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Ribozymes02:47

Ribozymes

12.8K
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can...
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Ribozymes02:47

Ribozymes

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DNA Isolation01:24

DNA Isolation

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Restriction Enzymes01:11

Restriction Enzymes

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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.
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Introduction to Enzymes01:22

Introduction to Enzymes

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The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...
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Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

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The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
 
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Related Experiment Video

Updated: Nov 2, 2025

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
09:12

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

Published on: September 16, 2019

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Single-round deoxyribozyme discovery.

Tereza Streckerová1,2, Jaroslav Kurfürst1,3, Edward A Curtis1

  • 1Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic.

Nucleic Acids Research
|June 16, 2021
PubMed
Summary
This summary is machine-generated.

Researchers developed a simpler method to discover new catalytic DNA (deoxyribozymes) and RNA motifs. This approach uses smaller DNA libraries and high-throughput sequencing, accelerating the discovery of functional nucleic acid sequences.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Synthetic Biology

Background:

  • Artificial evolution experiments typically require large sequence libraries (∼10^15) and multiple selection rounds to identify functional nucleic acid variants.
  • The catalytic potential of DNA architectures (deoxyribozymes) is an area of interest for developing novel biocatalysts.

Purpose of the Study:

  • To investigate if functional DNA motifs can be isolated from significantly smaller libraries in a single selection round.
  • To test the hypothesis that simple DNA structures can yield catalytic activity when embedded within a scaffold.

Main Methods:

  • Designed DNA libraries with 12 or 15 randomized positions within a fixed scaffold.
  • Applied a single round of selection based on self-cleavage at an RNA linkage in the presence or absence of lead ions.
  • Purified active deoxyribozymes using PAGE and characterized them via high-throughput sequencing.

Main Results:

  • Identified deoxyribozymes with catalytic activities 8- to 30-fold lower than those from larger libraries.
  • Demonstrated that a less diverse pool (smaller library) can still yield functional motifs with a surprisingly small disadvantage.
  • Elucidated sequence requirements and secondary structures of the selected deoxyribozymes without additional experiments.

Conclusions:

  • A simplified approach using smaller DNA libraries and high-throughput sequencing can efficiently discover new catalytic DNA motifs.
  • This method accelerates the discovery of functional nucleic acid enzymes, reducing the need for extensive library sizes and multiple selection rounds.
  • The findings suggest broader applicability for discovering novel DNA and RNA catalytic motifs.