Complex biochemical circuit engineered
Our very first idea was inspired by the spirit of engineering within us. We aimed to develop a synthetic biochemical circuit that could be introduced into a clinical blood sample, detect the levels of a variety of molecules in the sample, and integrate that information into a diagnosis of the pathology.
Gates were to made from pieces of either short, single-stranded DNA or partially double-stranded DNA in which single strands stick out like tails from the DNA's double helix. The single-stranded DNA molecules act as input and output signals that interact with the partially double-stranded ones.
Given the appropriate conditions; an incoming strand with the right DNA sequence would zip itself up to one strand while simultaneously unzipping another, releasing it into solution and allowing it to react with yet another strand.
Circuits with their approach, but the largest - containing 74 different DNA molecules - can compute the square root of any number up to 15 (technically speaking, any four-bit binary number) and round down the answer to the nearest integer. The calculation takes about 10 hours, so it won't replace your laptop anytime soon. But the purpose of these circuits isn't to compete with electronics.
The molecular signals are never entirely on or off, as would be the case for ideal binary logic. But the new logic gates are able to handle this noise by suppressing and amplifying signals - for example, boosting a signal that's at 80 percent, or inhibiting one that's at 10 percent, resulting in signals that are either close to 100 percent present or nonexistent.
Ph based sensors
Forces of attraction and repulsion existing between certain nano-molecules and bio-molecules lead us to our next idea. These forces exist because of charge on nano-molecules and the amphiprotic nature of bio-molecules such as proteins. The nature of the force depends upon the ph of the medium.
We proposed to make design a dna structure which would be negatively charged as in accordance with the properties of dna and incorporate a drug into it as payload. For example in case of acidity, the ph sensitive structure would undergo a conformational change and release the drug into the affected environment.
Intra cellular imaging
We intended to use the ability of dna to enter a cell by transformation to tag the dna at an early stage of cell development.
We planned to anchor single stranded dna on a gold nano-particle and the complementary strand is affixed onto another such gold nano-particle. When the two strands bind, the nano-particles come close to each other and move further apart on the unbinding of the corresponding strands. This movement of the gold nano-particles can be traced and can be developed into a technique of intra cellular imaging.
A nanotribometer gives a measure of the friction forces (stiction) involved. Our goal was to make use of hydrogen bonding involved in dna in order to measure this force or in other words to design a dna based meter to measure stiction.
Dendrimers are branched tree shaped nanoparticles, which have an immense potential for use in clinical diagnostics and therapeutics. Researchers have also developed nano-particles called tecto-dendrimers which are formed by attaching different types of dendrimers with each other through their branches. Our ambition was to design tecto-dendrimers using dna strands.
Gates and switches out of dna
For making a switch at a molecular level; all that is needed is a configurational or constitutional change. In case of dna the change in question can be conversion from b-form (right handed) to z-form (left handed) in the presence of cobalt hexamine. This change according to us would have enabled the development of a switch.