A5000247452- DNA and Nucleic Acid Chemistry
- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- Biochemical and Molecular Research
- Virus-based gene therapy research
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Microbial Metabolic Engineering and Bioproduction
- Chemical Synthesis and Analysis
- Plant Gene Expression Analysis
- RNA Interference and Gene Delivery
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Cancer therapeutics and mechanisms
- Hybrid Renewable Energy Systems
- Microbial Natural Products and Biosynthesis
- Colorectal Cancer Treatments and Studies
- Fermentation and Sensory Analysis
- RNA modifications and cancer
- ATP Synthase and ATPases Research
- Genetic Syndromes and Imprinting
University of Pennsylvania
2023-2024
Harvard University
2012-2013
Johns Hopkins Medicine
2008-2010
Johns Hopkins University
2008-2010
Laboratory of Molecular Genetics
2007
Abstract The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding how Cas9 and deaminases collaborate shape editor (BE) outcomes has been lacking. Here, we support novel mechanistic model editing by deriving range hyperactive activation-induced (AID) editors (hBEs) exploiting their characteristic diversifying activity. Our involves multiple layers previously underappreciated...
5-Fluorouracil (5-FU), 5-fluorodeoxyuridine (5-dUrd), and raltitrixed (RTX) are anticancer agents that target thymidylate synthase (TS), thereby blocking the conversion of dUMP into dTMP. In budding yeast, 5-FU promotes a large increase in dUMP/dTMP ratio leading to massive polymerase-catalyzed incorporation uracil (U) genomic DNA, lesser extent 5-FU, which both excised by yeast DNA glycosylase (UNG), fragmentation cell death. contrast, toxicity RTX human mouse lines does not involve UNG,...
The prodrug 5-fluorouracil (5-FU), after activation into 5-F-dUMP, is an extensively used anticancer agent that inhibits thymidylate synthase and leads to increases in dUTP 5-F-dUTP levels cells. One mechanism for 5-FU action involves DNA polymerase mediated incorporation of genomic leading U/A, 5-FU/A, or 5-FU/G base pairs. These uracil-containing lesions are recognized excised by several human uracil excision repair glycosylases (hUNG2, hSMUG2, hTDG) toxic abasic sites may precipitate cell...
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Screening Array (MSA), focus on human screening discovery. This array utilizes extensive data from previous platform-based studies (EWAS). It incorporates knowledge latest single-cell cell type-resolution whole genome methylome...
Biosynthesis of the dipeptide antibiotic bacilysin, encoded by seven Bacillus subtilis genes bacA–G, involves diversion flux from prephenate to noncognate amino acid anticapsin. The anticapsin warhead is then ligated C-terminus l-alanine produce mature bacilysin. We have previously noted formation two diastereomers tetrahydrotyrosine (4S- and 4R-H4Tyr) tandem action four purified enzymes BacABGF. BacC (oxidase) BacD (ligase) been hypothesized be remaining late stage in bacilysin...
Uracil DNA glycosylase (UNG) is a powerful repair enzyme that has been shown to stabilize glycosyl cation reaction intermediate and related tight binding inhibitor using electrostatic interactions with the +1 −1, but not +2, phosphodiester group of single-stranded substrate Ap2+Ap1+Up1−ApA. These experimental results differed considerably from computational findings duplex DNA, where +2 phosphate was found transition state by ∼5 kcal/mol, suggesting UNG uses different catalytic strategies...
BacA and BacB, the first two enzymes of bacilysin pathway, convert prephenate to an exocylic regioisomer dihydrohydroxyphenylpyruvate (ex-H2HPP) on way epoxycyclohexanone warhead in dipeptide antibiotic, bacilysin. decarboxylates without aromatization, converting 1,4-diene endocyclic 1,3-diene Δ4,Δ8-dihydrohydroxyphenylpyruvate (en-H2HPP). BacB then performs allylic isomerization bring diene into conjugation with 2-ketone product Δ3,Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). To prove that...
The first four enzymes of the bacilysin antibiotic pathway, BacABGF, convert prephenate to a tetrahydrotyrosine (H4Tyr) diastereomer on way anticapsin warhead dipeptide antibiotic. BacB takes BacA product endocyclic-Δ4,Δ8-7R-dihydrohydroxyphenylpyruvate (en-H2HPP) and generates mixture 3E- 3Z-olefins exocyclic-Δ3,Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). NADH-utilizing BacG then catalyzes conjugate reduction, adding pro-S hydride equivalent C4 yield tetrahydrohydroxyphenylpyruvate (H4HPP),...
ABSTRACT The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding how Cas9 and deaminases collaborate shape editor (BE) outcomes has been lacking. Here, we support novel mechanistic model editing by deriving range hyperactive activation-induced (AID) editors (hBEs) exploiting their characteristic diversifying activity. Our involves multiple layers previously underappreciated...