I am researching DNA profiling and wanted to know what technologies
could be used for transcription of the DNA sequence of a living
subject via a ?micro single-use apparatus?. In short the method would
read the sequence (STR or SNP) of the DNA for identification purposes.
 It is my understanding that the development of nano scale probes for
visualization of DNA would allow the reading of the transcription of
the DNA.  What current or planned technologies would be applicable to
this?

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Clarification of Question by dnaid-ga on 07 Jul 2004 15:37 PDT

Working backwards, I am trying to find out what techniques are
available or are in development for determining the DNA sequence (DNA
profile, DNA fingerprint, SNP, or STR; i.e. just enough for a unique
identification) using a single MEMS device, microfluidic or otherwise.
 A related piece of information that would be very valuable is the
size (i.e. 1Mb) of the DNA sequence data required for unique
identification similar to the standards used in forensic testing.

The subject area of the answer is similar to the information contained
in the link below however the presentation is too broad:

http://www.cnsi-uc.org/events/nanoseminar/nanoseminar_spring04.htm#1

The question is pretty speculative, so I think people will have a
difficult time answering it. What I think you want to know is "what
are the future horizins for DNA sequencing." There area many promising
technologies for DNA identification and seqencing. For example, the
lab down the hall works with genetically altered fish, and they ID the
experimental fish from the control by snipping a piece of the tail,
and running a quick PCR on them. Several companies are looking to
incorporate PCR into microfluidic "chips" for genomic analysis.
Ideally, scientists would like to get away from PCR, which doesn't do
too well with STRs, for example. If enough genetic material is
available, novel ultrasensitive detection techniques can be used. Two
of the more interesting are the use of mass spectrometery

http://www.nanosphere-inc.com

and nanotechnology

http://www.nanosphere-inc.com.


Probably the most widly used technology out there now is the "gene
chip", in which specific strands of DNA are imoblized on a surface and
"Capture" the target DNA you want to know about. A good site for this
type of technology is found at

http://www.affymetrix.com/index.affx

If you wanted to know what proteins a cell was making (eg monitoring
the transcription of DNA to RNA, and, by extension the translation of
RNA to proteins), you could mointor the RNA (albeit with more
difficulty) in ways similar to those mentioned above.

I appologies for the brevity of my response to a really interesting
question. If time permits, Ill add more later.
Good luck

First, I have read your question and I think I get gist of what you're
looking for.  However, from reading your question, it seems to me that
you have a limited knowledge of DNA sequencing and transcription.
First, 'transcription' in it's literal term implies the production of
an RNA from a DNA sequence.  One can produce readible DNA sequences
from DNA, but this process is a bit complicated for me to describe.


a.) by "dna profilling" what do you mean?

    if you mean analysis of gene sequence and predisposition to
disease, this process becomes complicated depending on which gene
sequences you're interested in, OR, simply telling one individual from
another?

b.) by mentioning short tandem repeat(STR) and single nucleotide
polymorphism(SNP) i am assuming that it is the latter.  These
processes do not sequence or 'transcribe' DNA, but are rather methods
that analyze a fingerprint of DNA.

c.) there are a vast number of technologies that are available and
being explored not only for rapid dna sequencing, fingerprinting(as
you have brought up), but for the measurement of gene expression
levels(RNA) in situ.  As such, I'm a little vague on what you mean by
a "micro scale single use" device and the market you're trying to get
information on.

I'm not a google answer guy, I don't get paid, and I probably won't
answer this question if you're expecting more than what I know off the
top of my head. But, I would expect that if you're willing to chat a
bit, you might get a lot more than a hundred bucks worth of
information to get you started.

Chugs,
Bob

The techniques you are mentioning are being developed for very
different purposes and would likely not fall under a single group or
groups working on each MEMS device.

In the case of STR and SNP, these are simply tests that look at the
size of particular fragments of a genome.  As such biological material
must still be sampled and processed to isolate the DNA. I am not sure
I know what size of DNA and the resolution that is needed to make a
determination, but simply searching those topics(STR SNP, RFLP) should
get you there.

In the case of DNA sequencing, there are a number of different
technologies, ranging from high throughput methods of traditional
Sanger sequencing to super high tech stuff like sequencing by
hybridization, and mass spectrometry  All of these come with their own
limitations. I am not sure if people have applied rapid sequencing of
particular fragments to determine if there are enough significant
differences among individuals to make a determination. On the surface
it seems possible, but it would have to be tested and validated,
whereas SNP, ans STR really is already the gold standard. Again, these
processes require isolation of the fragments of interest, a rate
limiting step.

