Swati Mahendru

A bouquet of DNA structures: Emerging diversity

Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications.

Protein engineering and de novo designing of a biocatalyst.

Proteins as a biomolecule have been recognized as a “molecule with manifold biological functions”. The functions not only include the structural, regulatory and transportation processes inside the body but also its capacity as an extremely specific catalyst for various biochemical reactions. Nature has been quite admirably using proteins as biocatalysts which are known as enzymes. Properties like higher reaction rate, good specificity, faster kinetics, production of lesser by‐products and their non‐hazardous nature make enzymes the most suitable targets for a process chemist to exploit. At the same time, limitations like a narrow range of substrates, requirement of coenzymes, lesser stability, smaller shelf‐life, along with difficulties in procuring these enzymes, make this biocatalysis field quite challenging.

Genetic contribution of CYP1A1 variant on treatment outcome in epilepsy patients: a functional and interethnic perspective.

CYP1A1 gene is involved in estrogen metabolism, and previously, we have reported association of variant rs2606345 with altered anti-epileptic drugs (AED) response in North Indian women with epilepsy (WWE). The present study aims to replicate the pharmacogenetic association, perform functional characterization and study its distribution within ethnically diverse Indian population. The variant was genotyped in 351 patients to assess the pharmacogenetic association and 552 healthy individuals belonging to 24 different ethnic groups to examine the distribution in Indian population. We observed significant overrepresentation of ‘A’ allele and ‘AA’ genotype in poor responders in WWE at Bonferroni-corrected significance levels. The recessive allele was found to lower the promoter activity by ~70–80% which was further substantiated by thermally less stable hairpin formed by it (ΔTm=7 °C). Among all ethnic groups, west Indo–European (IE-W-LP2) subpopulation showed highest genotypic frequency of the variant making women from this community more prone to poor AED response. Our results indicate that rs2606345 influences drug response in WWE by lowering CYP1A1 expression.

Peptide Biomarkers: Exploring the Diagnostic Aspect.

BACKGROUND In the past few decades, with the upsurge of various deadly diseases, development of accurate diagnostic methods is inevitable for maintaining good health. There is an urgent requirement of specific and sensitive biomarkers in order to improve diagnosis, guide molecular targeted therapy, and predict and examine therapeutic response across a wide spectrum of disease. METHOD We undertook a structured search of bibliographic databases for peer-reviewed research literature to evaluate the significance of peptides as valuable tools for diagnostic applications as well as the techniques used for discovery of peptide biomarkers. RESULT On the basis of extensive literature survey, peptide biomarkers are classified according to their diagnosis approach. In addition, we summarize a few techniques used in peptide biomarker discovery such as peptidomics and peptide microarray. CONCLUSION Small size, stability, easy and inexpensive production, capability to migrate throughout the body, fast clearance from body and low immunogenicity, as well as the remarkable quality of peptides to mirror the change in protease expression or activation associated with a pathological process, have established them as a promising biomarker.

Multiple dimensions of functional relevance of genosensors

ABSTRACT Biosensors having the recognition element as DNA/RNA oligon-ucleotides are known as genosensors, which have been widely utilized for many applications including clinical diagnostic tool for diseases like cancer and a range of infectious diseases. This review aims to discuss the vast repertoire of nanomaterial based genosensors, their designing and numerous applications, including their usage in food quality assessment, environmental monitoring, as aptasensors for the recognition of nucleosides, as biomarkers for the identification of DNA methylation in epigenetics and molecular beacon nano-sensors for probing the living cancer cells etc. Genosensors are of utmost significance for solving various puzzles related to cellular processes and their control mechanisms.

Unusual Stability Exhibited by (AT)XN12(AT)Y Motif Associated With High Fetal Hemoglobin Levels

Abstract Quasi-palindromic sequences (AT)XN12(AT)Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults arise due to pathological conditions such as sickle cell disease and β-thalassemia. However, elevated levels of HbF are also associated with a reducing morbidity and mortality in patients with β-thalassemia and thus ameliorate the severity of the disease. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, and circular dichroism (CD) techniques, we demonstrated that it exhibits a hairpin-duplex equilibrium. Intramolecular species (hairpin) were observed in both low and high salt concentrations in gel assay studies displaying the unusual stability of intramolecular species even at the high counter-ion concentration. The unusual stability of hairpin secondary structures was also demonstrated by the monophasic nature of the melting profiles for the oligonucleotides which persisted at low as well as high salt and oligomer concentrations. Change in CD spectra as a function of oligomer concentration indicates that the bimolecular duplex formation is selectively favored over monomolecular hairpin formation at and above 9 µM oligomer concentration. Thus, we hypothesize that imperfect inverted repeat sequence (AT)XN12(AT)Y of HS2 of β-globin gene LCR forms the unusually stable hairpins which may result in the formation of a cruciform structure that may be recruited for binding by various nuclear proteins that could result in elevated HbF levels. Communicated by Ramaswamy H. Sarma. Graphical Abstract

