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Related Concept Videos

RNA Structure01:23

RNA Structure

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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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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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Transfer RNA Synthesis02:36

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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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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.
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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.
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Structural basis for substrate loading in bacterial RNA polymerase.

Dmitry G Vassylyev1, Marina N Vassylyeva, Jinwei Zhang

  • 1Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA. dmitry@uab.edu

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|June 22, 2007
PubMed
Summary

The trigger loop refolding mechanism in RNA polymerase is vital for substrate loading. Structural studies reveal distinct preinsertion and insertion states, offering targets for antibiotic development.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Understanding RNA polymerase substrate loading is key to transcription.
  • The precise mechanism remains a subject of debate.

Purpose of the Study:

  • To elucidate the mechanism of substrate loading in multisubunit RNA polymerase.
  • To determine the structural basis of substrate binding and inhibition.

Main Methods:

  • X-ray crystallography at 3.0-A resolution.
  • Biochemical assays.

Main Results:

  • Structures of Thermus thermophilus elongation complex (EC) with AMPcPP and AMPcPP/streptolydigin were determined.
  • AMPcPP binds in an active 'insertion' site via trigger loop (TL) refolding.
  • Streptolydigin stabilizes an inactive 'preinsertion' state by displacing the TL.

Conclusions:

  • TL refolding is essential for RNA polymerase catalysis.
  • A two-step preinsertion/insertion mechanism for substrate loading may be universal.
  • The preinsertion state is a potential target for novel antibiotics.