Uses in DNA super computers? (Score 2)

DNA is trivially custom-synthesized on solid supports. You rig chromophores or fluorophores to form Watson-Crick dimers instead of ATCG and roll rigid chromophore configuration and custom ordering any way you want. Bridge the base pairs with hydrogen bonding, dipole alignment, hydrophobic effects... be a chemist. We already have evidence of anomalous electronic conductivity in ordinary DNA (depends on base composition, which is a veeeery good sign). Want longer molecules? DNA-ligase and whatever. Let the enzymes do the fine work. After you get your Nobel Prize you want to manufacture, and you DON'T do it solid phase. You do it PCR with custom (patentable) templating. I bet you bust the conventional and closely held PCR application patents, too. GROW THE SUPERCONDUCTORS in bugs! Spinoff of fluorescent DNA and RNA probes for genome sequencing and clinical diagnostics ane therpaeutics - re photodynamic therapy targeted to oncogenes (especially gene hyper-repeat sequences).

Why use crappy phosphate-deoxyribose alt-copolyester? Peptide nucleic acids are vastly more robust and give you optional chiral centers for more goodies, like non-linear optical devices.

Hell, make a PNA 17-25 mer cocktail complimentary to a few critical HIV gene sequences and cure that, too, by knockout strategy (the Flavr-Savr HIV therapy). PNAs are uncharged and readily permeate cell membranes, they are totally untouched by nucleases and other catabolisms, and they are cheap to make. Turn off HIV RNA, turn off disease process progression. Boom. None of this downstream small molecule enzyme inhibitor bullshit that makes so much money for the pharm workers.

Original proposal is an interesting problem, and rather a small proportion of the population is up to it. When I started out in the business some 30 years ago, the process of discovery and original proposal awed me. It still does, and my track record has been exemplary. Perhaps the best answer is that you must read everything and be prepared for things to bump around in your head.

Example: My first original research proposal was to synthesize an obscure polycyclic alkaloid (in 32 steps! Silly synthesis is the refuge of a scoundrel) An ocean of blood flowed, and all of it was mine save for one redeeming skeletal inversion which was deemed "adequate." The next year, for my second original proposal, I proposed synthesizing C2 in cryogenic matrix and gas phase. C2 is hot stuff (literally) in flames and comet tails (Schwan lines), and its electronic structure was uncomputable at the time. When you warm the matrix fragments recombine to give acetylene diethers - which had not been synthesized at that time. The diethers dimerize to a squaric acid precursor, which was hot stuff re squarylium dyes for photoconductors. The tar from the reaction was worth at least ten times the cost of starting materials.

Know everything, and see where stuff rubs.

Almost any ten-carbon lump turns into adamantane in aluminum chloride/bromide slush. We can do better (though not cheaper) in ionic solvents like N-methl-N-(n-butyl)imidazolium tetrachloroaluminate with up to another added mole of AlCl3. The media support multiple carbocationic rearrangeents as a benign environment. What happens if you put micronized graphite into the slush and bubble in isobuytlene? Will you edge alkylate and solublize, or make 1-D tert-butylated diamond plates, or will something else happen? Look at all the applications of graphite fluoride and graphite intercalcates, as in high energy density battery systems and high number density low bulk mass hydrogen storage modalities.

Sargeson trapped Co(en)3(3+) as the inspired sepulchrate (formaldehyde plus ammonia), and then the brilliant sarcophogate (formaldehyde plus nitromethane; look down the triangular face of the coordination octahedron). Stop being an inorganiker and start being an organiker. That last gives you "para" nitro groups, which give you amines, which give you redox nylon (and azo linkages; polyisocyanates, polyurethanes, epoxies, acrylamides, and...) Nitrogen chemistry is incredibly rich - conjugated azo linkages, fluorescent heterocycles, stable free radicals, extrusion and caged radical recombination... As Co(en)3(3+) is trivially optically resolved, you also have potential non-linear optical films switchable through redox change. (Information storage, chemical transistors, sensors, clinical diagnostics, electrochromic windows...) It goes on and on... a whole lifetime of research. Nobody has diddled with it.

Look up the synthesis and reactions of of hydroxlyamine-O-sulfonic acid in Volume 1 (!) of Fieser and Fieser. Look at the mysteries of ammonia - inversion, nucleophilicity. Look at the Alpha Effect re hydrazine, hydroxylamine, and hydrogen peroxide. Look at Bredt's rule and all the interesting things it does at bridgeheads. Now, make it all rub against itself: Start with 1,4,7-triazacyclononane, which is easy enough though sloppy to make in bulk. Gently nitrosate it. The nitroso group goes on the first amine, then the adjacent amine (pre-organized to attack re Cram) attacks at the nitroso nitrogen to give you the hydroxylamine. Do the usual hydroxylamine-O-sulfonic acid synthesis and you tether the original nitroso nitrogen to the third amine with the original nitroso's oxygen as the leaving group. What have you got? You have four bridgehead nitrogens rigidly held, none of which can invert. The apical nitrogen is tethered only to other aliphatic nitrogens - which has never been done. It cannot invert and... for all that, it may have no nucleophilicity whatsoever because the Alpha Effect is euchered out by geometry and inductive electron withdrawal is mammoth. You could do it in undergrad lab.

I once watched a bunch of engineers with a very big budget try to excimer laser drill parallel or serial hundreds of 5 micron holes in PMMA intrastromal corneal implants (without the holes to move oxygen from outside and nutrients from inside the cornea dies and sloughs, which is tough on the rabbits). Buncha maroons. 5 microns is a magic number to an organiker, and I won't insult your intelligence with the trivial solution. The next Tuesday I delivered a foot-long bar of oriented two-phase PMMA which was cut and polished to spec, had its holes revealed, and got me into incredible hot water since my employer did not give shit one about the product but was really interested in the long term money budgeted by its parent company.

Take two cyclopentane rings (Framework Molecular Models do this nicely). Put 5 all-cis (vs the ring not olefin configuration, which need only be consistent) alkenes on one cylcopentane. Cap with the other. Now, twist slightly and watch the pi-oribtals. Is that a clever way to make dodecahedrane, or what? The alkenes came from alkynes. The alkynes were assembled with Schrock alkyne metathesis catalyst from the nitriles. Strain being what it is, you might want to have diacetylene linkages (copper-mediated oxidative coupling) and go for a bigger hydrocarbon bubble. Start with all-cis 1,3,5-cyclohexane and trace the diacetylene evolution (no strain here!) Consider 1,3,5-trans-2,4,6 all cis-substituted cyclohexane). Voila! You grow 1-D diamond (note the ring conformation and the special name given to that diamond structural variant).

I could go on for megabytes. All you need do is read the library, hold it all in your head, and wonder "what if..." where stuff rubs together. This is the first (easy) kind of genius. The second (hard) kind of genius is to see it all ab initio. I don't have a handle on that one.