For gene expression screening, chips are already available containing
probes for various RNA or cDNA library analysis.

This is a robust field of research and there are literally hundreds of
different approaches aimed at improving the efficiency of DNA
sequencing and analysis.  See companies, such as affymetrix, beckman
instruments, celera genomics(applied biosystems).

Anything much more than this would require me to do real work, and I
got enough of that to do already.

Chugs,
Bob

I ran across this in case anyone is interested.  Thanks to everyone
who has posted a response.

TRANSLATING BIOCHEMICAL RECOGNITION INTO NANOMECHANICAL ACTION

Translating Biochemical Recognition Into Nanomechanical Action
Array of tiny cantilevers imaged by scanning electron microscopy.
The cantilevers bend by docking of molecules.
We have discovered a new approach to transforming specific biochemical
recognition into a nanomechanical motion. To do this, we used
hybridization, the base pairing between two single strands of DNA that
results in the well-known double-helix structure. Hybridization is a
prominent example of molecular recognition.

The core of the device is an array of silicon cantilevers, each 500
microns long, 100 microns wide and less than 1 micron thick. Each
cantilever is coated on one side by specific biomolecules. When
immersed in solution, molecules of an injected substance dock to a
layer of receptor molecules that have been attached to one side of the
cantilever. Sensitizing an array of cantilevers, each with a different
receptor, allows docking of different substances in the same solution.
The increase of the molecular "packing density" leads to surface
stress and thus to bending of the cantilever.

Core of the instrument is the liquid cell in which the cantilevers are mounted.
The bending is of the order of 10-20 nanometers, which can be measured
accurately by well-established methods, such as laser beam deflection.
The hybridization was done with short strands of single-stranded DNA
(12mer oligonucleotides) and proteins known to recognize antibodies of
various mammals.

The scientific report on this work has been published in Science, Vol.
288, Number 5464, April 14, 2000. The authors of the report
"Translating Biomolecular Recognition into Nanomechanics" are Jürgen
Fritz, Marko Baller, Hans Peter Lang, Ernst Meyer and Hans-Joachim
Güntherodt of the University of Basel, and Hugo Rothuizen, Peter
Vettiger, Christoph Gerber, and James Gimzewski of IBM?s Zurich
Research Laboratory.

The technology underlying this new advance springs from development
work on nanomechanical olfactory sensors, as pursued by the research
teams at IBM in Zurich and at the University of Basel. To date,
applications of this work are mainly in quality and process control,
where the technology is used in sensing devices for gaseous analytes,
such as process gases or solvent vapors. Such devices are not limited
to gaseous environments, but also function in liquids. This led the
way to the research now reported in Science on using the biomechanical
sensors in biochemistry and medical diagnostics.
"Microbots and nanobots have been popularized in recent
science-fiction stories and movies, but technological issues remain an
obstacle to their realization," said James Gimzewski of IBM Research.
"The ability to use biology to perform specific mechanical tasks on
the nanometer scale with silicon provides a completely new approach to
operate machinery autonomously, without external power or computer
control. We have found a way to get DNA to do the work for us, so we
don't need batteries, motors, or the like to operate tiny machines."

GE Unveils Nanotech Device, May Shrink Future Chips (Excerpt reposted
from Yahoo Site)

NEW YORK (Reuters) - Scientists at General Electric Co. (NYSE:GE -
news) unveiled one of the smallest functioning devices ever made on
Wednesday. .............GE's device has potential, according to Paul
McEuen, a physics professor at Cornell University in New York state.
.....Unlike earlier designs, GE's nanotube can both emit and detect
light, GE said. That means it has potential to perform tasks like
shining small amounts of light on molecules, a possible application in
medicine, or security, McEuen said.

Aug. 10, 2004 

1.  The Nat'l. Inst. of Health presently may soon announce its grants
for the "$1,000 Genome Project."  Look at their web site weekly.

2.  Click to  www.visigenbio.com    (VisGen Biotechnologies, Inc.)

3.  There are a few private and public companies operating in a
"stealth mode" at this time that are seeking the holy grail of whole
genome sequencing which  would be to do single molecule genome
sequencing in real time at a very rapid rate of base-pair
identification, such as entire genome sequencing in a few days per
genome or less time for $1,000 per entire genome or less cost.  Such a
result would allow:  the "personalized medicine industry" to grow
quickly; quick identification of unconventional pathogens; and would
allow better comparative genomic analysis.

4.