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Nat Commun
January 2025
Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA.
Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity to ligand (EC) is controlled is critical to explain how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover roles by which RNA folding dynamics control riboswitch sensitivity in cells.
View Article and Find Full Text PDFBiochem J
January 2025
School of Science, University of Waikato, Hamilton, Waikato, 3216, New Zealand.
DNA-joining by ligase and polymerase enzymes has provided the foundational tools for generating recombinant DNA and enabled the assembly of gene and genome-sized synthetic products. Xenobiotic nucleic acid (XNA) analogues of DNA and RNA with alternatives to the canonical bases, so-called 'unnatural' nucleobase pairs (UBP-XNAs), represent the next frontier of nucleic acid technologies, with applications as novel therapeutics and in engineering semi-synthetic biological organisms. To realise the full potential of UBP-XNAs, researchers require a suite of compatible enzymes for processing nucleic acids on a par with those already available for manipulating canonical DNA.
View Article and Find Full Text PDFBioconjug Chem
January 2025
Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1,Canada.
The ability to label synthetic oligonucleotides with fluorescent probes has greatly expanded their nanotechnological applications. To continue this expansion, it is essential to develop approachable, modular, and tunable fluorescent platforms. In this study, we present the synthesis and incorporation of an amino-formyl-thieno[3,2-]thiophene (AFTh) handle at the 5'-position of DNA oligonucleotides.
View Article and Find Full Text PDFAnal Bioanal Chem
January 2025
Biospring Gesellschaft für Biotechnologie, Alt-Fechenheim 34, Frankfurt am Main, 60386, Germany.
The use of single-guide RNA (sgRNA) for gene editing using the CRISPR Cas9 system has become a powerful technique in various fields, especially with the growing interest in such molecules as therapeutic options in the last years. An important parameter for the use of these molecules is the verification of the correct sgRNA oligonucleotide sequence. Apart from next-generation sequencing protocols, mass spectrometry (MS) has been proven as a powerful technique for this purpose.
View Article and Find Full Text PDFAnal Chim Acta
February 2025
Department of Chemistry, Iowa State University, Ames, IA, 50011, USA. Electronic address:
Background: Infections from the hepatitis B virus (HBV) are a major risk factor for hepatocellular carcinoma, one of the most common types of liver cancer. Circulating cell-free DNA (ccfDNA) in human plasma can be used as a non-invasive biomarker for diagnosing HBV-related liver diseases. The isolation of target ccfDNA sequences is often challenging due to the co-extraction of highly abundant non-target DNA from samples.
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