A5081890628- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Interference and Gene Delivery
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Biochemical and Molecular Research
- Chemical Synthesis and Analysis
- Monoclonal and Polyclonal Antibodies Research
- ATP Synthase and ATPases Research
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Origins and Evolution of Life
- DNA Repair Mechanisms
- Bacterial Genetics and Biotechnology
- Biosensors and Analytical Detection
- Innovative Microfluidic and Catalytic Techniques Innovation
- Advanced Biosensing Techniques and Applications
- Crystallization and Solubility Studies
- RNA Research and Splicing
- X-ray Diffraction in Crystallography
- Viral Infectious Diseases and Gene Expression in Insects
- HIV/AIDS drug development and treatment
University of California, Irvine
2016-2025
Irvine University
2023
Arizona State University
2009-2018
University of California System
2018
Irvine Valley College
2018
University of California, Berkeley
2018
Center for Personalized Cancer Treatment
2015
University of California, Riverside
1997-2012
Innovative Medicines Canada
2012
Howard Hughes Medical Institute
2002-2009
Genetic information storage and processing rely on just two polymers, DNA RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution design, we show that genetic can be stored in recovered from six alternative polymers based simple nucleic acid architectures not found nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind targets with high affinity specificity, demonstrating...
Abstract Polymerases that synthesize artificial genetic polymers hold great promise for advancing future applications in synthetic biology. However, engineering natural polymerases to replicate unnatural is a challenging problem. Here we present droplet-based optical polymerase sorting (DrOPS) as general strategy expanding function employs an sensor monitor activity inside the microenvironment of uniform compartment generated by microfluidics. We validated this approach performing complete...
Synthetic biology aims to improve human health and the environment by repurposing biological enzymes for use in practical applications. However, natural often function with suboptimal activity when engineered into pathways or challenged recognize unnatural substrates. Overcoming this problem requires efficient directed evolution methods discovering new enzyme variants that a desired activity. Here, we describe construction, validation, application of fluorescence-activated droplet sorting...
Abstract The term “xeno‐nucleic acids”, abbreviated XNA, has grown in popularity to the point that it become a catch‐all phrase for almost any unnatural nucleic acid, raising question: what is XNA and how does differ from chemically modified DNA?
In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying information back forth between DNA xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, transcriptional efficiency this enzyme diminishes greatly when individual are replaced libraries sequences,...
Aptamers are often prone to nuclease digestion, which limits their utility in many biomedical applications. Here we describe a xeno-nucleic acid system based on α-l-threofuranosyl nucleic (TNA) that is completely refractory digestion. The use of an engineered TNA polymerase permitted the isolation functional aptamers bind HIV reverse transcriptase (HIV RT) with KD's ∼0.4-4.0 nM. were identified using display strategy provides powerful genotype-phenotype linkage. remain active presence and...
Isothermal amplification strategies capable of rapid, inexpensive, and accurate nucleic acid detection provide new options for large-scale pathogen detection, disease diagnosis, genotyping. Here we report a highly sensitive multicomponent XNA-based platform that combines analyte preamplification with X10–23-mediated catalysis to detect the viral responsible COVID-19. The platform, termed RNA-Encoded Viral Nucleic Acid Analyte Reporter (REVEALR), functions limit ≤20 aM (∼10 copies/μL) using...
Threose nucleic acid (TNA), which has a repeat unit one atom shorter than that of DNA, is capable Watson−Crick base pairing with RNA, and TNA. Because its chemical simplicity, TNA considered to be possible progenitor RNA. As an initial step toward developing the molecular tools necessary investigate functional capabilities by in vitro selection, we have screened variety DNA polymerases for synthesis activity on template. We wish report several show surprisingly good ability synthesize using...
On show: High-density peptide arrays capable of displaying many different amino acid sequences at well-defined and addressable locations on the same DNA nanostructure have been produced. The strategy used relies genetic information encoded in nucleic portion a DNA-tagged to position sequence predetermined location array. Supporting for this article is available WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z603919_s.pdf or from author. Please note: publisher not responsible content...
A full understanding of the proteome will require ligands to all proteins encoded by genomes. While antibodies represent principle affinity reagents used bind proteins, their limitations have created a need for new large numbers proteins. Here we propose general concept obtain protein that avoids animal immunization and iterative selection steps. Central this process is idea small peptide libraries contain sequences independent regions on surface these can be combined synthetic scaffolds...
The emerging field of synthetic genetics provides an opportunity to explore the structural and functional properties genetic polymers by in vitro selection. Limiting this process, however, is availability enzymes that allow for synthesis propagation information present unnatural nucleic acid sequences. Here, we report development a transcription reverse-transcription system can replicate composed threose acids (TNA). TNA potential progenitor RNA which natural ribose sugar found has been...
The ability to synthesize and propagate genetic information encoded in the framework of xeno-nucleic acid (XNA) polymers would inform a wide range topics from origins life synthetic biology. While directed evolution has produced examples engineered polymerases that can accept XNA substrates, these enzymes function with reduced activity relative their natural counterparts. Here, we describe biochemical strategy enables discovery improved for given unnatural polymerase function. Our approach...
Abstract The isolation of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that catalysis is not limited to natural biopolymers, but it remains unknown whether such systems can achieve robust Michaelis-Menten kinetics. Here, we describe an efficient RNA-cleaving 2’-fluoroarabino nucleic acid enzyme (FANAzyme) functions a rate enhancement >10 6 -fold over the uncatalyzed reaction and exhibits substrate saturation kinetics typical most enzymes. FANAzyme was generated...
ConspectusGenomes can be viewed as constantly updated memory systems where information propagated in cells is refined over time by natural selection. This process, commonly known heredity and evolution, has been the sole domain of DNA since origin prokaryotes. Now, some 3.5 billion years later, pendulum discovery swung a new direction, with carefully trained practitioners enabling replication evolution "xeno-nucleic acids" or "XNAs"—synthetic genetic polymers which sugar found RNA replaced...
Abstract Low activity has been the primary obstacle impeding use of DNA enzymes (DNAzymes) as gene silencing agents in clinical applications. Here we describe chemical evolution a DNAzyme with strong catalytic under near physiological conditions. The enzyme achieves ~65 turnovers 30 minutes, feat only previously witnessed by unmodified parent sequence forcing conditions elevated Mg 2+ and pH. Structural constraints imposed modifications drive catalysis toward highly preferred U GU D motif...
Chemical modifications are necessary to ensure the metabolic stability and efficacy of oligonucleotide-based therapeutics. Here, we describe analyses α-(l)-threofuranosyl nucleic acid (TNA) modification, which has a shorter 3'-2' internucleotide linkage than natural DNA RNA, in context small interfering RNAs (siRNAs). The TNA modification enhanced nuclease resistance more 2'-O-methyl or 2'-fluoro ribose modifications. TNA-containing siRNAs were prepared as triantennary N-acetylgalactosamine...
Supramolecular self-assembly is an integral step in the formation of many biological structures. Here we report a DNA pentaplex that derives from metal-assisted, hydrogen bond-mediated process. In particular, cesium ions are found to induce pentameric assembly bearing nonstandard nucleobase iso-guanine. The was designed by using simple algorithm predict structural requirements within quintet motif. design principles general and should extend complexes beyond pentaplex. Structures exhibiting...