Ribonucleotides

Ribonucleotides are the molecular building blocks of RNA, consisting of a ribose sugar, a nitrogenous base, and one or more phosphate groups. In cells, ribonucleotide triphosphates such as ATP, GTP, CTP, and UTP are incorporated into RNA by polymerases through phosphodiester-bond formation, with pyrophosphate release driving chain growth in the 5′ to 3′ direction. Beyond RNA synthesis, ribonucleotides participate in energy transfer, cellular signaling, and metabolic regulation, while serving as precursors for other nucleotide molecules. Studying their production, modification, and use helps explain gene expression, genome maintenance, metabolism, and the design of RNA-based research tools and therapeutics.

Ribonucleotides - Related Videos

Research

JoVE Journal - Biology

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

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Cited by 5 •

2018

Ribonucleotides are among the most abundant non-canonical nucleotides incorporated into the genome during eukaryotic nuclear DNA replication. If not properly removed, ribonucleotides can cause DNA damage and mutagenesis. Here, we present two experimental approaches that are used to assess the abundance of ribonucleotide incorporation into DNA and its mutagenic effects.

Research

JoVE Journal - Biology
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Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

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Cited by 5 •

2017

Here we describe a method amenable to simultaneously quantitate and genome-wide map ribonucleotides in highly intact DNA at single-nucleotide resolution, combining enzymatic cleavage of genomic DNA with its alkaline hydrolysis and subsequent 5´-end sequencing.

Research

JoVE Journal - Biology
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Substrate Generation for Endonucleases of CRISPR/Cas Systems

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Cited by 4 •

2012

CRISPR/Cas systems mediate adaptive immunity in Bacteria and Archaea. Many Cas proteins are proposed to act as endoribonucleases acting on crRNA precursors of varying length. Here we illustrate three different approaches to generate pre-crRNA substrates for the biochemical analysis of Cas endonuclease activity.

Research

JoVE Journal - Biology
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Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

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Cited by 10 •

2010

The fate of the replisome following a collision with a head-on RNA polymerase (RNAP) is unknown. We find that the replisome stalls upon collision with a head-on RNAP, but resumes elongation after displacing the RNAP from DNA. Mfd promotes replication restart by facilitating displacement of the RNAP after the collision.

Research

JoVE Journal - Biology
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Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies

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Cited by 489 •

2012

PCR has emerged as a common technique in many molecular biology laboratories. Provided here is a quick guide to several conventional PCR protocols. Because each reaction is a unique experiment, optimal conditions required to generate a product vary. Understanding the variables in a reaction will greatly enhance troubleshooting efficiency, thereby increasing the chance to obtain the desired result.

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