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Sandeep Verma

Publications and source records attributed to Sandeep Verma.

At least 19 recordsLinked to original sources
PubMed2007

meso-meso-Linked corrole dimers with modified cores: synthesis, characterization, and properties.

The synthesis and characterization of the first examples of core-modified corrole dimers linked through the meso positions are described. The dimers are obtained by a simple Ag(I)- or Fe(III)-catalyzed coupling reaction in near-quantitative yields. The corroles obtained are metalated with metal ions, such as Cu(II) and Ni(II). The electronic-absorption spectral studies reveal weak electronic interaction between the two subunits and the exciton coupling observed for the free-base corrole dimer (1717 cm(-1)) is lower than that for the corresponding protonated derivative (4081 cm(-1)). The solution-state structure derived from (1)H and two-dimensional NMR spectral studies reveals a noncoplanar arrangement of two corrole units. Geometry optimization at the B3LYP-631G level also confirms the noncoplanar arrangement of corroles with a dihedral angle of 64.8 degrees between two corrole planes. The electron paramagnetic resonance (EPR) and magnetic characterization studies on the paramagnetic copper-metalated dimer indicate that both copper ions behave as independent spins without any noticeable interaction. Results of fluorescence studies reveal a bathochromic shift of about 60 nm upon dimerization. The first hyperpolarizability (beta) measured by using the hyper Rayleigh scattering (HRS) method reveals doubling of the beta values on progressing from monomer to dimer, attributed to enhanced pi conjugation. The use of copper dimers in the photocleavage of DNA is also explored. It is shown that the bimetallic copper dimer selectively cleaves the nucleic acids without affecting the proteins, suggesting a possible application of the copper complex in the removal of nucleic acid contaminants from protein extracts through a simple photolytic pathway.

Catalysis↗
PubMed2006

Ordering in a glycine-rich peptide conjugate: microscopic, fluorescence, and metalation studies.

Glycine residues play an intriguing role in peptide/protein structure where they can act as tightly packing amino acids with flexible bond angles. For example, structural role of glycines is highlighted in natural silk fibers where different structural polymorphs have been reported. This study deals with a glycine-rich segment from the conserved octarepeat (PHGGGWGQ) in prion protein. We have synthesized a bis-conjugate 3, containing a truncated pentapeptide segment (GGGWG), to study its time-dependent solution phase aggregation by a combination of microscopic methods and fluorescence. This discontinuous peptide conjugate 3 exhibited interesting photophysical properties upon self-assembly allowing us to propose a possible model of peptide filament formation. Taking note of the fact that prion octarepeats bind copper, we also demonstrate the ability of this conjugate to bind copper and the growth and ultrastructure of metallized fibers formed upon incubation. Enforcing peptide fiber formation in metal binding motifs offers an entry into metal impregnated fibers for possible nanobiotechnological applications.

Amino Acid Sequence↗
PubMed2006

Phosphodiester modification by zinc metalated adenine polymer with carboxyl pendants.

This report describes a novel carboxyl pendant containing adenylated polymeric template, its metalation with Zn (II), and manifestation of catalytic activity for the hydrolysis of model phosphodiester, bis(p-nitrophenyl) phosphate (bNPP), and plasmid cleavage. Observation of a bell-shaped pH-K(obs) profile suggested influence of pH variation over hydrolysis rate. This metalated polymer also afforded facile relaxation of pBR322 supercoiled DNA, with an interesting reusability feature intricately associated with heterogeneous catalysis.

Adenine↗
PubMed2006

Interfacial electron transfer between the photoexcited porphyrin molecule and TiO2 nanoparticles: effect of catecholate binding.

Interfacial electron transfer (ET) dynamics of 5,10,15-trisphenyl-20-(3,4-dihydroxybenzene) porphyrin (TPP-cat) adsorbed on TiO2 nanoparticles has been studied by femtosecond transient absorption spectroscopy in the visible and near-IR region exciting at 400 and 800 nm. TPP-cat molecule forms a charge transfer (CT) complex with TiO2 nanoparticles through the catechol moiety with the formation of a five-membered ring. Optical absorption measurements have shown that the Q-band of TPP-cat interacts strongly with TiO2 due to chelation; however, the Soret band is affected very little. Optical absorption measurements indicate that the catechol moiety also interacts with TiO2 nanoparticles showing the characteristic band of pure catechol-TiO2 charge transfer (CT) in the visible region. Electron injection has been confirmed by monitoring the cation radical, instant bleach, and injected electron in the conduction band of TiO2 nanoparticles. Electron injection time has been measured to be < 100 fs and recombination kinetics has been best fitted with a multiexponential function, where the majority of the injected electrons come back to the parent cation radical with a time constant of approximately 800 fs for both excitation wavelengths. However, the reaction channel for the electron injection process has been found to be different for both wavelengths. Excitation at 800 nm, found to populate the CT state of the Q-band, and from the photoexcited CT state electron injection into the conduction band, takes place through diffusion. On the other hand, with excitation at 400 nm, a complicated reaction channel takes place. Excitation with 400 nm light excites both the CT band of Cat-TiO2 and also the Soret band of TPP-cat. We have discussed the reaction path in the TPP-cat/TiO2 system after exciting with both 400 and 800 nm laser light. We have also compared ET dynamics by exciting at both wavelengths.

