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Integrating Internal Fragments in the Interpretation of Top-Down Sequencing Data of Larger Oligonucleotides.
J Am Soc Mass Spectrom
October 2023
University of Connecticut, Storrs, Connecticut 06269, United States.
In the context of direct top-down analysis or concerted bottom-up characterization of nucleic acid samples, the waning yield of terminal fragments as a function of precursor ion size poses a significant challenge to the gas-phase sequencing of progressively larger oligonucleotides. In this report, we examined the behavior of oligoribonucleotide samples ranging from 20 to 364 nt upon collision-induced dissociation (CID). The experimental data showed a progressive shift from terminal to internal fragments as a function of size.
View Article and Find Full Text PDFSafety and Biodistribution of Nanoligomers Targeting the SARS-CoV-2 Genome for the Treatment of COVID-19.
ACS Biomater Sci Eng
March 2023
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States.
As the world braces to enter its fourth year of the coronavirus disease 2019 (COVID-19) pandemic, the need for accessible and effective antiviral therapeutics continues to be felt globally. The recent surge of Omicron variant cases has demonstrated that vaccination and prevention alone cannot quell the spread of highly transmissible variants. A safe and nontoxic therapeutic with an adaptable design to respond to the emergence of new variants is critical for transitioning to the treatment of COVID-19 as an endemic disease.
View Article and Find Full Text PDFNrnA Is a Linear Dinucleotide Phosphodiesterase with Limited Function in Cyclic Dinucleotide Metabolism in Listeria monocytogenes.
J Bacteriol
January 2022
Food Science Department, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Listeria monocytogenes produces both c-di-AMP and c-di-GMP to mediate many important cellular processes, but the levels of both nucleotides must be regulated. c-di-AMP accumulation attenuates virulence and diminishes stress response, and c-di-GMP accumulation impairs bacterial motility. An important regulatory mechanism to maintain c-di-AMP and c-di-GMP homeostasis is to hydrolyze them to the linear dinucleotides pApA and pGpG, respectively, but the fates of these hydrolytic products have not been examined in L.
View Article and Find Full Text PDFTrypanosomatid, fluorescence-based U-insertion/U-deletion RNA-editing (FIDE).
Bio Protoc
March 2021
Molecular Genetics, Technical University Darmstadt, Darmstadt, Germany.
Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is catalyzed by a 0.
View Article and Find Full Text PDFPdc2/Pat1 increases the range of decay factors and RNA bound by the Lsm1-7 complex.
RNA
October 2020
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA.
Pat1, known as Pdc2 in fission yeast, promotes the activation and assembly of multiple proteins during mRNA decay. After deadenylation, the Pat1/Lsm1-7 complex binds to transcripts containing oligo(A) tails, which can be modified by the addition of several terminal uridine residues. Pat1 enhances Lsm1-7 binding to the 3' end, but it is unknown how this interaction is influenced by nucleotide composition.
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