Photo-induced double-strand DNA and site-specific protein cleavage activity of L-histidine (mu-oxo)diiron(III) complexes of heterocyclic bases

Three oxo-bridged diiron(III) complexes of L-histidine and heterocyclic bases [Fe-2(mu-O)(L-his)(2)(B)(2)](ClO4)(2) (1-3), where B is 2,2'-bipyridine (bpy),1,10-phenanthroline (phen), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), were prepared and characterized. The bpy complex 1 was structurally characterized by X-ray crystallography. The molecular structure showed a {Fe-2(mu-O)} core in which iron(III) in a FeN4O2 coordination is bound to tridentate monoanionic L-histidine and bidentate bpy ligands. The Fe center dot center dot center dot Fe distance is similar to 3.5 angstrom. The Fe-O-Fe unit is essentially linear, giving a bond angle of similar to 172 degrees. The complexes showed irreversible cyclic voltammetric cathodic response near -0.1 V vs. SCE in H2O-0.1 M KCl. The binuclear units displayed antiferromagnetic interaction between two high-spin (S = 5/2) iron(III) centers giving a -J value of -110 cm(-1). The complexes showed good DNA binding propensity giving a binding constant value of similar to 10(5) M-1. Isothermal titration calorimetric data indicated single binding mode to the DNA. The binding was found to be driven by negative free energy change and enthalpy. The dpq complex 3 showed oxidative double-strand DNA cleavage on exposure to UV-A and visible light. The phen complex 2 displayed single-strand photocleavage of DNA. The DNA double-strand breaks were rationalized from theoretical molecular docking calculations. Mechanistic investigations showed formation of hydroxyl radicals as the reactive species through photodecarboxylation of the L-histidine ligand. The complexes exhibited good binding propensity to bovine serum albumin (BSA) protein in Tris-HCl/NaCl buffer medium. The dpq complex 3 showed UV-A light-induced site-specific oxidative BSA cleavage forming fragments of similar to 45 kDa and similar to 20 kDa molecular weights via SOH pathway.

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.

DNA structural variability as a factor in gene expression and evolution

Redundant DNA can buffer sequence dependent structural deviations from an ideal double helix. Buffering serves a mechanistic function by reducing extraneous conformational effects which could interfere with readout or which would impose energetic constraints on evolution. It also serves an evolutionary function by allowing for gradual variations in conformation-dependent regulation of gene expression. Such gradualism is critical for the rate of evolution. The buffer structure concept provides a new interpretation for repetitive DNA and for exons and introns.

Application of various viscosity theories to the viscosity data of methyl methacrylate-acrylonitrile random copolymersstar

Values of Ko, Flory constant related to unperturbed dimensions, are evaluated for methyl methacrylate-acrylonitrile random copolymers using Flory-Fox, Kurata-Stockmayer and Inagaki-Ptitsyn methods and compared with the Ko values obtained by Stockmayer-Fixman method. Ko values are seen to be less in solvents which have large a (Mark-Houwink exponent) values. A correlation between Ko and a is developed to arrive at a more reliable estimate of Ko for this copolymer system.

A sensitive immunochemical method for detecting 5mC in DNA fragments

Abstract is not available.

Non-linear resonance in strings under narrow band random excitation, part I: Planar response and stability

Non-linear planar response of a string to planar narrow band random excitation is investigated in this paper. A response equation for the mean square deflection σ2 is obtained under a single mode approximation by using the equivalent linearization technique. It is shown that the response is triple valued, as in the case of harmonic excitation, if the centre frequency of excitation Ω lies in a certain specified range. The triple valued response occurs only if the excitation bandwidth β is smaller than a critical value βcrit which is a monotonically increasing function of the intensity of excitation. An approximate method of investigating the almost sure asymptotic stability of the solution is presented and regions of instability in the Ω-σ2 plane have been charted. It is shown that planar response can become unstable either due to an unbounded growth of the in-plane component of motion or due to a spontaneous appearance of an out-of-plane component.

Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

Behaviour of methylmethacrylate-acrylonitrile random copolymers in dilute solution

Studies on the dilute solution properties of methylmethacrylate-acrylonitrile random copolymers of three different compositions, 0.236, 0.5 and 0.74 mole fraction (m.f.) of acrylonitrile (AN) designated as MAa, MAb and MAc, respectively, have been made in good solvents and theta solvents. MAa has been studied in benzene (Bz) and ethylacetate (EAc). MAb in acetonitrile (MeCN), dimethyl sulphoxide (DMSO) and a binary solvent mixture of Bz and dimentyl formamide (DMF) in the volume ratio 6.5:1 designated as BM1 and MAc in MeCN, DMSO and Bz + DMF in the volume ratio 1.667:1 designated as BM2. The Mark-Houwink exponent ‘a’ reveals that Bz is a theta solvent for MAa at 20°C. For MAb and MAc, BM1 and BM2, respectively have ‘a’ values of 0.5 at all three temperatures studied (30°, 40° and 50°C). It is not clear whether they represent theta states or preferential adsorption plays a role complicating the behaviour in solution. The values of A2 are very low in MeCN considering that it is a very good solvent for the copolymer, ‘a’ values for MAb and MAc being 0.75 and 0.7, respectively.

Nonstationary Random Critical Seismic Excitations

A method is presented to find nonstationary random seismic excitations with a constraint on mean square value such that the response variance of a given linear system is maximized. It is also possible to incorporate the dominant input frequency into the analysis. The excitation is taken to be the product of a deterministic enveloping function and a zero mean Gaussian stationary random process. The power spectral density function of this process is determined such that the response variance is maximized. Numerical results are presented for a single-degree system and an earth embankment modeled as shear beam.

Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation

pBR322 form V DNA is a highly torsionally strained molecule with a linking number of zero. We have used sequence- specific DNA methylases as probes for B-DNA in this molecule, exploiting the inability of methylases to methylate single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA. Some sequences in form V DNA were shown to be totally in the B-form, others were totally in an altered, unmethylatable conformation, while still other sites appeared to exist partly in altered and partly in normal B-conformation. Some potential Z-forming sequences (alternating pyrimidine/purine) of less than seven base-pairs were not in the Z conformation in form V DNA, whereas others did adopt an altered structure, indicating a modulating influence of flanking sequences. Furthermore, regions of imperfect alternating pyrimidine/purine structure were sometimes capable of adopting an altered structure. In addition, some regions of altered structure had no apparent Z-forming sequences, nor were they in polypurine stretches, which have also been proposed to form left-handed DNA. These non-B-DNA conformations may represent novel left-handed helical structures or sequences that become single stranded under torsional strain. Long regions of either altered (unmethylatable) DNA or B-DNA were not always observed. In fact, one region showed three transitions between B-like DNA and altered structure within 26 base-pairs.

A detailed study of Li-DNA fibres at various salt concentrations reveals a non-helical B-DNA and a possible similarity of solution and solid state structures

A thorough investigation of salt concentration dependence of lithium DNA fibres is made using X-ray diffraction. While for low salt the C-form pattern is obtained, crystalline B-type diffraction patterns result on increasing the salt concentration. The salt content in the gel (from which fibres are drawn) is estimated by equilibrium dialysis using the Donnan equilibrium principle. The salt range giving the best crystalline B pattern is determined. It is found that in this range meridional reflections occur on the fourth and sixth layer lines. In addition, the tenth layer meridian is absent at a particular salt concentration. These results strongly suggest the presence of non-helical features in the DNA molecule. Preliminary analysis of the diffraction patterns indicates a structural variability within the B-form itself. Further, the possibility of the structural parameters of DNA being similar in solid state and in solution is discussed.

Sex Determination - A Hypothesis Based On Noncoding Dna

Certain recent models of sex determination in mammals, Drosophila melanogaster, Caenorhabditis elegans, and snakes are examined in the light of the hypothesis that the relevant genetic regulatory mechanisms are similar and interrelated. The proposed key element in each of these instances is a noncoding DNA sequence, which serves as a high-affinity binding site for a repressor-like molecule regulating the activity of a major "sex-determining" gene. On this basis it is argued that, in several eukaryotes, (i) certain DNA sequences that are sex-determining are noncoding, in the sense that they are not the structural genes of a sex-determining protein; (ii) in some species these noncoding sequences are present in one sex and absent in the other, while in others their copy number or accessibility to regulatory molecules is significantly unequal between the two sexes; and (iii) this inequality determines whether the embryo develops into a male or a female.