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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-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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.
The technique helps...
Applications Of NMR In Biology01:25

Applications Of NMR In Biology

Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
The...
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...

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Structural and functional investigation of the hepatitis C virus IRES.

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Solution structure of the A loop of 23S ribosomal RNA.

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Related Experiment Video

Updated: Jul 15, 2026

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

RNAPack: an integrated NMR approach to RNA structure determination.

P J Lukavsky1, J D Puglisi

  • 1Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.

Methods (San Diego, Calif.)
|February 28, 2002
PubMed
Summary

RNAPack is a new software package that speeds up RNA structure determination using nuclear magnetic resonance (NMR) spectroscopy. This tool simplifies complex NMR experiments, enabling faster and more accurate analysis of RNA structures.

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Last Updated: Jul 15, 2026

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Published on: December 2, 2009

RNA Secondary Structure Prediction Using High-throughput SHAPE
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Area of Science:

  • Structural Biology
  • Biophysics
  • Molecular Biology

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining RNA structure and dynamics.
  • High-resolution RNA structure determination using NMR is often time-consuming and requires extensive expertise.
  • Existing NMR methods necessitate complex programming and calibration procedures.

Purpose of the Study:

  • To develop a user-friendly package of automated NMR experiments to accelerate RNA structure determination.
  • To streamline the process of data collection and calibration for RNA NMR studies.
  • To enhance the accessibility and efficiency of NMR spectroscopy for analyzing large RNA systems.

Main Methods:

  • Designed and programmed a software package named RNAPack for RNA NMR experiments.
  • Included semiautomated single, double, and triple resonance NMR experiments.
  • Integrated an autocalibration feature for rapid, single-step experiment calibration on Varian NMR spectrometers.

Main Results:

  • RNAPack significantly accelerates NMR data collection and minimizes user errors through autocalibration.
  • Successfully determined the solution structures of hepatitis C viral RNA domains in under 3 months.
  • Demonstrated the package's effectiveness for high-resolution RNA solution structure determination.

Conclusions:

  • RNAPack makes NMR spectroscopy a more rapid and attractive tool for structural analysis of RNA.
  • The software facilitates the integration of atomic-resolution structural data into biochemical studies of large RNA molecules.
  • RNAPack enhances the efficiency and accuracy of RNA structure determination by NMR spectroscopy.