A5004593987- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- Biochemical and Structural Characterization
- Microbial Natural Products and Biosynthesis
- Glycosylation and Glycoproteins Research
- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Hepatitis B Virus Studies
- Advanced Proteomics Techniques and Applications
- Plant biochemistry and biosynthesis
- Chemical Synthesis and Analysis
- Machine Learning in Bioinformatics
- interferon and immune responses
- Cancer Research and Treatments
- Antimicrobial Peptides and Activities
- vaccines and immunoinformatics approaches
- Molecular Biology Techniques and Applications
- DNA Repair Mechanisms
- Microbial Metabolism and Applications
University of Illinois Urbana-Champaign
2023-2024
Scripps College
2017-2020
Abstract Specialized or secondary metabolites are small molecules of biological origin, often showing potent activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis these natural products is governed by sets co-regulated physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs a standardized machine-readable way, Minimum Information Biosynthetic Gene cluster (MIBiG) data standard repository was initiated...
The RiPP precursor recognition element (RRE) is a conserved domain found in many prokaryotic ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic gene clusters (BGCs). RREs bind with high specificity affinity to sequence within the N-terminal leader region of peptides. Lasso biosynthesis involves an RRE-dependent peptidase, which discretely encoded or fused RRE as di-domain protein. Here we leveraged thousands predicted BGCs define RRE:leader peptidase...
Abstract Ribosomally synthesized and post-translationally modified peptides (RiPPs) comprise a structurally functionally diverse group of natural products. Lasso represent one about 50 known molecular classes RiPPs, which display characteristic [1] rotaxane conformation formed by lasso cyclase. This unique, threaded endows with biological activities remarkable thermal proteolytic stability. The prediction peptide properties, such as substrate compatibility particular cyclase or desired...
Abstract Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more‐diverse physical structures. However, native polymerases generally cannot synthesize significant lengths with modified nucleotide triphosphates. Previous efforts have identified a mutant polymerase I from Thermus aquaticus (SFM19) as capable synthesizing range short, 2′‐modified DNAs; however, it is limited in length products synthesize. Here, we rationally designed...
DNA is a foundational tool in biotechnology and synthetic biology but limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified polymerases that can enzymatically synthesize long oligonucleotides of modified (M-DNA) are resistant Most applications require M-DNA be reverse transcribed, typically using RNA transcriptase, back into natural for sequence analysis or further manipulation. Here, we tested commercially available DNA-dependent their ability transcribe...
Modified‐DNA polymerases have been evolved that can synthesize long strands of modified oligonucleotides. The resulting DNA (M‐DNA) has many high‐value potential applications, such as clinical diagnostics and therapeutics. To fully apply M‐DNA, it must be reverse transcribed back into natural DNA. Previously, error prone transcriptases required for this step, then the to amplified in a separate amplification reaction. Using synthetic template with 2′F nucleotides, we tested panel...
Recently, several modified‐DNA (M‐DNA) polymerases have been identified which can synthesize long M‐DNAs. While these discoveries enabled new applications of M‐DNA, enzymes typically poor fidelity, possessing error rates orders magnitude worse than native enzymes. However, to date, efforts both quantify rate, as well experimental approaches towards understanding the origin fidelity M‐DNA polymerases, limited. Here, we use a high‐throughput sequencing assay characterize rate leading showed...