Biology subjects

Kar, D. M.

Publications and source records attributed to Kar, D. M..

3 recordsLinked to original sources

bioRxiv2024

Self-Documenting Plasmids

SO_SCPLOWUMMARYC_SCPLOWPlasmids are the workhorse of biotechnology. These small DNA molecules are used to produce recombinant proteins and to engineer living organisms. They can be regarded as the blueprints of many biotechnology products. It is, therefore, critical to ensure that the sequences of these DNA molecules match their intended designs. Yet, plasmid verification remains challenging. To secure the exchange of plasmids in research and development workflows, we have developed self-documenting plasmids that encode information about themselves in their own DNA molecules. Users of self-documenting plasmids can retrieve critical information about the plasmid without prior knowledge of the plasmid identity. The insertion of documentation in the plasmid sequence does not adversely affect their propagation in bacteria and does not compromise protein expression in mammalian cells. This technology simplifies plasmid verification, hardens supply chains, and has the potential to transform the protection of intellectual property in the life sciences.

synthetic biology↗

bioRxiv2023

Computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (ppar-γ)

Diabetes mellitus is one of the complex metabolic disorders associated with individuals leading sedentary lifestyles. It leads to several complications rendering the normal function of vital organs like heart, liver, kidney, eye and brain. Scientists and doctors across the globe are involved in research for understanding the complex genetics of this disorder and formulating newer therapeutics accordingly. The finding of potential chemical entities and their underlying agonists or antagonist activities significantly controls the disorder but with some consequences. Thus there is demand for natural compounds and indigenous treatment methods for controlling the disorder with least or no adverse consequences. In the current work we present computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (PPAR-{gamma}). A group of four gamma-oryzanol compound structures reported in PubChem database were downloaded and docked in the ligand binding site of five different human PPAR-{gamma} structures reported in PDB database. It was observed that most of the gamma-oryzanol compounds occupied themselves in the ligand binding P1, P2, P3, P4 sites with similar orientations as that of co-crystal agonists. Their binding conformations were assisted by some reasonable docking scores (-7 to -11 kcal/mol) and hydrogen bond interactions with some important conserved amino acid residues lining the ligand binding site. Additionally we have done a comparative molecular dynamics studies to reveal the flexibility of gamma-oryzanol in the ligand binding site in comparison to the co-crystal agonist and a scaffold analysis using the structure of six agonists and gamma-oryzanol for fetching potential scaffolds which may helpful in designing of new chemical entities.

bioinformatics↗

bioRxiv2019

Securing the exchange of synthetic genetic constructs using digital signatures

Synthetic biology relies on an ever-growing supply chain of synthetic genetic material. Technologies to secure the exchange of this material are still in their infancy. Solutions proposed thus far have focused on watermarks, a dated security approach that can be used to claim authorship, but is subject to counterfeit, and does not provide any information about the integrity of the genetic material itself. We describe how data encryption and digital signature algorithms can be used to ensure the integrity and authenticity of synthetic genetic constructs. Using a pilot software that generates digital signatures and other encrypted data for plasmids, we demonstrate that we can predictably extract information about the author, the identity, and the integrity of plasmid sequences from sequencing data alone without a reference sequence, all without compromising the function of the plasmids. We discuss how this technology can be improved, applied, and expanded to support the new bioeconomy.

synthetic biology↗