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Related Concept Videos

RNA Structure01:23

RNA Structure

79.3K
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...
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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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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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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.7K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Structure modeling of RNA using sparse NMR constraints.

Benfeard Williams1,2, Bo Zhao2,3, Arpit Tandon1,2

  • 1Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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|November 23, 2017
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Summary

A new platform, iFoldNMR, uses NMR data to accurately model complex RNA structures quickly. This method aids in understanding the function of diverse RNA molecules.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • RNA molecules fold into specific three-dimensional shapes crucial for their biological functions.
  • Accurate prediction of RNA structures, especially those with complex motifs like non-canonical base pairs and pseudoknots, is a significant challenge in molecular biology.

Purpose of the Study:

  • To develop a rapid and accurate computational platform for modeling complex RNA structures.
  • To utilize Nuclear Magnetic Resonance (NMR) data to guide structure modeling of RNA molecules.

Main Methods:

  • Introduction of iFoldNMR, an all-atom discrete molecular dynamics (DMD) platform guided by NMR data.
  • Employing sparse distance constraints derived from imino resonances in NMR experiments.
  • Directing the DMD simulation to identify low-energy RNA conformers.

Main Results:

  • Demonstrated sufficiency of sparse imino resonance constraints for RNA structure modeling.
  • Successful recapitulation of experimentally determined structures for RNAs up to 56 nucleotides.
  • Achieved all-heavy-atom RMSDs between 2.4 and 6.5 Å for modeled structures.

Conclusions:

  • iFoldNMR provides an efficient approach for high-throughput RNA structure modeling.
  • The platform facilitates the analysis of newly discovered functional RNAs.
  • NMR-guided DMD modeling offers a powerful tool for understanding RNA structure-function relationships.