sequences.
2007
We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long range sequences.