(r9) Barrick Lab :: DNAConcentrationDetermination

---+Overview

The lab currently has 3 ways of determining DNA concentration available: *Qubit, !NanoDrop, and Agarose gel electrophoresis*. Each of these methods has advantages and disadvantages as follows: 
|*Method*|*Advantages*|*Disadvantages*|
|*Qubit*|Ability to detect lowest concentrations|Dilution required to determine concentrations.(Instrument calculates stock concentration)|
|^ |Highly tolerant of salts, solvents, and RNA contamination|Requires creation of 2 point standard curve so a bit annoying if only have a single sample|
|^ |Most accurate method(accurate within 10% based on single dilution curve)¡|Takes slightly longer than !NanoDrop|
||||
|* !NanoDrop*|Fastest method|Instrument not in our lab|
|^ |Largest range of acceptable concentrations|Not as accurate as Qubit(error rate of 40 - 160% below 30ng/µl based on single dilution curve)¡|
|^ |Requires only 1 µl of sample|Salt, RNA, and Solvents all alter the apparent concentration|
||||
|*Gel*|Salts, solvents, and RNA play no role in determining concentration|Requires estimation of concentration based on similar banding pattern to ladder|
|^ | |Requires previous use of other method or outright guess to know how much sample to load|
|^ | |Most time consuming|
|^ | |low percentage agarose gels are necessary for identifying genomic DNA which is also highly subjective to diffusion|
¡see attached excel sheet for details

---+ Qubit

   * Full manual can be found [[http://products.invitrogen.com/ivgn/product/Q32866][here]].
   * Two main protocols exist for determining DNA concentration *Broad Range (BR)* and *High Sensitivity*.
      * The protocols are identical, but require the use of different buffer, dye, and standards.
      * The correct protocol to use will be based on expected concentration, but for most work, *BR* is appropriate.
   * Between 1 and 20 µl of sample is required, with 2 µl being the amount typically used by the lab.

---++ *BR* Protocol
   * With this assay, the instrument can read *diluted concentrations* between 10pg/µl and 10ng/µl.
      * Maximum detection window: 0.1ng/µl to 2,000ng/µl (with decreased confidence above 1,000ng/µl) for 20µl and 1µl sample respectively.
      * Typical detection window: 1ng/µl to 1,000ng/µl (with decreased confidence above 500ng/µl) for 2µl of sample.

   1. Make working stock by diluting 1µl of BR dye into 199µl dsDNA BR Buffer for each sample and standard.
      * be sure to make enough working stop for all your samples plus 2 standards.
   1. Aliquot 190 µl working stock into Qubit tubes for both standards.
   1. Aliquot 198 µl working stock into Qubit tubes for each sample.
   1. Add 10 µl of appropriate standard to each standard tube. Briefly vortex after adding.
      %BR% %X% _Should be done before samples to ensure at least 3 minute incubation at RT_
   1. Add 2 µl of each sample to each sample tube. Briefly votrex after adding.
   1. On the instrument select home on the bottom left, then select dsDNA BR assay, and yes to reading new standards
      %BR% %T% _If intending to transfer data to memory card, it is best to clear the data first by selecting data on the bottom right and then clear data._
   1. Follow on screan instructions to read both standards and first sample.
      %BR% %X% Temperature affects the assay, so avoid warming the tubes by holding them excessively in your hands prior to placing them in the instrument, and select 'read' quickly after
      1. After first sample is read, the units and dilution factor can be entered by selecting 'calculate stock concentration'
      1. selecting 'save' will allow easy transfer to a usb memory card after all samples are read.
   1. Continue reading all samples.
   1. If transferring to memory card, select Data from bottom right, memory stick icon will have a green circle next to it, select all data to be transferred (check box top left can be very helpful) and click the usb memory card icon. 

