January 31, 2008

Artificial letters added to the four natural DNA bases

Two artificial DNA "letters" that are accurately and efficiently replicated by a natural enzyme have been created by US researchers. Adding the two artificial building blocks to the four that naturally comprise DNA could allow wildly different kinds of genetic engineering, they say.

This combines with the previous articles about using DNA to assemble millions of three dimensional nanoparticles, being able to synthesize strings of DNA over 500,000 base pairs long and all molecular programmable DNA construction.

I would say that the combined work indicates that we are completely within the age of DNA nanotechnology (using DNA for programmatic molecular control and construction).

As these processes are further mastered, there is the potential to quickly scale up to rapid construction of many trillions of components (various nanoparticles and strands of DNA).

The ability to scale these approaches is illustrated by : The world’s first gene detection platform made up entirely from self-assembled DNA nanostructures has been made. The other interesting aspect is to generalize the techniques used to rapidly create 100 trillion reactive and functional DNA components with easily readable results.

Frustrated by the slow pace designing and synthesising potential new bases one at a time, Romesberg borrowed some tricks from drug development companies. The resulting large scale experiments generated many potential bases at random, which were then screened to see if they would be treated normally by a polymerase enzyme.

With the help of graduate student Aaron Leconte, the group synthesized and screened 3600 candidates. Two different screening approaches turned up the same pair of molecules, called dSICS and dMMO2.

The molecular pair that worked surprised Romesberg. "We got it and said, 'Wow!' It would have been very difficult to have designed that pair rationally."

But the team still faced a challenge. The dSICS base paired with itself more readily than with its intended partner, so the group made minor chemical tweaks until the new compounds behaved properly.

We probably made 15 modifications," says Romesberg, "and 14 made it worse." Sticking a carbon atom attached to three hydrogen atoms onto the side of dSICS, changing it to d5SICS, finally solved the problem. "We now have an unnatural base pair that's efficiently replicated and doesn't need an unnatural polymerase," says Romesberg. "It's staring to behave like a real base pair."

The team is now eager to find out just what makes it work. "We still don't have a detailed understanding of how replication happens," says Romesberg. "Now that we have an unnatural base pair, we are continuing experiments to understand it better."

In the near future, Romesberg expects the new base pairs will be used to synthesize DNA with novel and unnatural properties. These might include highly specific primers for DNA amplification; tags for materials, such as explosives, that could be detected without risk of contamination from natural DNA; and building novel DNA-based nanomaterials.

More generally, Romesberg notes that DNA and RNA are now being used for hundreds of purposes: for example, to build complex shapes, build complex nanostructures, silence disease genes, or even perform calculations. A new, unnatural, base pair could multiply and diversify these applications.

The most challenging goal, says Romesberg, will be to incorporate unnatural base pairs into the genetic code of organisms. "We want to import these into a cell, study RNA trafficking, and in the longest term, expand the genetic code and 'evolvability' of an organism."

Scripps Research Institute

Romesberg Lab

Expanding the genetic alphabet

Unnatural base design and characterization

The Kool research group


Snake Oil Baron said...

Fascinating work.