Light games with DNA

The diagnosis of hereditary diseases and the identification of genetic fingerprints hinge on high-sensitivity DNA imaging biotechnologies. These imaging tools detect specific genes in cells using fluorophores—fluorescent tags that can illuminate DNA structures—and quenchers that interact with these tags to prevent them from emitting light, effectively working as an ‘off switch’.

In a development that expands the detection toolbox and the genetic alphabet, a team led by Ichiro Hirao from the RIKEN Systems and Structural Biology Center, Yokohama, has now designed an artificial base pair between a fluorophore (Dss) and quenchers (Pn and Px)¹. This method incorporates the pair into complementary DNA strands using polymerases and demonstrates that either Pn or Px can decrease the fluorescence of Dss upon hybridization.

Hirao and his team previously developed artificial base pairs involving Dss because of its strong fluorescence, which could illuminate DNA and RNA structures. “This time, we can put out the candle lit by Dss using the quencher as its pairing partner at will,” he says.

Hirao notes that this ability is unique because fluorescent dye Dss and quencher Pn face each other on their respective ssDNA strand, forming an artificial DNA base pair that also works in biological systems. He says that this close proximity results in strong ‘contact quenching’ of the fluorophore.

Usually, researchers have attached fluorophores and quenchers to natural bases through a linker that mediates so-called fluorescence resonance energy transfer (FRET) between dyes. However, this process lacks efficiency compared to contact quenching. Also, according to Hirao, unlike the Dss–Pn system, typical fluorophore–quencher pairs cannot be introduced at specific positions in DNA strands using polymerases, limiting their applications.

After establishing that the pairs were compatible with natural DNA synthesis techniques, Hirao’s team integrated the Dss–Pn pair in the stem of molecular beacons—hairpin-shaped single-stranded DNA (ssDNA) structures that fluoresce upon hybridization with DNA targets. They found that the beacons detected the targets with high sensitivity and differentiated ssDNA containing one mismatched base.

Next, the researchers tested the performance of Dss–Px in polymerase chain reaction (PCR)—a powerful DNA amplification technique. Dss-bearing ssDNA fragments became less fluorescent upon assimilation of Px into synthesized DNA chains, allowing the team to monitor the amplification process in real time.

“One of our present tasks is to apply this system to in vivo cell experiments,” says Hirao. “If it is possible, we will be able see the on–off of a specific gene expression.”

The corresponding author for this highlight is based at the Nucleic Acid Synthetic Biology Research Team, RIKEN Systems and Structural Biology Center

Journal information

1. Kimoto, M., Mitsui, T. Yamashige, R., Sato, A., Yokoyama, S. & Hirao, I. A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology. Journal of the American Chemical Society 132, 15418–15426 (2010).

Media Contact

gro-pr Research asia research news

All latest news from the category: Life Sciences and Chemistry

Articles and reports from the Life Sciences and chemistry area deal with applied and basic research into modern biology, chemistry and human medicine.

Valuable information can be found on a range of life sciences fields including bacteriology, biochemistry, bionics, bioinformatics, biophysics, biotechnology, genetics, geobotany, human biology, marine biology, microbiology, molecular biology, cellular biology, zoology, bioinorganic chemistry, microchemistry and environmental chemistry.

Back to home

Comments (0)

Write a comment

Newest articles

Lighting up the future

New multidisciplinary research from the University of St Andrews could lead to more efficient televisions, computer screens and lighting. Researchers at the Organic Semiconductor Centre in the School of Physics and…

Researchers crack sugarcane’s complex genetic code

Sweet success: Scientists created a highly accurate reference genome for one of the most important modern crops and found a rare example of how genes confer disease resistance in plants….

Evolution of the most powerful ocean current on Earth

The Antarctic Circumpolar Current plays an important part in global overturning circulation, the exchange of heat and CO2 between the ocean and atmosphere, and the stability of Antarctica’s ice sheets….

Partners & Sponsors