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A cell-free biosensor signal amplification circuit with polymerase strand recycling.
Nat Chem Biol
January 2025
Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
Cell-free systems are powerful synthetic biology technologies that can recapitulate gene expression and sensing without the complications of living cells. Cell-free systems can perform more advanced functions when genetic circuits are incorporated. Here we expand cell-free biosensing by engineering a highly specific isothermal amplification circuit called polymerase strand recycling (PSR), which leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits.
View Article and Find Full Text PDFA direct approach toward investigating DNA-ligand interactions surface-enhanced Raman spectroscopy combined with molecular dynamics simulations.
Phys Chem Chem Phys
January 2023
Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands.
View Article and Find Full Text PDFA Combination of Membrane Filtration and Raman-Active DNA Ligand Greatly Enhances Sensitivity of SERS-Based Aptasensors for Influenza A Virus.
Front Chem
June 2022
Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.
Biosensors combining the ultrahigh sensitivity of surface-enhanced Raman scattering (SERS) and the specificity of nucleic acid aptamers have recently drawn attention in the detection of respiratory viruses. The most sensitive SERS-based aptasensors allow determining as low as 10 virus particles per mL that is 100-fold lower than any antibody-based lateral flow tests but 10-100-times higher than a routine polymerase chain reaction with reversed transcription (RT-PCR). Sensitivity of RT-PCR has not been achieved in SERS-based aptasensors despite the usage of sophisticated SERS-active substrates.
View Article and Find Full Text PDFDetecting the formation of human c-KIT oncogene promoter G-Quadruplex by Taylor dispersion analysis.
Talanta
October 2021
Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. Electronic address:
The formation of G-quadruplex (G4) structures in oncogenic G-rich promoter regions are implicated in their biological functions, especially the inhibition of transcription. The binding of cations is thought to contribute to the stabilization of the G4 formation and competition against the duplex formation in the genomic sequence. Furthermore, it might affect the recognition of DNA-binding proteins.
View Article and Find Full Text PDFBerberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA.
Molecules
April 2021
Department of Chemistry-Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering (Cµ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms ( = 2-7 × 10 M) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex . The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA.
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