Photochemical addition of amino acids and peptides to homopolyribonucleotides of the major DNA bases

Abstract— The photochemical quantum yields for addition of glycine and the L-amino acids commonly occurring in proteins (excluding proline) to polyadenylic acid, polycytidylic acid, polyguanylic acid and polyribothymidylic acid have been determined in deoxygenated phosphate buffer at Λ 254 nm and pH 7, using a fluorescamine assay technique. Polyadenylic acid was reactive with eleven of the twenty amino acids tested, with phenylalanine, tyrosine, glutamine, lysine and asparagine having the highest quantum yields. Polyguanylic acid reacted with sixteen amino acids; phenylalanine, arginine, cysteine, tyrosine, and lysine displayed the largest quantum yields. Polycytidylic acid showed reactivity with fifteen amino acids with lysine, phenylalanine, cysteine, tyrosine and arginine having the greatest quantum yields. Polyribothymidylic acid, reactive with fifteen of nineteen amino acids surveyed, showed the highest quantum yields for cysteine, phenylalanine, tyrosine, lysine and asparagine. None of the polynucleotides were reactive with aspartic acid or glutamic acid.
The quantum yields for photoaddition of eighteen dipeptides of the form glycyl X (X being one of the amino acids commonly occurring in proteins, including proline), and of L-alanyl-L-tryptophan, L-seryl-L-seryl-L-serine, L-threonyl-L-threonyl-L-threonine, L-cystine- bis -glycine, and N_α-acetyllysine to polyadenylic acid, polycytidylic acid and polyguanylic acid were measured. All of these were found to add photochemically to each of these polymers. Polyribothymidylic acid, tested with eleven of these peptides and with N_α-acetyllysine, was found to be reactive with all.     

Indirect spectrofluorimetric determination of arsenic at nanotrace levels in alloys, underground water, industrial waters and sewage sludge

An inexpensive and virtually specific nonextractive Spectrofluorimetric method for the determination of As(III) (1 ng/ml-1 g/ml) in 0.18–1.08N H₂SO₄ has been developed. A known excess of Cr(VI) is allowed to quantitatively oxidize As(III) in the essential presence of a mixture of iodide and chloride as catalyst, followed by the addition of excess 2-(-pyridyl) thioquinaldinamide and measurement of the fluorescence intensity (_em(max) = 488 nm _ex(max) = 360 nm) caused by Cr(VI) remaining after As(III) oxidation. The measurement is repeated without As(III) addition and the decrease in fluorescence intensity gives the As(III) concentration with the help of a calibration graph. The method is very precise and accurate (S. D. = ± 0.474, R. S. D. = 0.95%, for the analysis of 50ng/ml As(III), 11 replicates). The detection limit is 0.3ng/ml As(III). Large excesses of over fifty cations, anions and some complexing agents do not interfere. The method has been successfully applied for arsenic determination in various complex matrices: environmental waters, sewage sludges and several certified reference materials (alloys). This method has also been extended to determine As(V), after its reduction to As(III), in water samples, waste discharge water and sewage sludges.Presented at International Conference Arsenic in Ground Water: Cause, Effect and Remedy, Calcutta, India, February, 1995     

Formation of a DNA layer on Langmuir-Blodgett films and its enzymatic digestion

Here, we report a system we have developed where long double-stranded DNAs (dsDNAs) are immobilized on a monolayer of Zn-arachidate. We have applied the Langmuir-Blodgett technique to form the monolayer of Zn-arachidate where Zn(II) is bound to arachidic acid through charge neutralization. Because tetrahedral Zn(II) participates in DNA recognition through coordination, we have been able to layer DNA over the Zn-arachidate monolayer. The DNA layer shows a typical compression and expansion cycle in a concentration-dependent fashion. Interestingly, the DNA monolayer is available for enzymatic degradation by DNaseI. The detection of DNA and its accessibility towards biological reaction is demonstrated by imaging through fluorescence microscopy. The conformation of the DNA, immobilized on the monolayer, was studied with the help of atomic force microscopy (AFM). We observed that the dsDNAs were aligned in a stretched manner on the surface. To investigate further, we also demonstrate here that the small single-stranded DNA (ssDNA) immobilized on the air-water interface can act as a target molecule for the complementary ssDNA present in the subphase. The study of DNA hybridization done with the help of fluorescence spectroscopy clearly supports the AFM characterization.     

