Koch Lab:Protocols - Revision history

Andy Maloney: /* General Lab Techniques */

2011-01-24T18:40:30Z

General Lab Techniques

←Older revision		Revision as of 18:40, 24 January 2011
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	*[[/How to Clean Glassware\|Cleaning Glassware]]		*[[/How to Clean Glassware\|Cleaning Glassware]]
	*[[/How to use a pipette\|Using Pipettes]]		*[[/How to use a pipette\|Using Pipettes]]
		+	*[[/Changing the Hg bulb\|Changing the Hg bulb]]
	*[[/Laser Safety\|Laser Safety]]		*[[/Laser Safety\|Laser Safety]]
	*[[/How to Autoclave\|How to Autoclave]]		*[[/How to Autoclave\|How to Autoclave]]

Brian P. Josey: /* General Lab Techniques */

2010-06-30T17:58:58Z

General Lab Techniques

←Older revision		Revision as of 17:58, 30 June 2010
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	*[[/How to Autoclave\|How to Autoclave]]		*[[/How to Autoclave\|How to Autoclave]]
	*[[/How to Clean the Autoclave\|How to Clean the Autoclave]]		*[[/How to Clean the Autoclave\|How to Clean the Autoclave]]
		+	*[[/Recycling\|Recycling]]

	==Molecular Biology Protocols==		==Molecular Biology Protocols==

Anthony Salvagno: /* Standard Techniques */

2009-10-28T17:58:30Z

Standard Techniques

←Older revision		Revision as of 17:58, 28 October 2009
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	===Standard Techniques===		===Standard Techniques===
	*PCR		*PCR
-	*Gel Electrophoresis	+	*[[User:Anthony Salvagno/Notebook/Research/Notes About Gels\|Gel Electrophoresis]]
	*Cloning		*Cloning
	*Transformation into E. Coli		*Transformation into E. Coli

Brian P. Josey: /* General Lab Techniques */

2009-10-27T18:25:33Z

General Lab Techniques

←Older revision		Revision as of 18:25, 27 October 2009
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	*[[/Laser Safety\|Laser Safety]]		*[[/Laser Safety\|Laser Safety]]
	*[[/How to Autoclave\|How to Autoclave]]		*[[/How to Autoclave\|How to Autoclave]]
		+	*[[/How to Clean the Autoclave\|How to Clean the Autoclave]]

	==Molecular Biology Protocols==		==Molecular Biology Protocols==

Anthony Salvagno: /* Computational Protocols */

2009-10-26T22:14:38Z

Computational Protocols

←Older revision		Revision as of 22:14, 26 October 2009
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	*[[/Gel Imaging System\|Gel Imaging System]]		*[[/Gel Imaging System\|Gel Imaging System]]

-	==~~[[/~~Computational Protocols~~\|Computational Protocols]]~~==	+	==Computational Protocols==
	*Shotgun DNA Mapping		*Shotgun DNA Mapping
	*Kinesin Processivity		*Kinesin Processivity
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	*Motion Detection Camera		*Motion Detection Camera
	*[[/Loading rate clamp\|Loading Rate Clamp]]		*[[/Loading rate clamp\|Loading Rate Clamp]]
		+	* 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])


	</div>		</div>

Anthony Salvagno: /* Old Page to be deleted */

2009-10-26T22:13:24Z

Old Page to be deleted

←Older revision		Revision as of 22:13, 26 October 2009
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	*[[/Loading rate clamp\|Loading Rate Clamp]]		*[[/Loading rate clamp\|Loading Rate Clamp]]

-	~~=Old Page to be deleted=~~
-	Everything below this point will be deleted by Friday Oct 23. If you have something recorded below that you want saved, please move information to the appropriate location above. All of the wiki links below should be under the DNA Protocols above as of now, but if anything is left out please contribute.

-	~~===Labeling DNA for single-molecule stretching===~~
-	~~Various methods to label dsDNA with digoxigenin (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.
-	** (Useful for a couple of the above protocols): [[/Oligonucleotide Annealing\|Oligo Annealing]]
-	~~===Labeling DNA for unzipping===~~
-	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.
-	* [[/Unzipping constructs\|Creating dig / biotin unzipping constructs for unzipping long DNA segments]]
-	* [[/Fork unzipping constructs\|Hybridized unzipping forks]]
-
-	~~===DNA 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.
-	*[[/Microsphere-DNA tethering\|Microsphere-DNA tethering]]
-	*[[/Glass-DNA-PDMS tethering\|Glass-DNA-PDMS tethering]]
-
-	~~===Probing protein-DNA interactions by unzipping single DNA molecules===~~
-	~~Detailed protocols for "popping" experiments -- that is, unzipping DNA molecules with DNA-binding proteins present~~
-
-	~~===Single-molecule manipulation buffers===~~
-	~~Various buffers used in single-molecule manipulation experiments~~
-
-	~~===Kinesin aggregation via DLS===~~
-	~~Measuring kinesin aggregation via dynamic light scattering (DLS) (As in our [http://dx.doi.org/10.1016/j.fgb.2007.02.004 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 [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])
-	* Making a flow cell to hydrate a SUMMiT MEMS device
-	* [[Koch Lab:Research/AOD tidbits\|Some things about AODs]]
	</div>		</div>

