Swarna Basu

Detection of Quadruplex DNA by Luminescence Enhancement of Lanthanide Ions and Energy Transfer from Lanthanide Chelates

Small amounts of quadruplex DNA have been detected using luminescence enhancement of aqueous lanthanide ions and energy transfer from lanthanide chelates. The 22mer human telomeric DNA, AGGG(TTAGGG)(3), was detected using europium ions at concentrations as low as 20 ppb DNA. Detection with terbium ions was not possible due to the inherent weak luminescence intensities of lanthanides. Two different terbium chelates were used to overcome this challenge. When quadruplex DNA was added to the chelates there was a change in the excited-state lifetime of the chelate with subsequent energy transfer to the DNA. Experiments showed an increase in the amount of energy transferred from the chelate to the human telomeric DNA and other quadruplex sequences increased as a function of DNA concentration.

Static and Dynamic Quenching of Tryptophan Fluorescence in Various Proteins by a Chromium (III) Complex

ABSTRACT The interaction of a chromium (III) complex, (R,R)-N,N′-Bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-diaminochromium (III), with human serum albumin, bovine serum albumin, lysozyme, and free tryptophan was studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants were calculated using Stern-Volmer kinetics. The complex bound more tightly to the serum albumins than to lysozyme or free tryptophan, but only one binding site was determined in all systems. The interaction was also determined to be thermodynamically favorable, and the binding constants were on the order of 103–106. The fluorescence quenching was static in nature with Forster distances in the 1.8–2.0 nm range.

Vibrational dynamics of 9-fluorenemethanol using infrared-ultraviolet double-resonance spectroscopy.

Vibrational spectroscopy of jet-cooled 9-fluorenemethanol and its clusters 9-fluorenemethanol-H2O, 9-fluorenemethanol-CH3OH, 9-fluorenemethanol-C2H5OH, and 9-fluorenemethanol-C3H7OH has been carried out using an IR-UV double-resonance method. The spectrum of the OH stretching vibration, v(OH), has been measured for the 9-fluorenemethanol monomer and for each of the clusters. Two conformers of 9-fluorenemethanol, symmetric (sym) and unsymmetric (unsym), have been identified using a combination of spectroscopy and quantum chemical calculations with B3LYP and HF methods using the 6-31G(d) basis set. Vibrational dynamics resulting from IR excitation has also been studied using the S0-S1 transition probed by a nanosecond-time-delayed UV laser. The data suggest that isomerization occurs as a result of the IR excitation, but the breadth of the probe spectra makes an unequivocal conclusion difficult. The effect of hydrogen bonding on the v(OH) of 9-fluorenemethanol has also been studied in clusters with water, methanol, ethanol, and propanol by measuring the IR spectra. Cluster dissociation dynamics have also been studied following IR excitation. It is observed that upon excitation of the cluster of a particular conformation the monomer product is generally produced in both conformer forms. Energetic considerations indicate that isomerization occurs before dissociation.

3-Ethylindole electronic spectroscopy: S1 and cation torsional potential surfaces

The tryptophan derivative 3-ethylindole was studied in the first excited electronic state and the cation ground state using resonance enhanced multiphoton ionization (REMPI) and zero electron kinetic energy (ZEKE) spectroscopy. Weakly bound clusters of 3-ethylindole with argon (n=1–3) have also been studied. The monomer spectroscopy revealed that two conformations of the 3-ethylindole exist in the jet cooled sample. Density-functional theory (DFT) calculations have been used to calculate the ground- and ionic-state geometries and energies. The calculations reveal the two conformations to be a planar and a nonplanar orientation of the ethyl substituent relative to the indole plane. The ZEKE spectrum of the nonplanar form has an extensive progression in the vibration associated with ethyl torsion and indicates a significant geometry change in the ethyl chain torsion upon ionization. The ethyl chain torsional potential is mapped out using DFT calculations, and the ion surface is adjusted such that calculated...

