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Principal Investigator: SMITA S PATEL
Organization: RUTGERS BIOMEDICAL AND HEALTH SCIENCES
Fiscal Year: 2024
Award: $828,047
Funding agency: National Institute of General Medical Sciences
Project Summary
The overarching goal of our research is to understand the mechanisms of helicases and polymerases in
processes such as viral RNA recognition, DNA transcription, and replication. The unifying approach is the
quantitative characterization of the enzymatic reactions using rigorous biochemical and biophysical methods
such as transient state kinetics, single-molecule kinetics, computational kinetic modeling, and cryo-electron
microscopy. The integration of structural and functional studies allows the development of a complete
mechanistic picture. In project 1, we are studying viral RNA recognition by RIG-I like receptors which are
helicases serving as the first responders of viral RNA infections. The RIG-I like receptors recognize pathogen-
associated molecular patterns on viral genomes and replication intermediates and respond by triggering an
immune response to create an antiviral state. Our research focuses on understanding the mechanisms of RNA
recognition and ATPase/helicase functions of RIG-I like receptors using biochemical, structural, and cell-
signaling assays. We are elucidating the intrinsic mechanisms in RIG-I that enable self versus non-self
recognition and developing new strategies to understand how they are activated and regulated. In project 2,
we are studying the mechanism and regulation of mitochondrial DNA transcription catalyzed by RNA
polymerases that resemble phage T7 but regulated by transcription factors. Transcription initiation and
transition into elongation are key stages that are regulated by transcription factors. We are using cryo-electron
microscopy, and ensemble/single-molecule kinetics to elucidate the structure and dynamics at these stages of
transcription using in vitro reconstituted yeast and human mitochondrial RNA polymerases. In project 3, we
are studying the mechanism of DNA replication by phage T7 and human mitochondrial replisomes. We study
how helicase and polymerase work together to catalyze strand-displacement DNA synthesis, in particular, how
they are energetically coupled. We are studying the mechanism of DNA synthesis by mitochondrial DNA
polymerase to understand the role of helicase, Twinkle, and mitochondrial single-strand binding protein. An in-
depth understanding of the enzymatic mechanisms is critically necessary to understand mitochondrial DNA
deletions caused by defects in helicase and polymerase. This research will provide the mechanistic framework
to quantitatively model the reactions of replication, transcription, and pathogen recognition that will guide in the
development of therapies for viral infections, cancer, mitochondrial diseases.
Terms: <ATP phosphohydrolase><ATPase><Adenosine Triphosphatase><Anti-viral Agents><Assay><Bacteriophage T7><Basal Transcription Factor><Basal transcription factor genes><Binding Proteins><Bioassay><Biochemical><Biochemical Reaction><Biological Assay><Cancers><Cell Communication and Signaling><Cell Signaling><Coliphage T7><Coupled><Cryo-electron Microscopy><Cryoelectron Microscopy><DNA><DNA Helicases><DNA Polymerases><DNA Replication><DNA Synthesis><DNA Unwinding Proteins><DNA biosynthesis><DNA unwinding enzyme><DNA-Dependent DNA Polymerases><DNA-Dependent RNA Polymerases><DNA-Directed DNA Polymerase><DNA-Directed RNA Polymerase><Defect><Deoxyribonucleic Acid><Development><Disease><Disorder><Electron Cryomicroscopy><Enterobacteria phage T7><Enzymatic Reaction><Enzyme Gene><Enzymes><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Genetic Transcription><Goals><Human><Immune response><Immunologic Receptors><Immunological Receptors><Immunological response><In Vitro><Innate Immunity><Intracellular Communication and Signaling><Kinetics><Knowledge><Ligand Binding Protein><Ligand Binding Protein Gene><Maintenance><Malignant Neoplasms><Malignant Tumor><Mitochondria><Mitochondria RNA><Mitochondrial DNA><Mitochondrial Diseases><Mitochondrial Disorders><Mitochondrial RNA><Modeling><Modern Man><Molecular><Native Immunity><Natural Immunity><Non-Polyadenylated RNA><Non-Specific Immunity><Nonspecific Immunity><Nucleic Acids><Pattern><Polymerase><Process><Production><Property><Protein Binding><RNA><RNA Expression><RNA Gene Products><RNA Polymerases><RNA Virus Infections><RNA viral infection><Reaction><Receptor Protein><Regulation><Research><Ribonucleic Acid><Role><Signal Transduction><Signal Transduction Systems><Signaling><Structure><T7 Phage><Transcription><Transcription Factor Proto-Oncogene><Transcription Initiation><Transcription factor genes><Vaccine Adjuvant><Viral><Viral Diseases><Viral Genome><Virus Diseases><Virus Replication><Work><Yeasts><anti-viral compound><anti-viral drugs><anti-viral medication><anti-viral therapeutic><anti-virals><biological signal transduction><biophysical approaches><biophysical methodology><biophysical methods><biophysical techniques><bound protein><cryo-EM><cryoEM><cryogenic electron microscopy><develop therapy><developmental><enzyme mechanism><first responder><helicase><host response><immune activator><immune receptor><immune system response><immunoresponse><intervention development><kinetic model><malignancy><mitochondrial><mtDNA><mtRNA><neoplasm/cancer><pathogen><receptor><reconstitute><reconstitution><single molecule><social role><therapy development><transcription factor><treatment development><viral RNA><viral infection><viral multiplication><viral replication><virus RNA><virus genome><virus infection><virus multiplication><virus-induced disease>