Andy Maloney: /* KochLab Techniques */

2009-10-23T16:33:36Z

KochLab Techniques

←Older revision		Revision as of 16:33, 23 October 2009
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	*[[/Kinesin\|Kinesin protocols]]		*[[/Kinesin\|Kinesin protocols]]
	*[[/DNA Protocols\|DNA Protocols]]		*[[/DNA Protocols\|DNA Protocols]]
		+	*[[/Flow cell\|Flow cell]]

	==Equipment Setup==		==Equipment Setup==

Anthony Salvagno: /* General Lab Techniques */

2009-10-23T15:55:55Z

General Lab Techniques

←Older revision		Revision as of 15:55, 23 October 2009
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	==General Lab Techniques==		==General Lab Techniques==
		+	Every lab has its own standards when it relates to lab safety, cleanliness, and shared equipment protocols. Below we've documented our specific techniques with regards to these general lab standards:
	*[[/How to Clean Glassware\|Cleaning Glassware]]		*[[/How to Clean Glassware\|Cleaning Glassware]]
	*[[/How to use a pipette\|Using Pipettes]]		*[[/How to use a pipette\|Using Pipettes]]

Anthony Salvagno: /* Old Page to be deleted */

2009-10-22T21:37:50Z

Old Page to be deleted

←Older revision		Revision as of 21:37, 22 October 2009
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	=Old Page to be deleted=		=Old Page to be deleted=
	Everything below this point will be deleted by Friday Oct 23. If you have something recorded below that you want saved, please move information to the appropriate location above. All of the wiki links below should be under the DNA Protocols above as of now, but if anything is left out please contribute.		Everything below this point will be deleted by Friday Oct 23. If you have something recorded below that you want saved, please move information to the appropriate location above. All of the wiki links below should be under the DNA Protocols above as of now, but if anything is left out please contribute.
-	~~==[[/Sequences\|DNA Sequences]]==~~
-
-	~~==Molecular protocols==~~

	===Labeling DNA for single-molecule stretching===		===Labeling DNA for single-molecule stretching===
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	* Making a flow cell to hydrate a SUMMiT MEMS device		* Making a flow cell to hydrate a SUMMiT MEMS device
	* [[Koch Lab:Research/AOD tidbits\|Some things about AODs]]		* [[Koch Lab:Research/AOD tidbits\|Some things about AODs]]
-
-	~~==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.
-	* 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])
-
-
-	~~==Microfluidics protocols in Lopez Keck lab/Koch lab==~~
-	*For specific protocol see the following link
-	*[[Koch Lab:Protocols/Photo lithography\|Photo lithography]]
-	*[[Koch Lab:Protocols/PDMS\|PDMS]]
-
	</div>		</div>

Anthony Salvagno: /* Equipment Setup */

2009-10-22T20:29:56Z

Equipment Setup

←Older revision		Revision as of 20:29, 22 October 2009
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	==Equipment Setup==		==Equipment Setup==
-	*[[/Optical Tweezers]]	+	*[[/Optical Tweezers\|Optical Tweezers]]
-	*[[/Microscopy]]	+	*[[/Microscopy\|Microscopy]]
-	*[[/Gel Imaging System]]	+	*[[/Gel Imaging System\|Gel Imaging System]]
		+
	==[[/Computational Protocols\|Computational Protocols]]==		==[[/Computational Protocols\|Computational Protocols]]==
	*Shotgun DNA Mapping		*Shotgun DNA Mapping

←Older revision		Revision as of 18:40, 24 January 2011
Line 9:		Line 9:
	*[[/How to Clean Glassware\|Cleaning Glassware]]		*[[/How to Clean Glassware\|Cleaning Glassware]]
	*[[/How to use a pipette\|Using Pipettes]]		*[[/How to use a pipette\|Using Pipettes]]
		+	*[[/Changing the Hg bulb\|Changing the Hg bulb]]
	*[[/Laser Safety\|Laser Safety]]		*[[/Laser Safety\|Laser Safety]]
	*[[/How to Autoclave\|How to Autoclave]]		*[[/How to Autoclave\|How to Autoclave]]