A5003328243- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- DNA and Nucleic Acid Chemistry
- Surface Chemistry and Catalysis
- Molecular Junctions and Nanostructures
- Protein Structure and Dynamics
- Virus-based gene therapy research
- Chemotherapy-induced organ toxicity mitigation
- Ferrocene Chemistry and Applications
- RNA regulation and disease
- DNA Repair Mechanisms
- Metal complexes synthesis and properties
- thermodynamics and calorimetric analyses
- Electrochemical sensors and biosensors
- Plant Virus Research Studies
- RNA Research and Splicing
- Curcumin's Biomedical Applications
- SARS-CoV-2 and COVID-19 Research
- Analytical Chemistry and Sensors
- Gene Regulatory Network Analysis
- Molecular Sensors and Ion Detection
- Advanced Electron Microscopy Techniques and Applications
- vaccines and immunoinformatics approaches
University of California, Riverside
2020-2025
The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, can bind and cleave partially complementary off-target sequences, which raises safety concerns for use clinical applications. Here, we report crystallographic structures bound bona fide substrates, revealing that binding enabled range noncanonical base-pairing interactions within guide:off-target heteroduplex. Off-target...
Abstract The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field nucleic acid-based detection. Here, we report on enhancement trans-cleavage Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate due to its improved affinity (Km) for structures, provide mechanistic insights our findings through Molecular Dynamics simulations. Using probes significantly enhance signal transduction...
Abstract CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by sequential mechanism in which initial cleavage of the non-target strand followed target cleavage. How spatially distant traverses toward catalytic core presently not understood. Here, continuous tens microsecond-long molecular dynamics and free-energy simulations reveal an α-helical lid, located within domain, plays pivotal role traversal...
The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables target recognition nuclease activation, we used cryo-electron microscopy to capture wild-type Acidaminococcus sp. intermediates DNA delivery into RuvC active site. Stages formation-starting from 5-bp seed-are marked by distinct REC domain arrangements. Dramatic flexibility limits contacts until...
Abstract CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed combining CRISPR-Cas9 with a transfer RNA (tRNA) adenosine deaminase enzyme and through directed evolution, conferring the ability deaminate DNA. However, molecular mechanisms driving efficient deamination in evolved remain unresolved. Here, extensive simulations biochemical experiments reveal biophysical basis behind astonishing...
ADVERTISEMENT RETURN TO ISSUEPREVFirst ReactionsNEXTFighting COVID-19 Using Molecular Dynamics SimulationsMolecular dynamics simulations revealed a promising immune target on the SARS-CoV-2 spike protein, proposing novel strategies for vaccine development.Pablo R. ArantesPablo ArantesDepartment of Bioengineering, University California Riverside, 900 Avenue, 92512, United StatesMore by Pablo Arantes, Aakash SahaAakash SahaDepartment Sahahttp://orcid.org/0000-0003-0776-9771, and Giulia...
CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which promising the diagnosis of SARS-CoV-2 coronavirus through DETECTR technology. Here, collective ensemble multimicrosecond molecular dynamics characterizes key dynamic determinants allowing processing in CRISPR-Cas12a. We show that DNA binding induces switch conformational Cas12a, results activation peripheral REC2 and Nuc domains to enable cleavage acids. The simulations reveal large-amplitude...
Abstract Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role molecular dynamics (MD) simulations in discovering mechanism allosteric communication within CRISPR‐Cas9, leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps CRISPR‐Cas9 function: affecting DNA recognition, mediating...
CRISPR−Cas12a effects RNA-guided cleavage of dsDNA in cis , after which it remains catalytically active and non-specifically cleaves ssDNA trans . Native host-defence by Cas12a employs cleavage, can be repurposed for the genome editing other organisms, used vitro DNA detection. orthologues have high structural similarity a conserved mechanism yet highly different efficacies when applied or By comparing three well characterised (FnCas12a, LbCas12a, AsCas12a), we sought to determine what...
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required simulate degrees freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) approach on massively parallelized cloud computing platform efficiently calculate thermodynamics and metadynamics biochemical first validate our approach, calculated free-energy surfaces alanine...
Abstract CRISPR-Cas12a is a powerful RNA-guided genome-editing system, also emerging as robust diagnostic tool that cleaves double-stranded DNA using only the RuvC domain. This opens an overarching question on how spatially distant target strand (TS) traverses toward catalytic core. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal ⍺-helical lid, located within domain, plays pivotal role in traversal TS by anchoring crRNA:TS hybrid elegantly...
Carrying out metadynamics calculations of large chemical systems with ab initio methods is computationally prohibitive due to the extensive sampling required simulate degrees freedom in these systems. To address this computational bottleneck, we utilize a GPU-enhanced density functional tight binding (DFTB) approach on massively-parallelized cloud computing platform efficiently calculate thermodynamics and biochemical first validate our approach, free energy surfaces alanine dipeptide show...
ABSTRACT The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, can bind and cleave partially complementary off-target sequences, which raises safety concerns for use clinical applications. Here we report crystallographic structures bound bona fide substrates, revealing that binding enabled range non-canonical base pairing interactions within guide–off-target heteroduplex....
TASK-3 generates a background K
Chemotherapy is a type of cancer treatment that kills rapidly proliferating cells.Being non-specific mode treatment, it can cause damage to healthy cells like bone marrow cells, epithelial hair follicles etc., resulting in various side effects.Cisplatin, platinum coordination complex, common chemotherapeutic drug used the several types cancers, including testicular, ovarian and bladder cancer.Cisplatin interferes with DNA replication by forming cross-linking form 1, 2-intrastrand crosslinks...