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Related Concept Videos

Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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The DNA Helix01:16

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Related Experiment Video

Updated: May 12, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

RNA structure determination using nuclease digestion.

Timothy W Nilsen

    Cold Spring Harbor Protocols
    |April 3, 2013
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces a method for mapping RNA structures using commonly available ribonucleases (RNases). This technique helps determine RNA secondary structures and protein-binding potential.

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    Analyzing and Building Nucleic Acid Structures with 3DNA
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    Analyzing and Building Nucleic Acid Structures with 3DNA

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    Published on: December 9, 2022

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    Analyzing and Building Nucleic Acid Structures with 3DNA
    16:24

    Analyzing and Building Nucleic Acid Structures with 3DNA

    Published on: April 26, 2013

    Area of Science:

    • Molecular Biology
    • Biochemistry

    Background:

    • Determining RNA structure is crucial for understanding RNA function, including protein interactions and structural similarities between sequences.
    • Many ribonucleases (RNases) previously used for RNA structure mapping are no longer available.

    Purpose of the Study:

    • To present a method for mapping RNA structures using readily available RNases.
    • To enable parallel analyses of single- and double-stranded RNA regions.

    Main Methods:

    • Utilizing three common RNA endonucleases: RNase T1 (single-stranded specific), RNase V1 (double-stranded specific), and RNase I.
    • Initiating RNA cleavage with RNases, terminating with aurintricarboxylic acid, and detecting cleavage products via denaturing polyacrylamide gel electrophoresis.
    • Employing H2O as a mock-treated control.

    Main Results:

    • Demonstrated the utility of RNase T1 and RNase V1 for distinguishing between single- and double-stranded RNA regions.
    • Established a reliable method for RNA structure probing using accessible enzymes.

    Conclusions:

    • The described method provides a robust approach to RNA structure determination using commonly available RNases.
    • This technique facilitates the assessment of RNA-protein interactions and comparative structural analysis.