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Conformational properties of 2',5'-linked 3'-deoxyribonucleotides have been compared with their natural isomer using CD spectroscopy. It is inferred from the salt induced titration curves that the 2',5'-linked-3'deoxyribonucleotides have rigid phosphodiester backbone.

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Escherichia coli-DNA-T protein is a key component of a multiprotein complex called the primosome which is involved in the initiation of DNA replication. The thermal and urea induced unfolding transition of this protein in the presence and absence of Mg2+ was studied using circular dichroism (CD) and fluorescence spectroscopy as probes. Quenching of the intrinsic fluorescence of DNA-T was observed in the thermal unfolding while formation of a hyperfluorescent form of the protein was found in the urea induced unfolding process. The CD studies showed a monophasic transition curve for thermal unfolding in the presence and absence of Mg2+. Biphasic curves indicative of the formation of intermediates was observed in the urea induced unfolding. The results suggest that the pathways of unfolding of thermal- and urea-induced transitions are different. MgCl2, which affects the conformation of the protein and stabilises the secondary structure, also affects the unfolding pattern.

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The binding of methylene blue (MB) with tRNA was studied using absorption, fluorescence and circular dichroic spectroscopy. In the spectral titration of MB with tRNA, hypochromism was observed in the absorption maximum of the dye in the visible region till P/D = 4 and thereafter the intensity increased with a red shift at P/D > 9, indicating electrostatic and intercalative binding at low and high P/D ratios, respectively. Analysis of absorption data, following Schwarz's procedure, showed that the electrostatic binding is cooperative in nature (cooperatively parameter q = 50) with a binding constant K = 7.77 x 10(3) M-1. A non-linear Scatchard plot was observed for the intercalative binding (at P/D > 4), probably due to a difference in the spectral characteristics of the dye intercalated between the base pairs and that between the bases in the single stranded domains. Quenching of fluorescence was observed for both the binding processes. In the circular dichroism spectra of tRNA-MB complexes at high P/D (approximately 30), nonconservative positive ICD bands were seen at 620 and 680 nm while at low P/D (approximately 2), two conservative negative CD bands at 300 and 660 nm and two bisignate bands with cross overs at 565 and 605 nm were observed. The short wavelength component of the bisignate band at 565 nm is negative while that of the 605-nm band is positive, indicating that the former arises from left handed and the latter from the right handed helical disposition of dye molecules along the tRNA backbone. The changes in the CD spectrum of tRNA on dye binding could be due to a conformational change of the nucleic acid or a negative CD being induced at that region.

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The binding of methylene blue (MB) to poly(rA) was studied using UV and CD spectroscopy at neutral and acidic pH, in which poly(rA) exists as a single strand and a duplex respectively. UV spectroscopic studies and analysis of equilibrium binding data show that salt increases the cooperativity parameter but reduces the binding between the cationic dye and the negatively charged phosphate groups. The binding constant for the single strand-MB complex decreased from 1.15 x 10(5) M-1 to 7.62 x 10(3) M-1 while the cooperativity parameter increased from 9 to 71, when salt concentration was increased from 1 mM to 200 mM. At neutral pH, changes in the induced circular dichroism of MB-poly(rA) complex with ionic strength show predominance of electrostatic binding to the phosphate group externally on the poly(rA) chain; a partial intercalation between the adenine bases is also indicated. A red shift in the visible absorption band and the ICD profile of the double stranded poly (rA)-MB complex suggest an electronically coupled intercalation mode for the dye binding at pH 4.2.

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The interaction of two anthraquinone dyes, bromaminic acid 1-amino-4-bromo anthraquinone-2-sulphonic acid (BA) and 1-amino-4-(4'-aminophenylamino)-anthraquinone-2,3'-disulphonic acid (ASSO), with poly-L-lysine (PLL), poly-L-ornithine (PLO) and poly-L-arginine (PLA) has been studied. The flexibility of the side chain (chain length) and the geometry of the charge centre (tetrahedral/planar) of the polypeptide were found to affect the interaction. Further, both dyes induce ordered conformation (alpha or beta) for the three polypeptides, but the final conformation was found to depend on the polypeptide as well as the number of anionic sites on the ligand. While the bidentate ASSO-polypeptide complexes acquire beta-conformation, the monodentate BA distinguished between the three substrates and induces beta-conformation only for PLO.

