Biomod/2011/IITM/AcidArtists/Brainstorming

Complex biochemical circuit engineered

Summary 1) in the future a synthetic biochemical circuit 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. 2)Now gates are 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. 3)The molecules are just floating around in solution, bumping into each other from time to time Occasionally, an incoming strand with the right DNA sequence will zip itself up to one strand while simultaneously unzipping another, releasing it into solution and allowing it to react with yet another strand 4)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; 5) 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.

Comments: [1]Seems like a good idea. Plus, circuitry means mathematical modelling. You guys might be interested in this for the future too. Nice work Amit.

Also, what is DNA Origami's contribution here? Is it to make the molecules that are part of the circuit? [2] This looks great! I am glad we are already looking around and brainstorming ideas--I have been looking into methods similar to those described below as well as they seem very promising

Mini-Time-Controlled-Reactor

Summary Can we make a structure which is like a mini-time-controlled-reactor? Maybe we can make a nano scale structure which has 2 compartments containing reactants, which open on our signal. This can have many applications... for e.g. [a random idea] if some drug needs to be such that only freshly made compounds are effective, we can load then in our machinery and make sure that they react when we want them to.....

Ph based sensors

In nanotech there are nano materials which can attract as well as repel bio molecules. Nano particles are charged particles and as bio molecules such as proteins have amphiprotic nature and so depending on the ph of the medium, it can either attract or repel the bio molecule. What if we can make some structure out of DNA(net charge negative as DNA is negatively charged) and has some drug as its payload. One of the applications of such a DNA nano material which we could think is a drug which can cure acidity. As Ph is low so there will be net positive charge on the bio molecules which in turn will get attracted towards our DNA nanomaterial and the drug will destroy the bio molecule.

Water Purification

Now a day’s water is purified using gold nano tubes ( core has Au(0), surface has Au(I) and coordinated with citrate to give an overall negative charge). If we can make some structure and use gold as a payload on DNA maybe we can purify water.

Bio molecules and Nobel metal nano particle forms nano-bio conjugates

Depending upon the size of the bio molecule aggregates are formed. And these aggregates give specific colour to the solution. As DNA has polymerization property so it might give colour to a solution.

Enzyme catalysis

DNA-protein interaction is well known. Can we use this property so as to increase the efficiency of an enzyme.

Intra cellular imaging

As DNA can easily enter inside a cell by transformation, we can use this property of DNA to tag a cell at early stage of development.

Single stranded DNA is anchored on a gold nano particle and the complementary strand is anchored on another gold nanoparticle. When the two DNA strands bind, the nano particles come close to each other and when they unbind they again move further apart. This can be of great use.

Contraption using DNA nanotech

We will achieve a specified goal using parts made up of DNA. For example in my last post I introduced a way of aggregating nanoparticles (Single stranded DNA is anchored on a gold nano particle and the complementary strand is anchored on another gold nanoparticle). When gold particles aggregate u get to see some colour in the solution and this change in colour can be used to do some other step using ( some light sensitive sensor). Like this after a series of steps we will finally achieve our goal.

Nanotribometer

Nanotribometer gives the measure of the friction force( stiction). We can make use of hydrogen bonding in DNA to measure this force or in other words a meter made up of DNA to calculate stiction.

Dendrimers

Dendrimers are branched tree shaped nanoparticles, which have an immense potential for use in clinical diagnostics and therapeutics. Researchers have also developed nanoparticles called tectodendrimers which are formed by attaching different types of dendrimers with each other through their branches. What if we can make tectodendrimers out of DNA?.

Making Gates and switches out of DNA

We require either conformational change or configurational change or constitutional change in order to make a switch at molecular level. Because DNA can be easily converted from Bform( right handed) to Zform(left handed) by the presence of cobalt hexamine, Can we use this property off DNA to make a switch?

Azobenzene can also be used to make switches. As the incorporation of azobenzene unit into a crown ether gives azacrown molecule. E isomer of azacrown molecule does not have space to accommodate the alkali metal captions whereas Z isomer shows an affinity. Based on similar lines can we make a molecule using azobenzene and DNA, whose one form has different properties then the other form. ( Nikhil has also posted one idea on azobenzene). Gates : A rotaxane contains one or more bead-like components which can be threaded into a rod. A rotaxane has a rod, stoppers and beads. We can make rod, stoppers using DNA and proteins can be used as beads. Using the protein DNA interaction we can make gates. Please read more on rotaxene in order to get a feel of this idea.

Please let me know if I am not making myself clear at any point.