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Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

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Related Experiment Video

Updated: Jul 8, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Unveiling substrate RNA binding to H/ACA RNPs: one side fits all.

Hong Li1

  • 1Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA. hongli@sb.fsu.edu

Current Opinion in Structural Biology
|January 8, 2008
PubMed
Summary

H/ACA RNP pseudouridylases modify RNA, using a one-sided attachment model. RNP proteins are crucial for precise substrate positioning in the active site, as revealed by structural and biochemical studies.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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Related Experiment Videos

Last Updated: Jul 8, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • H/ACA RNP pseudouridylases are essential enzymes that modify various RNA molecules, including pre-ribosomal and small nuclear RNAs.
  • These enzymes play critical roles in RNA processing and function within the cell.
  • Previous structural data suggested a general model for H/ACA RNP-RNA interaction.

Purpose of the Study:

  • To elucidate the specific roles of individual H/ACA RNP proteins in RNA substrate binding and positioning.
  • To understand the mechanism by which H/ACA RNPs achieve precise placement of complex RNA substrates into their active sites.
  • To integrate structural and biochemical data for a comprehensive understanding of H/ACA RNP function.

Main Methods:

  • Utilizing X-ray crystallography and cryo-electron microscopy to determine high-resolution structures of H/ACA RNPs bound to RNA.
  • Employing biochemical assays to assess the catalytic activity and substrate binding affinities of wild-type and mutant H/ACA RNP proteins.
  • Combining structural insights with mutational analysis to dissect protein-RNA interactions.

Main Results:

  • Structural data reveal a conserved one-sided attachment model for H/ACA RNP-RNA capture.
  • Key RNP proteins were identified as essential for guiding the RNA substrate into the precise orientation within the catalytic active site.
  • Biochemical studies confirmed the functional importance of these RNP proteins in substrate recognition and positioning.

Conclusions:

  • H/ACA RNP proteins are indispensable for the accurate recruitment and placement of RNA substrates, ensuring efficient pseudouridylation.
  • The elucidated mechanism highlights the intricate interplay between RNA structure and protein factors in guiding enzymatic activity.
  • These findings provide a detailed molecular basis for H/ACA RNP function in RNA modification.