Vivian T. Dien
A5004611505- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Chemical Synthesis and Analysis
- Microbial Metabolic Engineering and Bioproduction
- Antimicrobial Peptides and Activities
- Adsorption and biosorption for pollutant removal
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Advanced Biosensing Techniques and Applications
- Geochemistry and Elemental Analysis
- Single-cell and spatial transcriptomics
- Heavy metals in environment
- Click Chemistry and Applications
Elements Biosciences (United States)
2023-2024
Scripps Research Institute
2017-2020
Massachusetts Institute of Technology
2013
Fluorescent bioorthogonal smart probes across the visible spectrum will enable sensitive visualization of metabolically labeled molecules in biological systems. Here we present a unified design, based on principle photoinduced electron transfer, to access panel highly fluorogenic azide that are activated by conversion corresponding triazoles via click chemistry. Termed CalFluors, these possess emission maxima range from green far red wavelengths, and biomolecule detection under no-wash...
Abstract We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along DNA template and identifying each nucleotide within template. Nucleotide identification uses multivalent ligands on dye-labeled cores to form polymerase–polymer–nucleotide complexes bound clonal copies targets. These polymer–nucleotide substrates, termed avidites, decrease required concentration reporting nucleotides from micromolar nanomolar yield negligible dissociation...
Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue stably maintaining an unnatural base pair (UBP) in its DNA, transcribing corresponding nucleotides into codons anticodons mRNAs tRNAs, then using them to produce proteins containing noncanonical amino acids (ncAAs). Here report systematic extension effort optimize SSO exploring variety deoxy- ribonucleotide analogues. Importantly, this includes first vivo...
We have developed a family of unnatural base pairs (UBPs), exemplified by the pair formed between dNaM and dTPT3, for which pairing is mediated not complementary hydrogen bonding but hydrophobic packing forces. These UBPs enabled creation first semisynthetic organisms (SSOs) that store increased genetic information use it to produce proteins containing noncanonical amino acids. However, retention was poor in some sequence contexts. Here, optimize SSO, we synthesize two novel...
We have developed an unnatural base pair (UBP) and a semisynthetic organism (SSO) that imports the constituent nucleoside triphosphates uses them to replicate DNA containing UBP. However, propagation of UBP is at least in part limited by stability triphosphates, which are degraded cellular secreted phosphatases. To circumvent this problem, we now report synthesis evaluation with their β,γ-bridging oxygen replaced difluoromethylene moiety, yielding dNaMTPCF2 dTPT3TPCF2. find although cannot...
We report the use of a simple yet highly effective magnetite-waste tea composite to remove lead(II) (Pb2+) ions from water. Magnetite-waste composites were dispersed in four different types water–deionized (DI), artificial rainwater, groundwater and freshwater–that mimic actual environmental conditions. The water samples had varying initial concentrations (0.16–5.55 ppm) Pb2+ mixed with for at least 24 hours allow adsorption reach equilibrium. stable all 3 months could be easily removed...
Abstract We present avidity sequencing - a novel chemistry that separately optimizes the process of stepping along DNA template and identifying each nucleotide within template. Nucleotide identification uses multivalent ligands on dye-labeled cores to form polymerase-polymer complexes bound clonal copies targets. These polymer-nucleotide substrates, termed avidites, decrease required concentration reporting nucleotides from micromolar nanomolar, yield negligible dissociation rates....
Abstract We present a novel sequencing chemistry implemented as part of the AVITI system. Relying on proximal DNA binding sites created through amplification solid support, avidity uses multivalent nucleotide ligands dye-labeled cores to simultaneously form polymerase-polymer complexes bound clonal copies targets. These polymer-nucleotide substrates, termed avidites, decrease required concentration reporting nucleotides by 100x and yield negligible dissociation rate. demonstrate use avidites...
Abstract The accuracy of a sequencing platform has traditionally been measured by the %Q30, or percentage data exceeding basecall 99.9%. Improvements to beyond Q30 may be beneficial for certain applications such as identification low frequency alleles improvement reference genomes. Here we demonstrate how achieved over 70% Q50 (99.999% accuracy) on AVITI™ sequencer. This level required us not only improve quality but also mitigate library preparation errors and analysis artifacts.