A5013255600- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- DNA Repair Mechanisms
- Cancer, Hypoxia, and Metabolism
- Nanoplatforms for cancer theranostics
- Cancer Research and Treatments
- RNA Research and Splicing
- Pancreatic and Hepatic Oncology Research
- Adenosine and Purinergic Signaling
- Ubiquitin and proteasome pathways
- Molecular Biology Techniques and Applications
- Metal-Catalyzed Oxygenation Mechanisms
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- Biochemical and Molecular Research
- Bacterial Genetics and Biotechnology
- Genome Rearrangement Algorithms
- Acute Lymphoblastic Leukemia research
- Tryptophan and brain disorders
- Histone Deacetylase Inhibitors Research
- Antimicrobial Peptides and Activities
- Algorithms and Data Compression
Stanford University
2016-2025
Howard Hughes Medical Institute
2022-2024
Yale University
2022-2024
Stanford Health Care
2024
New York University
2019
ConspectusNucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful effective, its reliance on heating cooling cycles places some constraints utility. For example, step of PCR can destroy biological molecules under investigation heat/cool are not applicable in living systems. Thus, isothermal approaches to DNA RNA widespread study. Perhaps simplest these rolling circle approaches, including (RCA)...
Over the past three decades, researchers have found that some engineered aptamers can be made to work well in test tubes but these same might fail function cells. To help address this problem, we developed 'Graftamer' approach, an experimental platform exploits architecture of a natural riboswitch enhance vitro aptamer selection and accelerate vivo testing. Starting with combinatorial RNA pools contain structural features guanine interspersed regions random sequence, performed multiplexed...
DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) ends (GA:TC) have been reported previously, and those diffracted to 4.9 Å at beamline NSLS-I-X25. Here, we analyze the effect of varying end lengths sequences as well impact 5′- 3′-phosphates on crystal formation resolution. Tensegrity triangle motifs having 1-, 2-, 3-, 4-nt all form crystals. X-ray diffraction data from same reveal that...
Significance We address a fundamental biological issue: the source of free energy enabling high-fidelity DNA replication. polymerase errors occur at about 1 per 1,000–10,000 bp, indicating “right” vs. “wrong” differences ΔΔ G inc = 3–5 kcal/mol. A recent paper using high inorganic pyrophosphate concentrations to “equilibrate” right and wrong forward reverse incorporation reactions concluded that base pairing in alone is sufficient account for fidelity. By performing an explicit analysis...
The efficacy of strategies targeting oncogenic RAS, prevalent in lung adenocarcinoma (LUAD), is limited by rapid adaptive resistance mechanisms. These include loss RAS addiction and hyperactivation downstream signaling pathways, such as PI3K/AKT. We previously reported that RAS-driven LUAD cells possess an enhanced reliance on MTH1, the mammalian 8-oxodGTPase, to prevent genomic incorporation oxidized nucleotides, MTH1 depletion compromises tumorigenesis signaling. Here, we show elevated...
Impaired DNA repair activity has been shown to greatly increase rates of cancer clinically. It hypothesized that upregulating in susceptible individuals may be a useful strategy for inhibiting tumorigenesis. Here, we report selected tyrosine kinase (TK) inhibitors including nilotinib, employed clinically the treatment chronic myeloid leukemia, are activators enzyme Human MutT Homolog 1 (MTH1). MTH1 cleanses oxidatively damaged cellular nucleotide pool by hydrolyzing oxidized...
A new strategy is reported for the production of luminescence signals from DNA synthesis through use chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, leaving group. ATP-releasing nucleotides (ARNs) were synthesized as derivatives four canonical nucleotides. All are good substrates polymerase, with Km values averaging 13-fold higher those natural dNTPs, and kcat within 1.5-fold native Importantly, ARNs found to yield very little background signal luciferase....
We document the preparation and properties of dimerized pentaphosphate-bridged deoxynucleotides (dicaptides) that contain reactive components two different nucleotides simultaneously. Importantly, dicaptides are found to be considerably more stable hydrolysis than standard dNTPs. Steady-state kinetics studies show dimers exhibit reasonably good efficiency with Klenow fragment DNA polymerase I, we identify thermostable enzymes process them efficiently at high temperature. Experiments dAp5dT...
The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal effects with unintended proteins; however, little attention has been paid intracellular RNAs as potential off targets that may contribute toxicity. To begin assess this, we developed a reactivity-based RNA profiling (RBRP) methodology, applied it uncover transcriptome interactions set FDA-approved small-molecule in vivo. We show these protein-targeted...
Engineered aptamers for new compounds are typically produced by using in vitro selection methods. However, that developed might not function as expected when introduced into complex cellular environments. One approach addresses this concern is the design of initial RNA pools contain structural scaffolds from naturally occurring riboswitch aptamers. Here, we provide guidance on and experimental principles developing riboswitch-inspired ligands. The protocol (based Capture-SELEX) generalizable...
Drug candidates that fail in clinical trials for efficacy reasons might still have favorable safety and bioavailability characteristics could be exploited. A failed drug candidate repurposed if a receptor, such as an aptamer, were created binds the compound with high specificity. Branaplam is small molecule was previously development to treat spinal muscular atrophy Huntington's disease. Here, we report of (48-nucleotide) RNA aptamer branaplam dissociation constant ∼150 nM. Starting...
ATP-releasing nucleotides are employed to detect single nucleotide polymorphisms in a novel method that is sensitive, rapid, and isothermal.
Abstract Pancreatic ductal adenocarcinoma (PDAC) is an aggressive KRAS-driven cancer that remains one of the most lethal all human malignancies. Oncogenic KRAS relies on elevated reactive oxygen species (ROS) to support pro-tumorigenic signaling. However, these ROS levels can also evoke tumor suppressive oxidative stress; thus cancers must evolve protective redox adaptations mitigate ROS-induced anti-tumor consequences. Here we report a unique adaptation centered maintenance nucleotide pool...
Abstract Oncogenic RAS signaling is mediated by reactive oxygen species (ROS) signaling. However, oncogenic ROS also evoke tumor suppressive damage, necessitating adaptive redox protective mechanisms. We previously reported that MTH1, the main mammalian 8-oxodGTPase, comprises one such critical adaptation. High MTH1 expression significantly correlates with poor disease-free survival in several KRAS-driven tumors. have shown RAS-driven xenograft cancer models for maintenance of ROS-driven and...
Abstract Pancreatic ductal adenocarcinoma (PDAC) is an aggressive KRAS-driven cancer that remains one of the most lethal all human malignancies. Oncogenic KRAS relies on elevated reactive oxygen species (ROS) to support pro-tumorigenic signaling. However, these ROS levels can also evoke tumor suppressive oxidative stress; thus cancers must evolve protective redox adaptations mitigate ROS-induced anti-tumor consequences. Here we report a unique adaptation centered maintenance nucleotide pool...
Abstract A new strategy is reported for the production of luminescence signals from DNA synthesis through use chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, leaving group. ATP‐releasing nucleotides (ARNs) were synthesized as derivatives four canonical nucleotides. All are good substrates polymerase, with K m values averaging 13‐fold higher those natural dNTPs, and k cat within 1.5‐fold native Importantly, ARNs found to yield very little background signal...