Two-Photon Fluorescence Tracking of Colloidal Clusters

In situ dynamics of colloidal cluster formation from nanoparticles is yet to be addressed. Using two-photon fluorescence (TPF) that has been amply used for single particle tracking, we demonstrate in situ measurement of effective three-dimensional optical trap stiffness of nanoparticles and their aggregates without using any position sensitive detector. Optical trap stiffness is an essential measure of the strength of an optical trap. TPF is a zero-background detection scheme and has excellent signal-to-noise-ratio, which can be easily extended to study the formation of colloidal cluster of nanospheres in the optical trapping regime. TPF tracking can successfully distinguish colloidal cluster from its monomer.     

Discrete Molecular Copper(II) Complex for Efficient Piezoelectric Energy Harvesting Above Room-Temperature

Developing robust, wearable, and biocompatible energy harvesting devices with bulk oxides (ceramics and perovskites) is extremely hard to achieve due to their zero mechanical flexibility, heavy metal toxicity, and tunability of properties. Alternatively, discrete inorganic complexes can be an excellent choice to overcome the above-stated issues, thanks to appropriate molecular engineering. Herein, we report an above-room-temperature ferroelectric discrete molecular complex [Cu(L-phe)(bpy)(H₂O)]PF₆⋅H₂O ( 1 ) which is suitable for piezoelectric energy harvesting due to its large values of piezoelectric co-efficient (d₃₃=10 pm V⁻¹) and spontaneous polarization (P_s=1.3 μC cm⁻²). Among the devices prepared with the composite films of polyvinyl alcohol (PVA) and various weight % composition of 1 , the 10 Wt % composite shows the highest output voltage of 8 V, a power density of 0.85 μW cm⁻², and output current of 5 μA, which is highest for any discrete inorganic complex reported to date.     

Cyanometallate incorporated supramolecular networks based on a nitroalkyl-substituted CuN4 precursor: Synthesis, crystal structure, thermal and electrochemical studies

Two new copper(II) complexes, viz. [Cu(nelin)(H₂O)₂]₂[Fe(CN)₆] · 6H₂O (2) and [{Cu(nelin)}₂Ni(CN)₄](ClO₄)₂ · 2H₂O (3), have been synthesized using [Cu(nelin)](ClO₄)₂ (1) (nelin = 1,9-diamino-5-methyl-5-nitro-3,7-diazanonane) as a nitroalkyl-substituted Cu^IIN₄ precursor, and their structures and supramolecular networks have been fully explored using the single crystal X-ray diffraction technique. The H-bonded 1D chains of 2 run along the a-axis, being generated from supramolecular synthons using cations and anions, and are further propagated into a 3D array to form irregular honeycomb-like channels which are divided into two halves, with each half accomodating a helical water chain running in opposite directions to each other. In complex 3, the trinuclear units are arranged in successive rows in a herringbone fashion and bifurcated hydrogen bonding through the uncoordinated terminals of the [Ni(CN)₄]²⁻ units give rise to a supramolecular (4,4) network. A comparison of the PXRD pattern of complex 2 and its dehydrated form indicate marked changes in the diffraction pattern with the development of a quasi glassy nature in the dehydrated form. The electrochemical properties of 1, 2 and 3 have been investigated in comparative ways using the cyclic voltammetric technique in aqueous and MeCN solutions with Ag/AgCl as a reference electrode. Electrochemical reduction generates the one-electron reduced nitro-radical anion. In water–alcohol glass at 77 K complex 2 exhibits a typical four-line hyperfine EPR spectra with g_|| = 2.11, g = 2.02, A_|| = 150 Oe and A = 5 Oe at ν = 9.45 MHz.     

