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A non-covalently bound redox indicator for electrochemical CRISPR-Cas12a and DNase I biosensors.
Anal Chim Acta
January 2025
Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322, USA; Department of Chemistry, University of Louisiana at Lafayette, 300 East St. Mary Blvd, Lafayette, LA, 70504, USA. Electronic address:
A rapid and accurate biosensor for detecting disease biomarkers at point-of-care is essential for early disease diagnosis and preventing pandemics. CRISPR-Cas12a is a promising recognition element for DNA biosensors due to its programmability, specificity, and deoxyribonuclease activity initiated in the presence of a biomarker. The current electrochemical CRISPR-Cas12a-based biosensors utilize the single-stranded DNA (ssDNA) self-assembled on an electrode surface and covalently modified with the redox indicator, usually methylene blue (MB).
View Article and Find Full Text PDFRapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.
Nat Struct Mol Biol
January 2025
Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
Following transcript release during intrinsic termination, Escherichia coli RNA polymerase (RNAP) often remains associated with DNA in a post-termination complex (PTC). RNAPs in PTCs are removed from the DNA by the SWI2/SNF2 adenosine triphosphatase (ATPase) RapA. Here we determined PTC structures on negatively supercoiled DNA and with RapA engaged to dislodge the PTC.
View Article and Find Full Text PDFChemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5' untranslated region.
Nat Commun
January 2025
Department of Medicinal Chemistry, University of Kansas, Lawrence, USA.
One of the hallmarks of RNA viruses is highly structured untranslated regions (UTRs) which are often essential for viral replication, transcription, or translation. In this report, we discovered a series of coumarin derivatives that bind to a four-way RNA helix called SL5 in the 5' UTR of the SARS-CoV-2 RNA genome. To locate the binding site, we developed a sequencing-based method namely cgSHAPE-seq, in which an acylating probe was directed to crosslink with the 2'-OH group of ribose at the binding site to create read-through mutations during reverse transcription.
View Article and Find Full Text PDFMolecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.
Mol Biotechnol
January 2025
Amity Institute of Biotechnology, Amity University, Kolkata, India.
Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones.
View Article and Find Full Text PDFOne-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation.
Nucleic Acids Res
January 2025
Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, The College of Life Sciences, Sichuan University, 24 South Section 1, 1st Ring Road, Chengdu, Sichuan 610064, P.R. China.
Region-specific RNA modifications are crucial for advancing RNA research and therapeutics, including messenger RNA (mRNA)-based vaccines and immunotherapy. However, the predominant method, synthesizing regionally modified mRNAs with short single-stranded DNA (ssDNA) splints, encounters challenges in ligating long mRNA fragments due to the formation of RNA self-folded complex structures. To address this issue, we developed an efficient strategy using an easily obtained long double-stranded DNA (dsDNA) as a ligation splint after in situ denaturing, while parts of this dsDNA are the templates for transcribing mRNA fragments.
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