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DNA microchips are small wafers that contain thousands of short DNA probes, about 20 or so nucleotides in length. They all correspond to genes. By washing cell extract over the microchip, those genes being actively synthesized will anneal to their complimentary probe due to sequence specificity. They
anneal to form a small double helix, and the presence of an annealed product can be measured by optical absorbance.
Recently in one of my genomics lectures, the prof said that they don't work as well as people often think, because of the difference in base pair binding. A-T pairs bind with 2 hydrogen bonds, while G-C pairs bind with 3, meaning a probe with large amounts of G-C content would hybridize more strongly than a largely A-T probe, because of the greater number of H-Bonds. Thus, it is hard to find a common temperature for the experiment if both of these kinds of probes are on one chip.
My suggestion here is to make modifications to Guanosine (G) and Cytosine (C) to produce new nucleotides. These are incorporated into the DNA probes in the place of G and C. The modifications result in only 2 H-bonds between modified G and cellular C, and vice versa. Alternatively, probe G and C could be made bulkier to produce steric interference while still retaining their 3 H-bonds with cellular C/G, effectively raising the energy state of hybridized C-G to that of A-T.
Making G-C binding energy comparable to A-T binding energy reduces restrictions placed on probe sequences.
The only problem here is that I don't have the organic chemical knowledge or mathematical tools to accurately compute what a change in one atom would do to the energy of hybridization. My first guess would be to replace N-5 in cytosine with Carbon, and the complimentary Nitrogen in Guanosine with Carbon as well.
O-Chemists...any ideas? (Mr angel chaser, I'm looking at you.)
Diagram showing the base pairs. [Cuit_au_Four, Apr 12 2008]
a liquid crystal chemical structure
just tether the amino acid to this n apply charge; study if it affects affinity [beanangel, Apr 14 2008]
water with magnet plus lipid is an order opportunity
gorgeous photo of water with magnet [beanangel, Apr 14 2008, last modified Feb 04 2012]
Electronic control of hybridisation [MaxwellBuchanan, Apr 14 2008]
||Yo [Cuit]. An excellent idea, but alas
extensively baked, or at least
undergoing baking. People have tried
modifying all the bases to make the
annealing temperatures more uniform,
with limited success. Other strategies
have included modifying the buffer
conditions (to favour A/T pairing and
make it more similar in energy to G/C
pairing), and also replacing some bases
with 'universal' bases, leaving the other
bases unaltered to confer specificity.
Some of this work goes back to the late
80's/early 90's when "sequencing by
hybridisation" was being tried, and
there's been a resurgence of interest
since the blossoming of array
technologies. Similar issues arise in
PCR primer design, and again modified
bases have been tried.
|| As far as I know, success has been
limited. Nowadays, it's more usual to
put the effort into probe selection (since
you normally have a wide choice of
available sequences for any given target
region) to try to achieve uniform Tm's.
||Also, factors other than base
composition can greatly affect
hybridisation. Secondary structure and
"base stacking" (interactions along the
strand rather than between strands) can
have considerable impacts.
||An excellent idea, nevertheless.
||(feels desperately inadequate to address this idea) Um.... I think if we use pulleys and add in a few spacer washers it should work.
||as ignorant as this will sound has
anyone tried either liquid crystals
decorated with nucleotides that can
have their electron density graph
adjusted with a
current like liquid crystals
||basically with liquid crystals the
molecular fronds plump or cluster or
compress with charge application; with
repeated testing this effect might
provide either the electron density
graph modification to equalize the (CG)
(AT) difference or actually slightly
sequester, kind of hide reminiscent of
protein, the (CG) (AT)ness to equality
||another possibility is putting a
teeny electric circuit with each dot of
the array to see if electrochemistry has
the desired effect
||then, just to be wild you could try
magnetism yep view [link] where
diamagnetic water migrates to the side
of a glass with a giant magnet; the
hydration pattern around (CG)(AT) is
certainly modifiable with magnetism but
you gotta view the [link]
||a blend of diamagnetic water with
another solvent could create
nonthermal magnetically wiggleable
amino acid reaction points
||rather than run the reaction at a
temperature to use thermal motion to
produces links you'd vibrate a
diamagnetic plus paramagnetic solvent
||Oddly enough, that has been tried.
There's a company called Nanogen that,
maybe 8 or 10 years ago, developed a
chip consisting of a set of
An applied voltage could be used to
attract an oligo to each pad, where it
could be attached chemically to act as
the target (thereby potentially
simplifying the step of making the
||More significantly, the applied voltage
could then also be used to attract the
probe to specific targets on the array,
or to drive the probe away, thereby
providing a sort of electronic control
over hybridisation stringency.
||I don't think they have as high a feature
density as conventional arrays, but the
voltage control is a neat trick. See link.
||I recently read a patent that used 0 to 100 micronewtons of force to do PCR cycling rather than warm cool cycles. I wonder if that would work with a blend of diamagnetic water with another solvent could create nonthermal magnetically wiggleable amino acid reaction points to create magnetic PCR
||It could go with genechips if the genechips had their ligands on lipid c-c-c-c-c-c-c-c-c-c-c-c-c-c thingies giving the gene chip the ability to be electronically (magnetically) contrast enhanceable
||What was the patent? And how was the force