DNA Fingerprints: Advances in their Forensic Analysis Using Nanotechnology

For deciphering the secrets of forensic science, nanotechnology has quite extensively been utilized. Generally, for identifying the fingerprints, a lot of combination of different materials and film assemblies have already been utilized. Since the mode of interaction between the nanoparticles and fingerprint marks, is still not clearly understood, fabricating the nanoparticle assemblies for their identification is quite challenging. Complete identification of fingerprint marks which are generally because of a combination of some kind of proteins and fatty acids, is still a difficult task and is only partially being done with the help of different techniques. Nanotechnology has already shown immense potential in many fields like medicine, molecular biology, genetics, material science etc. and it has also marked promising potential even in forensic analysis studies. This review aims to discuss the details of the process of fingerprint formation, their role in forensic analysis along with the latest advances in the field of nanotechnology for their identification. This information may enhance our understanding about the progress in the forensic analysis of fingerprints, which may further be utilized in solving the puzzle of various criminal cases.

Genetic Variations: Heroes or Villains

Gene pool of every organism has shown a wide occurrence of genetic variations. Variations have not only been associated with diseases like cancer, turner syndrome, sickle cell anaemia, cystic fibrosis etc., but some of them have even been proved to be beneficial in certain cases like for increasing bone density, lowering down cholesterol level, and for developing malaria resistance. Genetic variations or switches have also been explored for their significant role in evolution of human species. Monogenic diseases are the inherited disorders caused by the mutations in a single gene. Single Nucleotide Polymorphism, structural variants and genomic rearrangements are considered as some of the forms of genetic mutations. Genetic mutations are the fundamental cause of some monogenic disorders such as Schizophrenia, Alzheimer’s disease, Hutchinson-Gilford Progeria syndrome (HGPS), Proteus syndrome and Congenital generalized hypertrichosis (CGH). However, some variants have even offered protection against a disease like blocking of HIV infection due to mutations in co-receptors needed for entry of infection into the cells. This review aims to provide insights into the role of variants present in the genes associated with the monogenic disorders in order to determine the underlying mechanism of the disease, which might further pave a way for the scientists to discover the therapeutic approaches for dealing with the same.

Genomic Databases and Softwares: In Pursuit of Biological Relevancethrough Bioinformatics

With the completion of human genome project, a plethora of information had been available for exploring various unanswered questions related to cell and molecular biology. Bioinformatics has been instrumental in unravelling the genetic, phenotypic, structural and functional aspects of the whole genome by using this information. Genomics and proteomics have become one of the most relevant fields after the advancements in computational analysis, interpretation, and modelling software. It can not only quite categorically describe the position of nucleotides and amino acids throughout genomes and proteomes respectively, but it also helps in performing the phylogenetic analysis, search for associated transcription factors, multiple sequence alignments, and many other relevant explorations/hunts. The advances in the knowledge of genetics acquired from molecular biology and bioinformatics are applied and point towards potential therapeutic strategies such as genome editing. This review has an aim of discussing some of the bioinformatics databases and software, which has been utilized for exploring the position of a DNA sequence, any associated single nucleotide polymorphism (SNP) related to a disease, on or nearby situated transcription factor binding sites followed by multiple sequence alignment of this sequence with other organisms. This study provides the insights in to the functional elements of any DNA, RNA or Protein sequence prior to exploring the structural polymorphism, which may regulate the gene expression. Also, this review briefly discusses the tools used for programmable nuclease–based genome editing technology.

Advancements in Characterization Techniques of Biopolymers: CyclicVoltammetry, Gel Electrophoresis, Circular Dichroism and FluorescenceSpectroscopy

Biopolymers such as DNA, RNA and proteins are the key players in the cellular processes like cell differentiation, cell growth, maintenance, repair, recombination, transcription, translation, etc. Immense efforts have been made for their isolation, purification, quantification and structural as well as functional characterization. Profound insights into the structural and functional characterization of these biopolymers could help us understand the intricate cellular machinery. A wide range of biochemical, biophysical, electrochemical and molecular biology techniques have really been beneficial in exploring the key and interdependent relationships between the structure and function of these biopolymers. Each instrumentation technique has its own advantage and disadvantage in terms of their applications, selectivity and sensitivity. There had been a lot of advancements in these techniques for achieving their desired goals, but still, lots of limitations need our attention and further improvements. For understanding, the extremely complicated biological machinery at molecular and cellular level, every small fragment of a cell has to be studied separately with a lot of intricacies. In this review, we present a brief update of the advancements made in the large repertoire of Cyclic Voltammetry (CV), Gel electrophoresis, Circular Dichroism (CD) and Fluorescence spectroscopy techniques which might be relevant for updating our knowledge of the pre-existing and well-established tools utilized by the scientists across the world.