Competition between solvent quenching and indole quenching of 9-fluorenone: A spectroscopic and computational study

The interaction between 9-fluorenone, various indoles and solvents has been studied using steady-state fluorescence spectroscopy and quantum chemical calculations. It was determined that polar protic solvents such as methanol and ethanol significantly quenched the fluorescence of 9-fluorenone but various indoles reversed the solvent quenching. The effect of various solvents on the 9-fluorenone carbonyl vibration was investigated using infrared spectroscopy. Ab initio calculations using Gaussian03 were also carried out in order to determine the minimum energy conformations of these systems along with binding energies.

Detection of Quadruplex DNA by Gold Nanoparticles

Gold nanoparticles have been used as a probe to detect low (<10 ppb) concentrations of quadruplex DNA. These nanoparticles display a tendency to form aggregates in the presence of certain quadruplex forms, as observed via enhanced plasmon resonance light scattering (PRLS) signals. These nanoparticles showed differing degrees of interactions with different types of quadruplex and mixed sequences but no interaction with duplex DNA. Enhancement of PRLS signals greater than 50% was observed at nanomolar DNA concentration, and a lower limit of detection of 2.1 nM was established for three different quadruplex DNA sequences, including the thrombin-inhibiting single-stranded 15 mer aptamer DNA, d(GGTTGGTGTGGTTGG), and the double-stranded 12 mer DNA, d(G4T4G4). Two different sample preparation protocols were used for the PRLS experiments, and they yielded similar results.

Design and implementation of a cost-effective microscope for fabrication and imaging

The use of lasers and optical systems for advanced research and demonstrative purposes has traditionally been cost-prohibitive for many researchers. In this note, we present the design and optimization of a low-cost microscopy setup capable of imaging, fabrication or photopolymerization via multiphoton excitation of a photoactivator and the study of processes such as diffusion using fluorescence recovery after photobleaching (FRAP). The setup features a continuous wave (CW) Ar-ion laser, a pulsed Nd3+:YAG laser, an inverted microscope with a CCD camera and appropriate optics. The setup is cost-effective and puts a once-expensive setup within reach of more researchers interested in micron- and sub-micron-scale processes.

Conformational studies of the neutral and cation of several substituted fluorenes

Abstract The S 1 excited state and cation ground state of various fluorene derivatives have been studied experimentally using resonance enhanced multiphoton ionization and zero electron kinetic energy photoelectron spectroscopy. The compounds studied are 2-propylfluorene, 9-fluoreneacetic acid and 2-propionylfluorene. Density functional quantum chemical calculations using the gaussian 98 program have been used to calculate the ground state and cation energies of each conformer as well as the barrier to interconversion via a bond rotation. These calculations, coupled with the experimental results, have led to the identification and assignment of the various conformations of these molecules.

Interaction of Small Zinc Complexes with Globular Proteins and Free Tryptophan

A series of eight water soluble anionic, cationic, and neutral zinc(II) complexes were synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme, and free tryptophan (Trp) was investigated using steady-state fluorescence spectroscopy. Static and dynamic fluorescence quenching analysis based on Stern-Volmer kinetics was conducted, and the decrease in fluorescence intensity of the Trp residue(s) can be ascribed predominantly to static quenching that occurs when the Zn complex binds to the protein and forms a nonfluorescent complex. The role played by the nature of the ligand, the metal, and complex charge in quenching Trp fluorescence was investigated. The binding association constants () ranged from 104 to 1010 M−1 and indicate that complexes with planar aromatic features have the strongest affinity for globular proteins and free Trp. Complexes with nonaromatic features failed to interact with these proteins at or in the vicinity of the Trp residues. These interactions were studied over a range of temperatures, and binding was found to weaken with the increase in temperature and was exothermic with a negative change in entropy. The thermodynamic parameters suggest that binding of Zn complexes to the proteins is a highly spontaneous and favorable process.