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Related Concept Videos

RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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RNA Stability01:53

RNA Stability

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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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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.
DNA Structure
DNA...
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Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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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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Nucleic Acids02:43

Nucleic Acids

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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
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Related Experiment Video

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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Sequence-dependent conformational preferences of disordered single-stranded RNA.

Tong Wang1,2, Weiwei He3,4,2, Suzette A Pabit1

  • 1School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

Cell Reports. Physical Science
|December 27, 2024
PubMed
Summary
This summary is machine-generated.

Single-stranded RNA (ssRNA) structure is influenced by its sequence. Researchers used advanced methods to reveal distinct, sequence-dependent conformations in ssRNA, challenging simple polymer models.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Disordered single-stranded RNA (ssRNA) molecules perform vital functions dependent on their structures.
  • Characterizing the heterogeneous conformer populations of native ssRNAs presents significant challenges.
  • Understanding how sequence influences ssRNA structure is a key area of investigation.

Purpose of the Study:

  • To investigate the role of sequence in determining the structure and dynamics of single-stranded RNA.
  • To compare the structural properties (size, shape, flexibility) of RNA homopolymers and heteropolymers.
  • To develop detailed structural ensembles for ssRNAs using integrated experimental and computational approaches.

Main Methods:

  • Utilized solution-based measurements, including small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET).
  • Employed experimentally guided all-atom molecular dynamics (MD) simulations.
  • Constructed structural ensembles for a 30-nucleotide RNA homopolymer (rU30) and an A-/C-rich heteropolymer.

Main Results:

  • Average properties of the studied ssRNAs align with flexible polymer physics models.
  • Distinct, sequence-dependent conformations were identified at the molecular level.
  • The findings highlight that ssRNA conformations require more detailed representation than standard polymer models.

Conclusions:

  • The sequence of single-stranded RNA plays a critical role in shaping its overall structural properties.
  • Integrated experimental and simulation approaches are effective for characterizing complex ssRNA structures.
  • Future models of ssRNA should incorporate sequence-specific details for accurate representation.