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Related Concept Videos

RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Stability01:53

RNA Stability

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Stability01:53

RNA Stability

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...
RNA Structure01:19

RNA Structure

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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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Persistence length changes dramatically as RNA folds.

G Caliskan1, C Hyeon, U Perez-Salas

  • 1TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.

Physical Review Letters
|February 21, 2006
PubMed
Summary

Persistence length of bacterial group I ribozyme is determined using cation concentration. Magnesium ions dramatically alter persistence length, while sodium ions show gradual changes, aligning with polyelectrolyte theory.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Bacterial group I ribozymes are complex RNA molecules.
  • Understanding their structural dynamics is crucial for their function.
  • Cation concentrations significantly influence RNA structure and stability.

Purpose of the Study:

  • To determine the persistence length of bacterial group I ribozyme.
  • To investigate the effect of monovalent and divalent cations on ribozyme persistence length.
  • To correlate structural changes with cation concentration using physical models.

Main Methods:

  • Small-angle X-ray scattering (SAXS) to obtain distance distribution functions P(r).
  • Fitting SAXS data to the wormlike chain (WLC) model.
  • Analysis of persistence length (l(p)) as a function of Mg(2+) and Na(+) concentrations.

Main Results:

  • Persistence length (l(p)) changes significantly with Mg(2+) concentration, decreasing from ~21 Å (unfolded) to ~10 Å (compact/native states).
  • Na(+) concentration shows a more gradual effect on l(p).
  • Observed l(p) is inversely proportional to the square of the Debye-screening length (1/kappa(2)), consistent with polyelectrolyte theory.

Conclusions:

  • Cation-induced structural transitions in ribozymes are strongly dependent on the type and concentration of ions.
  • Magnesium ions play a critical role in compacting the ribozyme structure.
  • The study validates theoretical predictions of polyelectrolyte behavior in RNA molecules.