Journal Article↗
PubMed2005

Biomimetic synthesis and ultrastructural characterization of a zerovalent gold-hydroxyapatite composite.

This manuscript describes one-pot, in situ synthesis of organoapatite-gold nanoparticle composite and its characterization by XRD, energy dispersive X-ray analysis, atomic force, and scanning electron microscopy. This methodology offers a different approach into the synthesis of zerovalent metal-mineral-phase nanocomposites having potential application as osteointegrative ceramics.

Biomimetics↗
PubMed2005

Copper-metalated peptide palindrome derived from prion octarepeat: synthesis, aggregation, and oxidative transformations.

We report construction of a bis-pentapeptide conjugate 4 containing truncated pentapeptide sequence from prion octarepeats. Its copper-laden derivative 5 demonstrated a propensity for aggregate formation, which was studied by atomic force microscopy. Oxidative biochemical transformations catalyzed by 5 were evaluated by nucleic acid cleavage and by neurotransmitter oxidation, in the presence of external co-oxidants. Preliminary mechanistic analysis provides a hint for the involvement of reactive oxygen species in such transformations.

Amino Acid Motifs↗
PubMed2005

Enforcing solution phase nanoscopic aggregation in a palindromic tripeptide.

C-terminal dimerization of a tripeptide palindrome afforded fibrillation in solution through an assembly probably driven by hydrogen bonding and hydrophobic contributions; such an approach provides an expeditious entry into fabrication of fibrillating peptides from non-fibrillating peptide sequences.

Crystallography, X-Ray↗
PubMed2005

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis.

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.

Binding Sites↗
PubMed2004

Catalytic transformations with copper-metalated diglycine conjugates.

A series of copper-metalated, water-soluble bis-diglycine conjugates were synthesized and characterized through spectroscopic methods. These conjugates were evaluated for the cleavage of phosphodiester substrates, supercoiled plasmid relaxation in the presence of co-oxidants, and for the oxidation of a diphenolic substrate, 2,6-dimethoxyphenol. Appreciable rate enhancements were observed for these reactions and the oxidative nucleolytic cleavage activity and phenol oxidative coupling was presumably manifested via formation of reactive oxygen species.

Catalytic Domain↗
PubMed2004

Metalated hybrid polymers as catalytic reagents for phosphate ester hydrolysis and plasmid modification.

Pendant pyrazolylcyclophosphazene containing hybrid cross-linked polymer (CPPL) has been utilized for binding Zn(II). The metalated polymer (CPPL-Zn) has been found to be very effective catalyst for the hydrolysis of a RNA model phosphodiester substrate [2-(hydroxypropyl)-p-nitrophenyl phosphate, hNPP]. In addition, CPPL-Zn also cleaved supercoiled plasmid DNA pBR322 thus providing a novel structural motif of inorganic-organic hybrid polymers as synthetic nucleases.

Catalysis↗
PubMed2003

Adenine-copper coordination polymer as an oxidative nucleozyme: implications for simple prebiotic catalytic units.

Plasmid modification activity of a modified adenine-copper coordination polymer, in the presence of peracids and thiols, and ensuing preliminary mechanistic investigations are reported. These observations, when coupled with unique coordination pattern of the metal complex, have led us to propose that a synergistic interaction between nucleobases and metal ions may be responsible for primordial catalysis of certain key reactions of biochemical significance and could serve the function of a prototypical, prebiotic nucleozyme.

Adenine↗
PubMed2003

Plasmid relaxation induced by copper metalated diglycine conjugates under heterogeneous reaction conditions.

This paper reports synthesis and plasmid modification activities of a new class of insoluble copper-metalated diglycine conjugates, containing aliphatic linkers of varying length. Besides providing significant rate enhancement for model phosphate ester cleavage, these constructs also displayed efficient supercoiled plasmid scission, in the absence of co-oxidants, under heterogeneous catalytic conditions.

Catalysis↗
PubMed2003

Functional tuning of nucleic acids by chemical modifications: tailored oligonucleotides as drugs, devices, and diagnostics.

Chemical modifications of nucleic acids present vast opportunities for extending the functions and properties of these biomolecules. In general, efforts invested in this direction pertain to the introduction of reactive functional groups for further derivatizations of oligonucleotides with numerous reporter groups and for equipping nucleic acids with catalytic chemical moieties. This review deals with representative chemical modifications in the nucleobases, sugars, and the phosphate ester backbone and their application from novel catalytic RNA selection to nucleic acid-based biosensors.

Biosensing Techniques↗