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
The birth of a new protein
20.10.2017 | University of Arizona
Building New Moss Factories
20.10.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau
University of Maryland researchers contribute to historic detection of gravitational waves and light created by event
On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...
Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.
Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....
Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).
When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...
Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.
How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...
Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.
It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...
17.10.2017 | Event News
10.10.2017 | Event News
10.10.2017 | Event News
20.10.2017 | Information Technology
20.10.2017 | Materials Sciences
20.10.2017 | Interdisciplinary Research