Nanodrop - Revision history

Paul R Jaschke: /* Answer */

2011-02-01T23:23:08Z

Answer

←Older revision		Revision as of 23:23, 1 February 2011
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	Where A is the absorbance represented in absorbance units (A), E is the wavelength-dependent molar absorptivity coefficient (or extinction coefficient) with units of liter/mol-cm, b is the path length in cm, and c is the analyte concentration in moles/liter or molarity (M). <br>		Where A is the absorbance represented in absorbance units (A), E is the wavelength-dependent molar absorptivity coefficient (or extinction coefficient) with units of liter/mol-cm, b is the path length in cm, and c is the analyte concentration in moles/liter or molarity (M). <br>
	*For nucleic acid quantification, the Beer-Lambert equation is manipulated to give:<br>		*For nucleic acid quantification, the Beer-Lambert equation is manipulated to give:<br>
-	c = (A * e)/b <br>	+	c = A/(E * b) <br>
	Where c is the nucleic acid concentration in ng/microliter, A is the absorbance in AU, e is the wavelength-dependent extinction coefficient in ng-cm/microliter and b is the path length in cm. The generally accepted extinction coefficients for nucleic acids are:<br>		Where c is the nucleic acid concentration in ng/microliter, A is the absorbance in AU, e is the wavelength-dependent extinction coefficient in ng-cm/microliter and b is the path length in cm. The generally accepted extinction coefficients for nucleic acids are:<br>
	• Double-stranded DNA: 50 <br>		• Double-stranded DNA: 50 <br>

Jakob Suckale: /* Notes */ interference w RNA DNA purification chemicals

2010-07-02T15:41:25Z

Notes: interference w RNA DNA purification chemicals

←Older revision		Revision as of 15:41, 2 July 2010
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	== Notes ==		== Notes ==
		+
		+	[[Image:Nanodrop 1ul trizol in 1ml H2O.PNG\|300px\|thumb\|1µl trizol (phenol, chloroform, guanidine) in 1ml H2O]]
		+	[[Image:Nanodrop 1ul chloroform in 1ml H2O.PNG\|300px\|thumb\|1µl chloroform in 1ml H2O]]
		+
	===Measurement volume - 1 vs 2 µl===		===Measurement volume - 1 vs 2 µl===
	If your sample volume is very low, you may want to measure 1µl instead of the recommended 2µl. In my hands, however, this ''doubles the measurement error'' from about 0.5% to 1% standard deviation/mean. These figures are from repeated measurement of 2 RNA samples, which resulted in 3.5ng/µl SD for a mean of 689ng/µl (2µl volume) vs. 9.2ng/µl SD for a mean of 778ng/µl (1µl), n=5. -- [[User:Austin\|Jakob]] 2009/7		If your sample volume is very low, you may want to measure 1µl instead of the recommended 2µl. In my hands, however, this ''doubles the measurement error'' from about 0.5% to 1% standard deviation/mean. These figures are from repeated measurement of 2 RNA samples, which resulted in 3.5ng/µl SD for a mean of 689ng/µl (2µl volume) vs. 9.2ng/µl SD for a mean of 778ng/µl (1µl), n=5. -- [[User:Austin\|Jakob]] 2009/7

Jakob Suckale: /* Procedure */ illustration

2009-07-24T14:31:35Z

Procedure: illustration

←Older revision		Revision as of 14:31, 24 July 2009
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	== Procedure ==		== Procedure ==
		+	[[Image:DNANanodropExample1.PNG\|right\|thumb\|250px\|Typical DNA peak as measured by the Nanodrop on PC]]

	#Before starting the software module, clean the sample surfaces with DI water to remove any dried sample that might be present.		#Before starting the software module, clean the sample surfaces with DI water to remove any dried sample that might be present.
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	#Click Measure and record the concentration measured.		#Click Measure and record the concentration measured.
	#For DNA, the peak should be at 260 nm, and as a general rule, the 260/280 ratio should be between 1.8 and 2.0.		#For DNA, the peak should be at 260 nm, and as a general rule, the 260/280 ratio should be between 1.8 and 2.0.
-	~~#*A typical DNA peak can be found [[:Image:DNANanodropExample1.PNG\|here]].~~
	#To test multiple samples, just wipe the sensor in between measurements with a Kimwipe. Recalibration or re-blanking is not necessary.		#To test multiple samples, just wipe the sensor in between measurements with a Kimwipe. Recalibration or re-blanking is not necessary.
	#Clean the sample surfaces once more after you are finished.		#Clean the sample surfaces once more after you are finished.

