Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Illuminating the genetic alphabet

28.06.2010
Fluorescent unnatural base pairs light up the structures of DNA and RNA chains with minimal disturbance

The development of fluorescent tags—small, light-emitting molecules attached to DNA strands—has revolutionized cell biology over the past two decades, allowing precise tracking of labeled segments in living systems. Because fluorescent tags project outwards from the nucleic acid chains, they can interfere with the mobility and geometry of their targets, skewing the view of critical biological actions.

Now, a research team led by Ichiro Hirao at the RIKEN Systems and Structural Biology Center in Yokohama has synthesized an unnatural fluorescent base pair system that can be incorporated directly into DNA and RNA molecules1. Because this new addition to the genetic alphabet only minimally disturbs the delicate biochemical functions of cells, it holds great potential for advanced medical techniques such as DNA-based diagnostic testing.

Hirao and colleagues had previously discovered that a fluorescent 2-amino-6-thienylpurine molecule containing a thiophene ring, termed ‘s’, formed a base pair with a pyrrole–aldehyde compound known as ‘Pa’2. The new s–Pa pair could be site-specifically incorporated into RNA chains alongside the natural nucleotides; unfortunately, DNA replication processes with the s–Pa system were not as successful.

To solve this problem, the research team altered the structure of ‘s’, removing the amino group and a nitrogen in the purine ring, then adding an extra thiophene ring to give a new nucleotide, called ‘Dss.’ This highly fluorescent molecule retained the same complimentary base pairing with Pa, and could be easily transcribed into specific RNA positions by cell enzymes. Furthermore, single-nucleotide insertion experiments with Escherichia coli DNA polymerase I revealed that the Dss–Pa pairs could be replicated with nearly the same efficiency as natural bases.

Intriguingly, Dss also acted as a universal base—forming thermodynamically stable pairs with the four natural bases of DNA. Hirao says that the mechanisms of duplex DNA formation and polymerase reactions in replication and transcription with Dss are completely different than for natural systems.

Fluorescent imaging of functional DNA and RNA is becoming increasingly important as researchers seek to understand the conformations of these biopolymers in liquid environments. “The fluorescent intensity of the unnatural bases change greatly depending on the three-dimensional structure—providing a powerful tool to analyze the local structure of DNA and RNA molecules in solution,” says Hirao.

Hirao envisages a wide range of basic and applied technologies arising from these bright new pieces of genetic code. “We are now applying Dss to molecular beacons, realtime PCR, and structural analysis,” he says.

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., Yokoyama, S. & Hirao, I. A unique fluorescent base analogue for the expansion of the genetic alphabet. Journal of the American Chemical Society 132, 4988–4989 (2010)

2. Kimoto, M., Mitsui, T., Harada, Y., Sato, A., Yokoyama, S. & Hirao, I. Fluorescent probing for RNA molecules by an unnatural base-pair system. Nucleic Acids Research 35, 5360–5369 (2007)

gro-pr | Research asia research news
Further information:
http://www.rikenresearch.riken.jp/eng/research/6296
http://www.researchsea.com

More articles from Life Sciences:

nachricht Shrews shrink in winter and regrow in spring
24.10.2017 | Max-Planck-Institut für Ornithologie

nachricht 'Y' a protein unicorn might matter in glaucoma
23.10.2017 | Georgia Institute of Technology

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Salmonella as a tumour medication

HZI researchers developed a bacterial strain that can be used in cancer therapy

Salmonellae are dangerous pathogens that enter the body via contaminated food and can cause severe infections. But these bacteria are also known to target...

Im Focus: Neutron star merger directly observed for the first time

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...

Im Focus: Breaking: the first light from two neutron stars merging

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....

Im Focus: Smart sensors for efficient processes

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...

Im Focus: Cold molecules on collision course

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...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

3rd Symposium on Driving Simulation

23.10.2017 | Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

 
Latest News

Shrews shrink in winter and regrow in spring

24.10.2017 | Life Sciences

Microfluidics probe 'cholesterol' of the oil industry

23.10.2017 | Life Sciences

Gamma rays will reach beyond the limits of light

23.10.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>