Nanomicrobiology?

[Margret Storm]

These articles are very interesting:
http://jb.asm.org/content/184/19/5205
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246382/
http://www.uam.es/gruposinv/spmth/highlights/2008_Science_322_413/highlight.html

Has anyone here experimented with this technology themselves, or do you know anyone who has? What are your thoughts on the applications of the technology where it stands, or on how accessible it is? How viable would it be for modifying DNA/RNA sequences or proteins manually?

[Dave Casey]

Building one of these is near the top of my to-do list:

http://instructables.com/id/A-Low-Cost-Atomic-Force-Microscope-%E4%BD%8E%E6%88%90%E6%9C%AC%E5%8E%9F%E5%AD%90%E5%8A%9B%E9%A1%AF%E5%BE%AE%E9%8F%A1/step11/Prepare-for-making-your-own-educational-AFM/

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[Margret Storm]

Incredible! Thank you for the link!

On Saturday, July 26, 2014 4:14:00 PM UTC-4, da3v wrote:

Building one of these is near the top of my to-do list:

http://instructables.com/id/A-Low-Cost-Atomic-Force-Microscope-%E4%BD%8E%E6%88%90%E6%9C%AC%E5%8E%9F%E5%AD%90%E5%8A%9B%E9%A1%AF%E5%BE%AE%E9%8F%A1/step11/Prepare-for-making-your-own-educational-AFM/

On Saturday, July 26, 2014, Margret Storm <i.am....@gmail.com> wrote:

These articles are very interesting:
http://jb.asm.org/content/184/19/5205
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246382/
http://www.uam.es/gruposinv/spmth/highlights/2008_Science_322_413/highlight.html

Has anyone here experimented with this technology themselves, or do you know anyone who has? What are your thoughts on the applications of the technology where it stands, or on how accessible it is? How viable would it be for modifying DNA/RNA sequences or proteins manually?

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[Nathan McCorkle]

I've been training to operate a Focused Ion Beam milling machine. It can mill and deposit metal with a minimum spot size of about 10nanometers. I've been making probes with a pipette puller then milling the ends with a certain angle at a certain width along the probe tip.

I think FIBs can make AFM probes... I didn't see a picture/diagram of the tips they were using in those papers.

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[Margret Storm]

The third link's second image is of the atom used for manipulation.

[Nathan McCorkle]

Yes I saw that, but it doesn't seem to give a procedure used to produce it, unless that is another paper (maybe referenced in that paper)?

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[Margret Storm]

This is the paper they linked: http://www.uam.es/gruposinv/spmth/papers/2008_Science_332_413_Sugimoto_AFM.pdf

It says: "We performed the AFM experiments (9) in
dynamic mode under the frequency modulation
detection scheme (10),  keeping the cantilever
oscillation amplitude constant. Commercial silicon
cantilevers, which have very sharp tips at their
free ends, were used to image the Sn/Si (111)
[…] R30° surface (11) by detecting the
short-range chemical interaction force between
the closest tip and surface atoms (9)."

9: http://arxiv.org/pdf/cond-mat/9706132.pdf
10: http://arxiv.org/pdf/cond-mat/0311522v1.pdf
11:http://journals.aps.org/pr/abstract/10.1103/PhysRev.141.503 (can't find a full paper for this one, sorry)

[Nathan McCorkle]

http://scholar.google.com/scholar?q=32.768+khz+crystal+microscopy
http://research.sabanciuniv.edu/10163/1/Scanning_Hall_Probe_Microscopy_(SHPM)_Using_Quartz_Crystal_AFM_Feedback.pdf

crystal is <$1 USD
http://www.newark.com/fox-electronics/nc38lf-327/tuning-fork-32-768khz-12-5pf-thru/dp/61T5432

similar application but some better images of the tips:
http://www.hindawi.com/journals/ijo/2012/591083/
http://diyhpl.us/~nmz787/pdf/Integrating_micro-_and_nanoelectrodes_into_atomic_force_microscopy_cantilevers_using_focused_ion_beam_techniques.pdf

http://diyhpl.us/~nmz787/pdf/Development_of_a_regeneration-type_neural_interface_A_microtube_guide_for_axon_growth_of_neuronal_cells_fabricated_using_focused-ion-beam_chemical_vapor_deposition.pdf

Also this:
http://hansmalab.physics.ucsb.edu/afmhistory.html

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[Margret Storm]

Neat!! Thanks for the info =)

[bioscisam]

I've done a bit of AFM although it was in an institutional setting a few years ago and all the expensive kit was provided. It's a very intriguing technology along with other SPM methods. It's limitations seemed to be the depth of the image you can build up due to the physical limitations of the structure of the cantilever and at the time the newer SEMs for these methods seemed to give at least as good imaging plus deeper view of your sample's 'terrain'. The cantilevers that are used require microfabrication methods to make and are connected to a piezo material that feeds back signal depending on the feedback (can be physical but you can also look at electromagnetic feedback etc) from the sample.

I think the bottleneck in making these systems is being able to fabricate these probes.

Definitely an advanced project for hacking I'm really interested to see where it goes. It would be interesting to see if probes could be modified with biomolecular attachements and attempt to read feedback from interacting molecules or try to manipulate them, e.g pores that interact with DNA, enzymes or antibodies..

[Margret Storm]

Exactly!! It really bothers me how indirect most current methods of cell interaction are, especially when the subjects in question are already so complex. The possibilities of fine-tuned modification are so exciting!