Related Experiment Video
Updated: Jul 30, 2025
08:59
DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications
Published on: September 27, 2019
11.6K
Enzyme Cascade Reactions on DNA Origami Scaffold
Eiji Nakata1, Huyen Dinh1, Peng Lin1
1Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
Methods in Molecular Biology (Clifton, N.J.)
|May 11, 2023
Summary
Researchers developed DNA scaffolds to assemble multi-step enzyme cascade reactions. This method organizes enzymes from the xylose metabolic pathway for efficient biochemical processes.
Area of Science:
- Biochemistry
- Molecular Biology
- Synthetic Biology
Background:
- Enzyme cascade reactions are crucial for metabolic pathways.
- Organizing enzymes spatially can enhance reaction efficiency.
- DNA nanotechnology offers a platform for precise molecular assembly.
Purpose of the Study:
- To describe protocols for constructing enzyme cascade reaction systems on DNA scaffolds.
- To demonstrate the assembly of two-step and three-step enzyme cascades.
- To utilize a natural metabolic pathway (xylose) as a model system.
Main Methods:
- Enzyme cascade reactions were adapted from the xylose metabolic pathway.
- Two-step and three-step cascades were designed.
- DNA binding adaptors were used to assemble enzymes onto a DNA scaffold.
Main Results:
- Successful construction of enzyme cascade systems on DNA scaffolds.
- Demonstration of organizing enzymes from a natural metabolic pathway.
- Adaptors facilitated the assembly of multi-step enzymatic reactions.
Conclusions:
- DNA scaffolds provide a versatile platform for enzyme cascade construction.
- This approach enables the spatial organization of enzymes for enhanced function.
- The described protocols are applicable to various metabolic engineering and synthetic biology applications.
Related Concept Videos
02:37Restarting Stalled Replication Forks
5.9K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.9K
02:02DNA Topoisomerases
31.5K
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. ...
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
31.5K
00:55DNA Helicases
21.6K
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...
21.6K
03:01The Replisome
34.0K
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
34.0K
02:31Homologous Recombination
50.7K
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...
50.7K
01:02The DNA Replication Fork
36.2K
An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
36.2K