Polymorphism in [Co(SCN)4(ppz-H)2] (ppz,piperazine)

A one-pot reaction of [Co(NO₃)₂ · 6H₂O and piperazine] with NH₄SCN/NaSCN in water–methanol (1:1) solvent leads to two polymorphs of [Co(SCN)₄(ppz-H)₂] (ppz, piperazine) (I and II). X-ray crystal structure reveals both have same space group but the differences in the alignment of pendant SCN⁻ leads to two polymorphs. In I, trifurcated N–H?S hydrogen bonding plays a prominent role in crystal packing leading to S?S interactions between SCN fragments but in II, no such trifurcation arises and thereby the crystal packing occurs through hydrogen bonding interactions only leading to a distinctly different network topology. TG/DSC and FT-IR study reveal they are enantiotropically related.     

Instabilities and pattern miniaturization in confined and free elastic-viscous bilayers

We present an analysis of the instabilities engendered by van der Waals forces in bilayer systems composed of a soft elastic film (<10 microm) and a thin (<100 nm) viscous liquid film. We consider two configurations of such systems: (a) Confined bilayers, where the bilayer is sandwiched between two rigid substrates, and (b) free bilayers, where the viscous film is sandwiched between a rigid substrate and the elastic film. Linear stability analysis shows that the time and length scales of the instabilities can be tuned over a very wide range by changing the film thickness and the material properties such as shear modulus, surface tension, and viscosity. In particular, very short wavelengths comparable to the film thickness can be obtained in bilayers, which is in contrast to the instability wavelengths in single viscous and elastic films. It is also shown that the instabilities at the interfaces of the free bilayers are initiated via an in-phase "bending" mode rather than out-of-phase "squeezing" mode. The amplitudes of deformations at both the elastic-air and elastic-viscous interfaces become more similar as the elastic film thickness decreases and its modulus increases. These findings may have potential applications in the self-organized patterning of soft materials.     

Immobilized DNA switches as electronic sensors for picomolar detection of plasma proteins

The sensing principle of a new class of DNA conformational switches (deoxyribosensors) is based on the incorporation of an aptamer as the receptor, whose altered conformation upon analyte binding switches on the conductivity of an adjacent helical conduction path, leading to an increase in the measured electrical signal through the sensor. We report herein the rational design and biochemical testing of candidate deoxyribosensors for the detection and quantitation of a plasma protein, thrombin, followed by surface immobilization of the optimized sensor and its electrochemical testing in both a near-physiological buffer solution and in diluted blood serum. The very high detection sensitivity (in the picomolar range) and specificity, as well as the adaptability of deoxyribosensors for the detection of diverse molecular analytes both small and macromolecular, make this novel sensing methodology an extremely promising one. Such synthetic and robust DNA-based electronic sensors should find broad application in the rapid, miniaturized, and automated on-chip detection of many biomedically relevant substances (such as metabolites, toxins, and disease and tumor markers) as well as of environmental contaminants.     

Degradation of Methyl Parathion,a common pesticide and fluorescence quenching of Rhodamine B,a carcinogen using β-d glucan stabilized gold nanoparticles

Natural carbohydrate polymer β-d-glucan extracted from Tricholoma crassum (Berk.) Sacc. predominantly linked by β-glycosidic bonds have been used to synthesize gold nanoparticles (Au NPs). As glucan is water soluble, the Au NPs are prepared in water medium, a green solvent. The morphology and characterization of the synthesized Au NPs have been confirmed by various techniques, like TEM, EDX, XRD, UV–Vis and FT-IR spectroscopic studies. The obtained Au NPs exhibits chemosensing property against Methyl Parathion, a group of highly toxic organophosphorous pesticide, extensively used as an agricultural chemical. Degradation of parathion using Au NPs lead to water-soluble products thereby reducing the toxicity of Methyl Parathion by disrupting the thiophosphate-ester linkage. The synthesized Au NPs also act as a good fluorescence quencher of Rhodamine B, a common fluorophore and carcinogenic compound, obeying Stern-Volmer equations. The β-d-glucan capped Au NPs are safe having possible medicinal usage.