Posted: August 17, 2009

Extending DNA logic gate systems

(Nanowerk News) DNA logic gates can now detect more than just DNA segments, and by exploiting nature's design, their preparation could be simpler than ever.
Atsushi Ogawa and Mizuo Maeda from The Institute of Physical and Chemical Research (RIKEN), Saitama, and Ehime University, Japan, have developed existing DNA logic gate systems to create a detection system where gold nanoparticle aggregation provides a visual marker for a variety of biomarkers (Easy design of logic gates based on aptazymes and noncrosslinking gold nanoparticle aggregation).
3D molecule on logic gate background
Nanoscale logic gates can be made easily using aptazymes and nanoparticles.
Logic gates are used in digital circuits in computer chips. An input signal goes through a binary operation to give either a true (one) or false (zero) output. This system has been mimicked in biology using DNA inputs, outputs and switches. DNA logic gates detect oligonucleotides (short DNA segments) when they bind to the logic gate sensors. This concept has been developed to detect different molecules using aptamers - DNA or RNA molecules adapted to bind to other molecules and viruses. However, both DNA and aptamer logic gates have a drawback in that they rely on a hybridisation switch. When a target molecule binds, or hybridises, to the sensor, the event has to be transmitted to a reporter system, which must be specifically engineered for each sensor-target system.
To avoid the need to design a hybridisation switch, Ogawa and Maeda based their logic gate on a cleavase aptazyme. An aptazyme is an enzyme which naturally produces a response upon interaction with a specific target or marker molecule. The aptazyme can be adapted to respond to virtually any species of interest, from a single ion, to a drug metabolite, which could have implications for medical diagnostic techniques. In this case, when activated by its target molecule, the cleavase aptazyme cleaves a length RNA from its own structure.
The resulting free RNA transmits a signal to a reporter system; here, the pair used gold nanoparticles as reporters. They functionalised them with DNA strands that bind to the free RNA to form a duplex with a blunt end (where the ends of both strands are even rather than one strand being longer than the other). The duplexes facilitate nanoparticle aggregation, which can be seen with the naked eye by clearing of an otherwise cloudy reaction medium.
'We want to apply this method to construct more complex logic gates,' says Ogawa. 'Because the aggregation of gold nanoparticles depends on whether or not DNA on the nanoparticles forms a duplex with the cleaved RNA with a blunt end, we think an appropriate design of the cleaved RNA sequences may make them possible.'
Milan Stojanovic, an expert in diagnostic molecular devices based on nucleic acids, at Columbia University, New York, US, says that the work is an 'important contribution' towards a field that 'has a future if it moves in the direction of autonomous therapeutic devices, rather than towards competing with silicon.'
Source: Reprinted with permission from Chemical Sciences (Katie Dryden-Holt)
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