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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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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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Related Experiment Video

Updated: Jan 21, 2026

DNA Stable-Isotope Probing DNA-SIP
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RNA Stable Isotope Probing (RNA-SIP).

Noor-Ul-Huda Ghori1, Benjamin Moreira-Grez1, Paton Vuong1

  • 1Molecular Microbial Ecology Group, The UWA School of Agriculture and Enviornment (SAgE), The University of Western Australia, Crawley, WA, Australia.

Methods in Molecular Biology (Clifton, N.J.)
|August 14, 2019
PubMed
Summary

Stable isotope probing (SIP) uses labeled isotopes to track microbial metabolism and function in environmental samples. This culture-independent technique identifies active microbes and their roles by analyzing RNA incorporation of heavy isotopes.

Keywords:
16S rRNACommunity diversityCommunity functionGradient centrifugationIsotope-labeled substrateRNA-SIP

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Environmental Science

Background:

  • Uncultivated microorganisms play crucial roles in environmental processes.
  • Understanding microbial community composition and function is essential for environmental research.
  • Stable isotope probing (SIP) is a powerful technique for studying microbial activities.

Purpose of the Study:

  • To present a detailed protocol for performing RNA-SIP experiments.
  • To explain how RNA-SIP can identify and characterize uncultivated microorganisms.
  • To demonstrate RNA-SIP's capability in assessing microbiome function.

Main Methods:

  • Utilizing stable isotopes (e.g., carbon, nitrogen) of common elements.
  • Incorporating heavy isotopes into RNA through active microbial metabolism of labeled substrates.
  • Separating labeled RNA from unlabeled RNA using density gradient centrifugation.
  • Identifying and sequencing labeled RNAs to determine microbial identity and function.

Main Results:

  • RNA-SIP successfully labels RNA from metabolically active microorganisms.
  • Density gradient centrifugation effectively separates labeled from unlabeled RNA.
  • Sequencing of labeled RNA provides insights into microbial community composition and function.
  • This method allows for the study of uncultivated microbes in environmental samples.

Conclusions:

  • RNA-SIP is a robust, culture-independent method for linking microbial identity to function.
  • The technique provides simultaneous information on microbiome composition and metabolic activity.
  • Detailed protocols for RNA-SIP experiments enhance its applicability in environmental microbiology.