Jakob Suckale: /* Notes */

2009-07-24T14:29:26Z

Notes

←Older revision		Revision as of 14:29, 24 July 2009
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	== Notes ==		== Notes ==
-	===1 vs 2 µl ~~measurement volume~~===	+	===Measurement volume - 1 vs 2 µl===
	If your sample volume is very low, you may want to measure 1µl instead of the recommended 2µl. In my hands, however, this ''doubles the measurement error'' from about 0.5% to 1% standard deviation/mean. These figures are from repeated measurement of 2 RNA samples, which resulted in 3.5ng/µl SD for a mean of 689ng/µl (2µl volume) vs. 9.2ng/µl SD for a mean of 778ng/µl (1µl), n=5. -- [[User:Austin\|Jakob]] 2009/7		If your sample volume is very low, you may want to measure 1µl instead of the recommended 2µl. In my hands, however, this ''doubles the measurement error'' from about 0.5% to 1% standard deviation/mean. These figures are from repeated measurement of 2 RNA samples, which resulted in 3.5ng/µl SD for a mean of 689ng/µl (2µl volume) vs. 9.2ng/µl SD for a mean of 778ng/µl (1µl), n=5. -- [[User:Austin\|Jakob]] 2009/7

Jakob Suckale: /* Notes */ 1 vs 2µl

2009-07-24T14:26:35Z

Notes: 1 vs 2µl

←Older revision		Revision as of 14:26, 24 July 2009
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	== Notes ==		== Notes ==
		+	===1 vs 2 µl measurement volume===
		+	If your sample volume is very low, you may want to measure 1µl instead of the recommended 2µl. In my hands, however, this ''doubles the measurement error'' from about 0.5% to 1% standard deviation/mean. These figures are from repeated measurement of 2 RNA samples, which resulted in 3.5ng/µl SD for a mean of 689ng/µl (2µl volume) vs. 9.2ng/µl SD for a mean of 778ng/µl (1µl), n=5. -- [[User:Austin\|Jakob]] 2009/7

	===Liquid column not formed===		===Liquid column not formed===

Jakob Suckale: /* Notes */ notes into subheadings

2009-07-24T14:15:38Z

Notes: notes into subheadings

←Older revision		Revision as of 14:15, 24 July 2009
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	== Notes ==		== Notes ==
-	*If you see that a liquid column is not being formed, the surfaces may have been un-conditioned by protein or surfactants. Rub each surface 15-20 times with a dry Kimwipe to buff. Using 2 μL samples should ensure the formation of a column.	+
-	*Occasionally, the Nanodrop can give strange readings. One method to help prevent against this is (after you blank the instrument and wipe the sensor) to pipette on 2 μL of your blank once more and click measure. Then verify that the absorbance is at or near 0 for all wavelengths. If it is not, reclean the sensor and start again. Perhaps this effect is due to a liquid column not being formed?	+	===Liquid column not formed===
-	*We had issues of the Nanodrop freezing up sporadically during measurement such that the software became completely unresponsive and the machine was stuck in a measurement state. Tech support responded and said that static discharge can interfere with the computer/machine connection. They had previously sent out a batch of cables which were defective. ''The USB cable should be white not black.'' If your USB cable is black, you should probably call them up and ask for a replacement. --[[User:Austin\|Austin]] 15:17, 18 April 2006 (EDT)	+	If you see that a liquid column is not being formed, the surfaces may have been un-conditioned by protein or surfactants. Rub each surface 15-20 times with a dry Kimwipe to buff. Using 2 μL samples should ensure the formation of a column.
		+
		+	===Nanodrop gives strange readings===
		+	Occasionally, the Nanodrop can give strange readings. One method to help prevent against this is (after you blank the instrument and wipe the sensor) to pipette on 2 μL of your blank once more and click measure. Then verify that the absorbance is at or near 0 for all wavelengths. If it is not, reclean the sensor and start again. Perhaps this effect is due to a liquid column not being formed?
		+
		+	===Nanodrop freezing - cable problems===
		+	We had issues of the Nanodrop freezing up sporadically during measurement such that the software became completely unresponsive and the machine was stuck in a measurement state. Tech support responded and said that static discharge can interfere with the computer/machine connection. They had previously sent out a batch of cables which were defective. ''The USB cable should be white not black.'' If your USB cable is black, you should probably call them up and ask for a replacement. --[[User:Austin\|Austin]] 15:17, 18 April 2006 (EDT)

