Double-stranded DNA must disentangle itself into single strands during replication or repair to allow functional molecules to bind and perform their various operations. Cellular proteins specifically bind to single-stranded DNA to prevent their premature recombination.
Unfortunately, detailed studies of these DNA–protein interactions have been hindered by the need for expensive instrumentation and time-consuming labelling techniques. Yen Nee Tan at the A*STAR Institute of Materials Research and Engineering and co-workers1 have now developed a convenient method to characterize the interactions between single-stranded DNA and their binding proteins.
The researchers used the optical properties of gold nanoparticles to probe the mechanism of protein–DNA binding. When the nanoparticles were well dispersed in solution, they yielded a bright red color, but when aggregated, the solution changed to blue. Tan and co-workers discovered that when single-stranded DNA and its binding protein were both present in the solution, coupled with a salt that stimulates nanoparticle aggregation, the DNA remained red in color, indicating that the DNA–protein complexes had bound with the nanoparticles through electrosteric stabilization forces. In contrast, when the protein or single-stranded DNA was introduced alone in the salt solution, there was a greater shift to the blue-grey color, indicating nanoparticle aggregation (see image).
“The greatest challenge in this work was to determine the optimum conditions for single-stranded DNA to bind with its binding protein to form complexes that confer the highest stability to gold nanoparticles from salt-induced aggregation,” says Tan.
The researchers attribute binding of the nanoparticles and the DNA–protein complexes to the presence of sulphur-containing groups in the protein, which are known to create strong bonds with gold. The protein molecules alone are smaller in molecular size than the protein–DNA complexes, leading to a less effective steric stabilization of the nanoparticles.
Tan and co-workers showed that there was a minimum length of DNA sequence under which the binding protein–DNA adhesion mechanism could operate. They found that the binding protein had a preference for binding to specific chemical units (bases) which make up DNA, and were able to spot DNA sequence variations, called single nucleotide polymorphisms (SNPs), even at the extreme ends of the molecule which are difficult to identify. Double-stranded DNA with SNPs cannot bind together so closely. The binding protein can thus attach to the dissociated single-stranded DNA to form protein–DNA complexes, offering sites to which gold nanoparticles can adhere.
“We plan to further develop this assay into a hassle-free genotyping assay to detect SNPs in real biological samples containing long genomic DNA,” says Tan.
The A*STAR-affiliated researchers contributing to this research are from the Institute of Materials Research and Engineering
Further reports about: > DNA > DNA sequence > DNA–protein > Ferchau Engineering > Nanotechnology > Probing > SNP > double-stranded DNA > gold nanoparticle > materials research > protein complexes > protein molecule > protein–DNA complexes > single nucleotide polymorphism > single nucleotide polymorphisms > single-stranded DNA
Complementing conventional antibiotics
24.05.2018 | Goethe-Universität Frankfurt am Main
Building a brain, cell by cell: Researchers make a mini neuron network (of two)
23.05.2018 | Institute of Industrial Science, The University of Tokyo
A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.
The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...
At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.
At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...
There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?
At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...
So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics
Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...
The historic first detection of gravitational waves from colliding black holes far outside our galaxy opened a new window to understanding the universe. A...
02.05.2018 | Event News
13.04.2018 | Event News
12.04.2018 | Event News
24.05.2018 | Physics and Astronomy
24.05.2018 | Health and Medicine
24.05.2018 | Life Sciences