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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Nuclear Export of mRNA

Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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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.
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Related Experiment Video

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Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker
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DEAD-box proteins can completely separate an RNA duplex using a single ATP.

Yingfeng Chen1, Jeffrey P Potratz, Pilar Tijerina

  • 1Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

Proceedings of the National Academy of Sciences of the United States of America
|December 18, 2008
PubMed
Summary

DEAD-box proteins, essential for RNA metabolism, can unwind short RNA duplexes using a single ATP molecule. This ATP-dependent conformational change allows local RNA rearrangements without disrupting larger structures.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • DEAD-box proteins are crucial for RNA metabolism, utilizing ATP for RNA conformational changes.
  • Their mechanism is distinct from other helicases, involving local strand separation while remaining tethered.

Purpose of the Study:

  • To critically test the model of DEAD-box protein function by measuring ATP hydrolysis during short RNA helix separation.
  • To investigate the role of ATP in mediating RNA conformational changes.

Main Methods:

  • Measuring ATP hydrolysis by DEAD-box proteins (CYT-19, Mss116p, Ded1p) during the separation of short RNA helices (6-11 bp).
  • Comparing the activity of ATP with the non-hydrolyzable analog AMP-PNP.

Main Results:

  • DEAD-box proteins can achieve complete strand separation of short RNA duplexes using a single ATP molecule.
  • ATP strongly enhances strand separation activity, even without hydrolysis, suggesting a role in stabilizing active conformations.
  • AMP-PNP does not mimic ATP's effect, indicating hydrolysis or a specific ATP-bound state is important.

Conclusions:

  • DEAD-box proteins disrupt short RNA duplexes via a single cycle of ATP-dependent conformational changes.
  • This supports models where these proteins perform local rearrangements while tethered to RNA or RNP complexes.
  • This mechanism allows DEAD-box proteins to modulate RNA structure locally without global disruption.