	==Lab Nanodrop pages==		==Lab Nanodrop pages==

Jakob Suckale: illustration

2009-07-24T14:12:04Z

illustration

←Older revision		Revision as of 14:12, 24 July 2009
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		+	[[Image:Nanodrop.jpg\|thumb\|right\|300px\|NanoDrop ND-1000 spectrophotometer]]
		+
	== Websites ==		== Websites ==

Jakob Suckale: websites into list

2009-07-24T14:10:44Z

websites into list

←Older revision		Revision as of 14:10, 24 July 2009
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	== Websites ==		== Websites ==

-	General FAQ http://nanodrop.com/library/ND%201000%20FAQ.pdf	+	* General FAQ http://nanodrop.com/library/ND%201000%20FAQ.pdf
-		+	* User Manual http://nanodrop.com/Support.aspx?Type=User%20Guides&Cat=NanoDrop%201000
-	User Manual http://nanodrop.com/Support.aspx?Type=User%20Guides&Cat=NanoDrop%201000	+	* Reproducibility Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Reproducibility-Performance-Data.pdf
-		+	* Linearity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-linearity-Performance-Data.pdf
-	Reproducibility Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Reproducibility-Performance-Data.pdf	+	* Homogeneity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Homogeneity-Performance-Data.pdf
-		+	* NanoDrop Website http://www.nanodrop.com
-	Linearity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-linearity-Performance-Data.pdf	+
-		+
-	Homogeneity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Homogeneity-Performance-Data.pdf	+
-		+
-	NanoDrop Website http://www.nanodrop.com	+

	== Procedure ==		== Procedure ==

Russell Diemer: /* Answer */

2009-04-22T19:35:06Z

Answer

←Older revision		Revision as of 19:35, 22 April 2009
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	===''Answer''<br>===		===''Answer''<br>===

-	''From the nanodrop user manual'' (download at http://~~www.~~nanodrop.com/~~nd-1000-overview~~.~~html~~)	+	''From the nanodrop user manual'' (download at http://nanodrop.com/Support.aspx?Type=User%20Guides&Cat=NanoDrop%201000 )

	*General <br>		*General <br>

Russell Diemer: /* Websites */

2009-04-22T19:34:22Z

Websites

←Older revision		Revision as of 19:34, 22 April 2009
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	User Manual http://nanodrop.com/Support.aspx?Type=User%20Guides&Cat=NanoDrop%201000		User Manual http://nanodrop.com/Support.aspx?Type=User%20Guides&Cat=NanoDrop%201000

-	Reproducibility Performance ~~data~~ http://www.nanodrop.com/library/NanoDrop%201000-Reproducibility-Performance-Data.pdf	+	Reproducibility Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Reproducibility-Performance-Data.pdf

	Linearity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-linearity-Performance-Data.pdf		Linearity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-linearity-Performance-Data.pdf

	Homogeneity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Homogeneity-Performance-Data.pdf		Homogeneity Performance Data http://www.nanodrop.com/library/NanoDrop%201000-Homogeneity-Performance-Data.pdf
		+
		+	NanoDrop Website http://www.nanodrop.com

	== Procedure ==		== Procedure ==