Design principles for accurate folding of DNA origami
These videos have been matched automatically. Contact us if they are not relevant.
These videos have been matched automatically. Contact us if they are not relevant.
View abstract on PubMed
Summary
This summary is machine-generated.We developed new design principles for accurate three-dimensional DNA origami folding. Optimizing DNA strand routes using a thermodynamic model significantly improved folding accuracy and yield for fabricated shapes.
Area Of Science
- Biotechnology
- Nanotechnology
- Computational Biology
Background
- DNA origami enables precise nanoscale structure fabrication.
- Accurate folding of complex 3D DNA origami remains a challenge.
- Existing design heuristics lack comprehensive thermodynamic considerations.
Purpose Of The Study
- To establish design principles for accurate 3D DNA origami folding.
- To develop a computational framework for optimizing DNA strand routing.
- To improve the yield and reliability of DNA origami self-assembly.
Main Methods
- Reduced DNA strand routing to a shortest-path problem in a weighted graph.
- Employed a thermodynamic model to score DNA strand routes, considering binding, hybridization, and loop closure.
- Analyzed existing and novel design heuristics.
- Fabricated redesigned shapes and assessed folding accuracy via gel electrophoresis and electron microscopy.
Main Results
- Redesigned DNA origami shapes exhibited 6- to 30-fold improvements in folding yield compared to original designs.
- The thermodynamic scoring model effectively predicted and improved folding accuracy.
- Demonstrated the utility of optimizing staple routes for reliable DNA origami assembly.
Conclusions
- Optimized staple routes using the developed model significantly enhance DNA origami folding accuracy.
- The computational framework facilitates the design of complex 3D DNA origami structures.
- This methodology provides a pathway for predictable and high-yield DNA origami fabrication.
These videos have been matched automatically. Contact us if they are not relevant.
These videos have been matched automatically. Contact us if they are not relevant.
Related Concept Videos
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...
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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...
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...
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...