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Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.
Angew Chem Int Ed Engl
January 2025
Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India.
Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes.
View Article and Find Full Text PDFThermostable protein-stabilized gold nanoclusters as a peroxidase mimic.
Nanoscale Adv
November 2023
Physical Chemistry, Department of Chemistry, University of Konstanz 78457 Konstanz Germany
Protein-stabilized gold nanoclusters (AuNCs) are fascinating nanostructures with exciting properties owing to their ultra-small sizes and functional shell. However, their applications under extreme conditions are still complicated, waiting for programmable solutions. Therefore, the design of a multi-functional protein stabilizer for specific purposes gains attention to improve the stability and functionality of AuNCs.
View Article and Find Full Text PDFNon-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency.
Int J Mol Sci
September 2023
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia.
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase-DNA-dNTP complexes.
View Article and Find Full Text PDFRapid Cycle and Extreme Polymerase Chain Reaction.
Methods Mol Biol
April 2023
Crestwood Technology, Camden, ME, USA.
Rapid cycle polymerase chain reaction (PCR) amplifies DNA in 10-30 min, while extreme PCR is complete in less than 1 min. These methods do not sacrifice quality for speed; sensitivity, specificity, and yield are equivalent or better than conventional PCR. What is required (and not widely available) is rapid, accurate control of reaction temperature during cycling.
View Article and Find Full Text PDFAccurate gene consensus at low nanopore coverage.
Gigascience
November 2022
Gulliver Lab, ESPCI Paris, PSL University, CNRS, 75005 Paris, France.
Background: Nanopore technologies allow high-throughput sequencing of long strands of DNA at the cost of a relatively large error rate. This limits its use in the reading of amplicon libraries in which there are only a few mutations per variant and therefore they are easily confused with the sequencing noise. Consensus calling strategies reduce the error but sacrifice part of the throughput on reading typically 30 to 100 times each member of the library.
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