Koch Lab:Protocols

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(Computational protocols)
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==Protocols coming soon==
 
One of the goals of our lab is to share protocols in a form that makes it as easy as possible for other labs to build off of them.  These will be a combination of protocols that we will develop and also those that Steve has developed in the past but has not had a good opportunity to distribute yet. '''If any of the following protocols are of particular interest, [[Koch_Lab:Contact|drop us a line]] or make a note on the discussion page!'''  We also want to share software applications and computational modules (mostly LabVIEW) that would be useful to others.
One of the goals of our lab is to share protocols in a form that makes it as easy as possible for other labs to build off of them.  These will be a combination of protocols that we will develop and also those that Steve has developed in the past but has not had a good opportunity to distribute yet. '''If any of the following protocols are of particular interest, [[Koch_Lab:Contact|drop us a line]] or make a note on the discussion page!'''  We also want to share software applications and computational modules (mostly LabVIEW) that would be useful to others.
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===Molecular protocols===
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==Molecular protocols==
* Various methods to label dsDNA with dig and biotin for end-to-end stretching: [[/Dig-bio PCR|PCR with labeled primers]], klenow fill-in, ligating labeled duplexes (or hairpins), ligating multiply-tagged segments.
* Various methods to label dsDNA with dig and biotin for end-to-end stretching: [[/Dig-bio PCR|PCR with labeled primers]], klenow fill-in, ligating labeled duplexes (or hairpins), ligating multiply-tagged segments.
* More complicated construction of a molecules that will unzip when stretched, as in our 2002 Biophys. J. paper PMID 12124289.  Compared with DNA stretching, making a construct for unzipping presents many more potential pitfalls, and it is also challenging to get good yield.
* More complicated construction of a molecules that will unzip when stretched, as in our 2002 Biophys. J. paper PMID 12124289.  Compared with DNA stretching, making a construct for unzipping presents many more potential pitfalls, and it is also challenging to get good yield.
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* Measuring kinesin aggregation via dynamic light scattering (DLS) (As in our [http://dx.doi.org/10.1016/j.fgb.2007.02.004 kinesin paper])
* Measuring kinesin aggregation via dynamic light scattering (DLS) (As in our [http://dx.doi.org/10.1016/j.fgb.2007.02.004 kinesin paper])
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===Instrumentation protocols===
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==Instrumentation protocols==
* Preparing a low-tech (coverglass, slide, double-stick stape) sample chamber
* Preparing a low-tech (coverglass, slide, double-stick stape) sample chamber
* Flow cells for electromagnetic steering of microtubules labeled with magnetic microspheres.
* Flow cells for electromagnetic steering of microtubules labeled with magnetic microspheres.
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* [[Koch Lab:Research/AOD tidbits|Some things about AODs]]
* [[Koch Lab:Research/AOD tidbits|Some things about AODs]]
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===Computational protocols===
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==Computational protocols==
* [[/Loading rate clamp|Loading rate clamp]]--method for stretching single-molecule tethers such that the force-versus-time curves are linear segments.  Used in 2003 Phys. Rev. Let. paper, PMID 12906513, for unzipping with protein present, but can be used whenever the polymer physics are known ahead of time.
* [[/Loading rate clamp|Loading rate clamp]]--method for stretching single-molecule tethers such that the force-versus-time curves are linear segments.  Used in 2003 Phys. Rev. Let. paper, PMID 12906513, for unzipping with protein present, but can be used whenever the polymer physics are known ahead of time.
* Maximum likelihood anlaysis of single-molecule disruption data with Evan Evans' et al. Dynamic Force Spectroscopy (DFS) model.  Much better and easier than performing Gaussian fits to histograms.  Used in 2003 Phys. Rev. Let. paper, PMID 12906513.
* Maximum likelihood anlaysis of single-molecule disruption data with Evan Evans' et al. Dynamic Force Spectroscopy (DFS) model.  Much better and easier than performing Gaussian fits to histograms.  Used in 2003 Phys. Rev. Let. paper, PMID 12906513.
* Finite Element Magnetic Modeling (FEMM) for predicting forces on magnetic microspheres, as in [http://link.aip.org/link/?APL/89/173901 2006 Appl. Phys. Let.] ([http://www.chtm.unm.edu/publications/APL%2089_173901_Koch,%20Thayer,%20Corwin,%20de%20Boer_MEMS%20force%20sensor%20for%20mag%20bead%20calibration.pdf PDF])
* Finite Element Magnetic Modeling (FEMM) for predicting forces on magnetic microspheres, as in [http://link.aip.org/link/?APL/89/173901 2006 Appl. Phys. Let.] ([http://www.chtm.unm.edu/publications/APL%2089_173901_Koch,%20Thayer,%20Corwin,%20de%20Boer_MEMS%20force%20sensor%20for%20mag%20bead%20calibration.pdf PDF])
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Revision as of 00:41, 31 October 2007


Home Research Lab Members Publications Protocols Contact Funding
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One of the goals of our lab is to share protocols in a form that makes it as easy as possible for other labs to build off of them. These will be a combination of protocols that we will develop and also those that Steve has developed in the past but has not had a good opportunity to distribute yet. If any of the following protocols are of particular interest, drop us a line or make a note on the discussion page! We also want to share software applications and computational modules (mostly LabVIEW) that would be useful to others.

Molecular protocols

  • Various methods to label dsDNA with dig and biotin for end-to-end stretching: PCR with labeled primers, klenow fill-in, ligating labeled duplexes (or hairpins), ligating multiply-tagged segments.
  • More complicated construction of a molecules that will unzip when stretched, as in our 2002 Biophys. J. paper PMID 12124289. Compared with DNA stretching, making a construct for unzipping presents many more potential pitfalls, and it is also challenging to get good yield.
  • Tethering -- making single-molecule tethers via antidig-dig and biotin-streptavidin. Including all the tricks for washing glass, blocking, how much DNA to use, microsphere selection, microsphere preparation, etc.
  • Detailed protocols for "popping" experiments -- that is, unzipping DNA molecules with DNA-binding proteins present
  • Various buffers used in single-molecule manipulation experiments
  • Measuring kinesin aggregation via dynamic light scattering (DLS) (As in our kinesin paper)

Instrumentation protocols

  • Preparing a low-tech (coverglass, slide, double-stick stape) sample chamber
  • Flow cells for electromagnetic steering of microtubules labeled with magnetic microspheres.
  • Placing single 3 micron magnetic microspheres (or also 30 micron polystyrene) onto MEMS devices (with micromanipulators) as in 2006 Appl. Phys. Let. (PDF)
  • Making a flow cell to hydrate a SUMMiT MEMS device
  • Some things about AODs

Computational protocols

  • Loading rate clamp--method for stretching single-molecule tethers such that the force-versus-time curves are linear segments. Used in 2003 Phys. Rev. Let. paper, PMID 12906513, for unzipping with protein present, but can be used whenever the polymer physics are known ahead of time.
  • Maximum likelihood anlaysis of single-molecule disruption data with Evan Evans' et al. Dynamic Force Spectroscopy (DFS) model. Much better and easier than performing Gaussian fits to histograms. Used in 2003 Phys. Rev. Let. paper, PMID 12906513.
  • Finite Element Magnetic Modeling (FEMM) for predicting forces on magnetic microspheres, as in 2006 Appl. Phys. Let. (PDF)
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