User:Pranav Rathi/Notebook/OT/2013/01/09/DNA-Overstretching Experiments - Revision history

Pranav Rathi: /* Introduction */

2013-01-17T17:32:38Z

Introduction

←Older revision		Revision as of 17:32, 17 January 2013
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	\|autoplay=0		\|autoplay=0
	}}		}}
		+
		+	More on Optical Tweezers [https://picasaweb.google.com/101108414393941264686/OpticalTweezers02?authuser=0&feat=directlink]
		+

	==Proof of DNA-tethering==		==Proof of DNA-tethering==
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	----		----
-

	=Experiments=		=Experiments=

Pranav Rathi: /* Result: */

2013-01-17T01:28:05Z

Result:

←Older revision		Revision as of 01:28, 17 January 2013
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	Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts (15% efficiency). I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change.		Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts (15% efficiency). I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change.

-	Some tethers overstretched multiple times, i noticed every time the same tethers is overstretched the overstretching force depletes~~. It~~ is not ~~quite clear in some tethers but on average it sounds true~~.	+	Some tethers overstretched multiple times, i noticed every time the same tethers is overstretched the overstretching force depletes, but that is not case. I looked many many multiple overstretches and they looked very alike.

	=====Data:=====		=====Data:=====

Pranav Rathi: /* Result: */

2013-01-17T01:10:26Z

Result:

←Older revision		Revision as of 01:10, 17 January 2013
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	Sample is very successful tethering wise, lot of tethers, most of the tethers overstretched unlike the H2O sample. I got 31 good overstretches out of 84 attempts (40% efficiency); 3 times better than H2O sample. I selected some of the beast segments; force goes from 63 to 69pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change. On average the overstretching force is reported higher in D2O than H2O.		Sample is very successful tethering wise, lot of tethers, most of the tethers overstretched unlike the H2O sample. I got 31 good overstretches out of 84 attempts (40% efficiency); 3 times better than H2O sample. I selected some of the beast segments; force goes from 63 to 69pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change. On average the overstretching force is reported higher in D2O than H2O.

		+	=====Data:=====
		+	* Data acquisition parameters: DNA4.4kb(110ng/ml; 02/11/11) ,r=265nm ,medium D2o,TCH/BH 574nm,FH 200 ,loading rate .001, Temp=77~78 degF.
		+	* Data is in file: 1301115\007 to 013.
		+	* Good selected segments are: 0007-6, 0008-3,(0009-0,1,5,10), (0010-7,10), 0011-4, (0012-1,3,10) 0013-3.
		+	* Repeated overstretching segments are:
		+	0007-(6,7),0008-(3,4),0009-(1,2,3),0011-(4,5),0012-(1,2),(3,4),(10,11),0013-(3,4)
		+
		+	* The data link at server:http:
		+	[http://kochlab.org/files/data/Kochlab-daq2/rathi.pranav/Shotgun%20DNA%20Mapping/130115/,All%20segments%20report.html]
		+
		+	Overstretching-data and other information can be seen through evernotes:
		+
		+	<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>

Pranav Rathi: /* Result: */

2013-01-17T01:07:42Z

Result:

←Older revision		Revision as of 01:07, 17 January 2013
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	====Result:====		====Result:====
-	Sample is very successful tethering wise, lot of tethers, most of the tethers overstretched ~~good~~ unlike the H2O sample. I got 31 good overstretches out of 84 attempts (40% efficiency); 3 times better than H2O sample. I selected some of the beast segments; force goes from 63 to 69pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change. On average the overstretching force is reported higher in D2O than H2O.	+	Sample is very successful tethering wise, lot of tethers, most of the tethers overstretched unlike the H2O sample. I got 31 good overstretches out of 84 attempts (40% efficiency); 3 times better than H2O sample. I selected some of the beast segments; force goes from 63 to 69pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change. On average the overstretching force is reported higher in D2O than H2O.

Pranav Rathi: /* Result: */

2013-01-17T00:07:57Z

Result:

←Older revision		Revision as of 00:07, 17 January 2013
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	====Result:====		====Result:====
-		+	Sample is very successful tethering wise, lot of tethers, most of the tethers overstretched good unlike the H2O sample. I got 31 good overstretches out of 84 attempts (40% efficiency); 3 times better than H2O sample. I selected some of the beast segments; force goes from 63 to 69pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change. On average the overstretching force is reported higher in D2O than H2O.

