A5013819419- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Protein Structure and Dynamics
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Collagen: Extraction and Characterization
- Chemical Synthesis and Analysis
- Mycorrhizal Fungi and Plant Interactions
- Glycosylation and Glycoproteins Research
- Bacterial Genetics and Biotechnology
- RNA Interference and Gene Delivery
- RNA modifications and cancer
- DNA Repair Mechanisms
- RNA Research and Splicing
- biodegradable polymer synthesis and properties
- Seedling growth and survival studies
- Plant-Microbe Interactions and Immunity
- Soil Carbon and Nitrogen Dynamics
- Machine Learning in Bioinformatics
- Bone and Dental Protein Studies
- Immune Response and Inflammation
- Viral gastroenteritis research and epidemiology
Indian Institute of Science Bangalore
2012-2023
University of Rajasthan
2019
Centre for DNA Fingerprinting and Diagnostics
2019
Osmania University
2019
Bangalore University
2016
Institut de génétique et de développement de Rennes
2013
University of Toronto
2005-2010
Panjab University
1982-2008
University of Hyderabad
2008
University of Delhi
1993-2007
The role of thymine residues in the formation G-quartet structures for telomeric sequences has been investigated using model oligonucleotides type d(G4TnG4), with n = 1-4. Sequences d(G4T3G4) and d(G4T4G4) adopt a structure formed by hairpin dimerization 70 mM NaCl as judged characteristic circular dichroism signature 295 nm positive 265 negative bands while d(G4TG4) adopts parallel like d(G12) which exhibits strong band at 260 240 nm. sequence d(G4T2G4) mixture both conformations. stability...
Abstract Background In the post-genomic era, correct gene prediction has become one of biggest challenges in genome annotation. Improved promoter methods can be step towards developing more reliable ab initio methods. This work presents a novel prokaryotic method based on DNA stability. Results The region is less stable and hence prone to melting as compared other genomic regions. Our analysis shows that differences stability sequences non-promoter works much better existing programs, which...
Abstract A detailed analysis of structural and position dependent characteristic features helices will give a better understanding the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies geometry proteins on basis their Cα atoms alone. The Fortran program HELANAL can extract from PDB files then characterises overall each helix as being linear, curved or kinked, terms its local features, viz. helical twist rise, virtual torsion angle, origins...
Osteopontin (OPN) is important for the function of fibroblasts, macrophages and lymphocytes during inflammation wound healing. In recent studies experimental colitis we demonstrated exacerbated tissue destruction in OPN-null mice, associated with reduced tumour necrosis factor-alpha expression increased myeloperoxidase activity. The objective this investigation therefore was to determine importance OPN neutrophil function. Although, contrast macrophages, neutrophils expressed low levels...
It is shown that left-handed duplexes are possible for A, B, and D forms of DNA. These stereochemically satisfactory consistent with the observed x-ray intensity data. On scrutiny refined right-handed models B DNA by Arnott coworkers found to be unacceptable. was formulate a stereochemical guideline molecular model building based on theory analysis single-crystal structure data dinucleoside monophosphate higher oligomers. This led both right- duplexes. The so obtained superior earlier agree...
Osteopontin (OPN) is a glycophosphoprotein with multiple intracellular and extracellular functions. In vitro, OPN enhances migration of mouse neutrophils macrophages. cancer, facilitates cancer cells via its RGD sequence. The present study was designed to investigate whether osteopontin responsible for neutrophil macrophage infiltration in human particular glioblastoma. We found that vitro RGD-dependent. silico, we the gene one 5% most highly expressed genes 20 out 35 microarray data sets...
A nucleosome is the fundamental repeating unit of eukaryotic chromosome. It has been shown that positioning a majority nucleosomes primarily controlled by factors other than intrinsic preference DNA sequence. One key questions in this context role, if any, can be played variability nucleosomal structure. In study, we have addressed question analysing at dinucleotide and trinucleotide as well longer length scales dataset X-ray crystal structures. We observe structure displays remarkable local...
Spatial and temporal expression of genes is essential for maintaining phenotype integrity. Transcription factors (TFs) modulate patterns by binding to specific DNA sequences in the genome. Along with core motif, flanking sequence context can play a role DNA-TF recognition. Here, we employ high-throughput vitro silico analyses understand influence cognate sites three most prevalent eukaryotic TF families (zinc finger, homeodomain bZIP). In preferences each toward entire space were correlated...
An analysis of the amino acid distributions at 15 positions, viz., N", N′, Ncap, N1, N2, N3, N4, Mid, C4, C3, C2, C1, Ccap, C′, and C" in 1,131 α-helices reveals that each position has its own unique characteristics. In general, natural helix sequences optimize by identifying residues to be avoided a given minimizing occurrence these rather than maximizing preferred various positions. Ncap is most selective choice residues, with six acids (S, D, T, N, G, P) being this another 11 (V, I, F, A,...
Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis generation of non-uniform structures. A set local inter basepair parameters (viz. tilt, roll, twist, shift, slide rise) have been defined, use geometry coordinates two successive basepairs only generate polymeric structures with varying geometries for each the 16 possible dinucleotide steps. Intra parameters, propeller, buckle, opening...
Click to increase image sizeClick decrease size Acknowledgments Prasun Kumar acknowledges DBT-BINC, India for fellowship. We thank David Langelaan providing all the necessary files used in MC-HELAN paper, along with source code of program. Cheng-Wei pointing out database dependency problem related protein 1L0 V (pdb id). Ashish Shelar reading manuscript.
Eukaryotic genes can be broadly classified as TATA-containing and TATA-less based on the presence of TATA box in their promoters. Experiments both classes have revealed a disparity regulation gene expression cellular functions between two classes. In this study, we report characteristic differences promoter sequences associated structural properties categories six different eukaryotes. We analyzed three features, DNA duplex stability, bendability, curvature along with distribution A-tracts,...
In higher eukaryotes, gene architecture and structural properties of promoters have emerged as significant factors influencing variation in number transcripts (expression level) specificity expression a tissue breadth), which eventually shape the phenotype. this study, transcriptome data different types at various developmental stages A. thaliana, O. sativa, S. bicolor Z. mays been used to understand relationship between components its expression. Our findings indicate that plants, among all...
A new procedure for the identification of regular secondary structures using a C(α) trace has identified 659 π-helices in 3582 protein chains, solved at high resolution. Taking advantage this significantly expanded database π-helices, we have analysed functional and structural roles determined position-wise amino acid propensity within around them. These helices range from 5 to 18 residues length with average twist rise being 85.2 ± 7.2° 1.28 0.31 Å, respectively. total 546 (~ 83%) out occur...
Transcription is an intricate mechanism and orchestrated at the promoter region. The cognate motifs in promoters are observed only a subset of total genes across different domains life. Hence, sequence-motif based prediction may not be holistic approach for whole genomes. Conversely, DNA structural property, duplex stability characteristic can used to delineate them from other genomic sequences. In this study, we have algorithm 'PromPredict' broad range eukaryotes, representing various...