Related Experiment Video
Updated: Jun 20, 2026
05:33
Using Modified Synthetic Oligonucleotides to Assay Nucleic Acid-Metabolizing Enzymes
Published on: July 5, 2024
DNA-catalyzed sequence-specific hydrolysis of DNA
Madhavaiah Chandra1, Amit Sachdeva, Scott K Silverman
1Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Nature Chemical Biology
|August 18, 2009
Summary
Researchers developed novel deoxyribozymes (DNA enzymes) capable of sequence-specific DNA hydrolysis. These DNA catalysts exhibit high efficiency and require specific metal ions, mimicking natural bimetallic enzymes.
Area of Science:
- Biochemistry
- Molecular Biology
- Catalysis
Background:
- Deoxyribozymes (DNA catalysts) are known to cleave RNA phosphodiester bonds.
- Cleavage of peptide or DNA phosphodiester bonds by deoxyribozymes is significantly more difficult.
- Natural DNA nucleases often function as bimetallic protein enzymes.
Purpose of the Study:
- To identify novel deoxyribozymes capable of sequence-specific DNA hydrolysis.
- To characterize the catalytic efficiency and metal ion requirements of these DNA catalysts.
Main Methods:
- In vitro selection was employed to discover new deoxyribozymes.
- Catalytic activity and sequence specificity for DNA hydrolysis were assessed.
Main Results:
- Novel deoxyribozymes that sequence-specifically hydrolyze DNA were identified.
- These deoxyribozymes demonstrated multiple turnover capability.
- A significant rate enhancement (10^8 to 10^14) was observed for DNA cleavage.
- The DNA catalysts require both manganese (Mn2+) and zinc (Zn2+) ions for activity.
Conclusions:
- The discovery of deoxyribozymes that cleave DNA expands the known catalytic capabilities of DNA.
- The requirement for bimetallic cofactors (Mn2+ and Zn2+) highlights a parallel with natural metalloenzymes.
- These findings open new avenues for DNA-based catalysis and molecular tools.
Related Concept Videos
01:05Maxam-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...
Challenges of the Maxam-Gilbert Method
The...
02:25Overview of DNA Repair
In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
Chemically...
00:55DNA Helicases
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
02:02DNA Topoisomerases
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
01:03Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...