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Spermine induced B-Z transition of poly(dG-dC) in aqueous medium at and above physiological temperature, at cellular concentration levels in low ionic strength medium. The amine to phosphate ratio, A/P, at the midpoint of the transition decreases with increase in temperature. The enthalpy change was 45 +/- 8 kcal per mol of cooperative unit; the transition induced by spermine is highly cooperative with a cooperative unit length of 700 +/- 20 at 50 degrees C.

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The binding of antitumour drug mitoxantrone [1,4-dihydroxy-5, 8-bis [2-(2-hydroxy ethyl)amino)ethyl)amino)-9, 10-anthracenedione] to the synthetic polynucleotide poly[d(G-C)] was studied by circular dichroic titrations. The interaction induced intense chiroptical properties in the visible (688 nm) as well as the ultraviolet (260, 320 nm) region in an otherwise optically inactive drug. The interaction occurs in two stages, one below a drug/nucleotide ratio of 0.11 and other above this value. The second mode of interaction causes an almost cooperative enhancement of the visible induced circular dichroism (ICD).

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Computer modelling with an energy minimization procedure is used here to obtain stereochemical and energetic details for complexes of the dye Hoechst 33258 with different oligonucleotide sequences. An optimised model of the dye with d(A)5 X d(T)5 is in conformity with previous proposed models. It has bifurcated hydrogen bonds between N2H and N4H of benzimidazole rings with N3 of adenine and O2 of thymine. Relative binding energies with different oligonucleotides show preference for AT containing sequences, with an intermediate affinity between that for netropsin and distamycin-2. Reduced binding is observed at high ionic concentration. The benzimidazole rings are twisted with respect to the phenol ring in the optimal model. This gives desired curvature to the molecule which is stabilised by intermolecular forces.

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The saline extract (SE) of Mycobacterium tuberculosis H37Ra yielded four major fractions on Sephadex G-100, with average molecular weights of 48,000 (fraction I, F I) 32,000 (fraction II, F II), 15,000 (fraction III, F III) and 5,000 (fraction IV, F IV). FI and FII gave single bands on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, showed complete immunological cross-reactivity with each other and were more potent in reacting with antibodies in patients' (tuberculosis) sera than sonicate, SE, purified protein derivative, F III and F IV when tested in a competition enzyme-linked immunosorbent assay.

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Solution conformation of poly(L-lysyl-L-glutamic acid) (PLGU) and poly(L-lysyl-L-glutamine) (PLGN) was studied in water as a function of pH, added salt, detergents, methanol and trifluoroethanol (TFE). Both the polypeptides exhibit no ordered conformation in the pH range 1.5-12.5; salts and detergents did not have any marked effect. Replacement of side chain carboxyl by an amide group did not help in inducing PLGN to adopt a helical conformation even at pH as high as 12.0, unlike poly(L-lysine). The helicogenic solvents, methanol and TFE, induce formation of weak helices in PLGU as well as in PLGN. It is not unlikely that H-bonding between the side chains leads to stabilizing an unordered conformations.

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Tryptophan 108 of hen egg white lysozyme was selectively excited at 305 nm and fluorescence spectra were recorded as a function of pH (2-9) and concentration of urea (0-8 M). Urea at low concentrations (1-4 M) quenches markedly the Trp 108 fluorescence around pH 7; the gamma max, however, remained unaltered. The fluorescence quenching by urea is most likely due to local conformational changes around Trp 108 in active site region of the enzyme. Substantial unfolding of the enzyme, however, was brought about by 4 M urea below pH 3, and by 7 M urea at pH 10.3, as indicated by a marked red shift in the gamma max of the fluorescence emission.

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