Pranav Rathi: /* Result: */

2013-01-17T00:01:43Z

Result:

←Older revision		Revision as of 00:01, 17 January 2013
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	====Result:====		====Result:====
-	Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts. I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching~~. The highest force is the green curve which i think should not belong to this data because the FTC has a huge nick at the center which was very unusual~~ but ~~rest of~~ the data is good ~~with~~ the error range of stiffness. This data is analyzed under quick conversion, because we have not ~~done~~ the geometry going so the data might change.	+	Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts (15% efficiency). I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching but the data is good within the error range of stiffness. This data is analyzed under quick conversion, because we have not got the geometry going so the data might change.

-	Some tethers overstretched multiple times, i noticed every time the same tethers is overstretched the overstretching force depletes. it is not quite ~~noticing~~ in some tethers but on average it sounds true.	+	Some tethers overstretched multiple times, i noticed every time the same tethers is overstretched the overstretching force depletes. It is not quite clear in some tethers but on average it sounds true.

	=====Data:=====		=====Data:=====
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	<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>		<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>
-
-
-

	===Experiment:2===		===Experiment:2===

Pranav Rathi: /* Experiment:2 */

2013-01-16T22:44:51Z

Experiment:2

←Older revision		Revision as of 22:44, 16 January 2013
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	<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>		<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>
		+
		+
		+

	===Experiment:2===		===Experiment:2===

Pranav Rathi: /* Data: */

2013-01-16T22:44:09Z

Data:

←Older revision		Revision as of 22:44, 16 January 2013
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	<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>		<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>

		+	===Experiment:2===

		+	Overstrething in D2O
		+
		+	====Sample preparation====
		+	Single-chamber sample.
		+
		+	'''Bead:'''
		+	*D2O:
		+
		+	1.5ul of 265nm bead (1:5) from stock+13.5ul of BGB D2O=15ul of bead D2O (1:50)
		+
		+	'''DNA:'''
		+	ds-DNA 4.4kb (110ng/ml;02/11/11)
		+
		+	*D2O;
		+	1ul of DNA from stock (1:10) + 9ul of 1XPOP D2O =10ul of DNA D2O (1:100)
		+
		+	====Procedure====
		+	* The procedure is same as experiment 5(01/10/13)
		+
		+	====Result:====

Pranav Rathi: /* Result: */

2013-01-16T22:41:48Z

Result:

←Older revision		Revision as of 22:41, 16 January 2013
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	====Result:====		====Result:====
	Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts. I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching. The highest force is the green curve which i think should not belong to this data because the FTC has a huge nick at the center which was very unusual but rest of the data is good with the error range of stiffness. This data is analyzed under quick conversion, because we have not done the geometry going so the data might change.		Sample is very successful tethering wise, lot of tethers, but most of them broke during the beginning of overstretching after a good FTC. Very very few tethers overstretched; 11 good tethers out of 75 attempts. I selected some of the beast segments; force goes from 59 to 66pN at 1750nm LDNA at which the DNA starts overstretching. The highest force is the green curve which i think should not belong to this data because the FTC has a huge nick at the center which was very unusual but rest of the data is good with the error range of stiffness. This data is analyzed under quick conversion, because we have not done the geometry going so the data might change.
		+
		+	Some tethers overstretched multiple times, i noticed every time the same tethers is overstretched the overstretching force depletes. it is not quite noticing in some tethers but on average it sounds true.

	=====Data:=====		=====Data:=====

Pranav Rathi: /* Data: */

2013-01-16T22:38:29Z

Data:

←Older revision		Revision as of 22:38, 16 January 2013
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	=====Data:=====		=====Data:=====
		+	* Data acquisition parameters: DNA4.4kb(110ng/ml; 02/11/11) ,r=265nm ,medium H2o,TCH/BH 574nm,FH 200 ,loading rate .001, Temp=75~76 degF.
		+	* Data is in file: 1301115\001 to 006.
		+	* Good selected segments are: (0000-1,10),(0001-3,10,12),(0002-2,6),(0003-0,12,13, (0004-5)
		+	* Repeated overstretching segments (the segments in which same tether overstretched multiple times) are:(0000-(3,4),(10,11,12)); first number shows the overstretch first time consecutive ascending number shows 2nd, 3rd, so-forth and so-on time overstretch.
		+	* The data link at server:http:
		+	[http://kochlab.org/files/data/Kochlab-daq2/rathi.pranav/Shotgun%20DNA%20Mapping/130115/,All%20segments%20report.html]

		+	Overstretching-data and other information can be seen through evernotes:
		+
		+	<html><iframe height="300px" width=600px" src="http://www.evernote.com/shard/s24/sh/b188864a-8228-4570-87d0-5234228805a1/480f4bbe5ad4223b3ff163b0b0664195"></iframe></html>