---++ *HS* Protocol
   * With this assay, the instrument can read *diluted concentrations* between 1pg/µl and 500pg/µl.
      * Maximum detection window: 0.005ng/µl to 120ng/µl (with decreased confidence below 0.01ng/µl *and* above 100ng/µl) for 20µl and 1µl sample respectively.
      * Typical detection window: 0.05ng/µl to 60ng/µl (with decreased confidence below 0.1ng/µl above 50ng/µl) for 2µl of sample.
   1. Same protocol as BR, just substitute HS dye, and dsDNA HS buffer for the working stock, and be sure to use the HS standards instead of the BR standards

---+ !NanoDrop
   * 1 µl of sample required, capable of determing concentration between 5ng/µl and 3,000ng/µl according to manufacturer
      * 1µl vs 2µl of sample does not seem to make a difference in readings (see below) 
   * Concentration determination is affected by salts, solvents, and RNA present in the sample.
      * Looking at 260/280 and 260/230 ratios can give idea of contamination from these sources, but ratios only indicate problem.

---++ !NanoDrop Protocol
   1. Take samples, pippette tips, and tube of blank solution (typically water or elution buffer depending on what your DNA was eluted in) across hall in MBB to DNA sequencing core, and in the Zhang lab in WEL
   1. Log into computer and rinse pedestal and arm with di Water. Dry with kimwipes.
      * _In MBB login information is your personal eid and password._
      * _WEL requires no logon information, but does require a key to the Zhang lab._
   1. Initialize the !NanoDrop 1000 software by double clicking on the !NanoDrop icon.
   1. Select nucleic acid
   1. Pipette 1µl liquid from blank tube onto pedestal and lower the arm. 
   1. Hit 'ok' on computer to blank the instrument
   1. Use kimwipe to dry the pedestal. Reload a fresh 1µl aliquot from blank tube onto pedestal, and lower arm back down.
   1. Select Re-Blank from the top left of the window.
   1. Use kimwipe to dry pedestal. Load 1µl of sample onto pedestal and lower the arm.
   1. Enter sample name on the right hand side of the window, and select 'measure' on the top left.
   1. Inspect the curve to ensure it consists of a high reading on the left, a dip, another peak, and then a slope to the baseline.
   1. Record concentration of sample.
      %BR% %T% if determining multiple samples, you can wait till the end and use the 'report - show report - save report - save as csv table' option to have a record of all concentrations as well as 260/280 260/230 ratios.
   1. Repeat drying and loading of samples till done.

---+ Agarose Gel Electrophoresis
   * Capable of estimating DNA concentration between 125 and 30 ng irrespective of salts and solvents.
   * Detection based on actual ng, not on ng/µl.

---++ Agarose Gel Electrophoresis Protocol
   1. Pour agarose gel. 
      * Percentage of the gel should be based on range of linear separation. (see table below)
   1. Be sure to use marker with known amounts of each size marker (for instance the 1kb NEB marker)
   1. Load different amounts of DNA such that you estimate that at least 1 well has between 30ng and 125ng of DNA.
   1. Run gel till achieve good separation of marker.
   1. Take image of gel on imager.
      %BR% %X% Remember that low percentage gels will diffuse quickly necessitating quick return to electrophoresis.
   1. Estimate amount of DNA in each well as compared to known quantities of different bands.
   1. Determine concentration of DNA based on number of µl loaded in each well 

|*Gel Percent*|*Range of separation (kb)*|
|0.3|5-60|
|0.6|1-20|
|0.7|0.8-10|
|0.9|0.5-7|
|1.2|0.4-6|
|1.5|0.2-3|
|2.0|0.1-2|

---+ Comparisons

This section contains information regarding the comparison of the different protocols to assess their limitations.

   * Invitrogen Genomic DNA prep of REL606:
      1. 4 1ml aliquots of an overnight culture were isolated and eluted in 2 25µl elution buffer and pooled together to hopefully eliminate some variation of preparation.
      1. Qubit and !NanoDrop readings were taken in triplicate for 2µl and 1µl aliquots with the following results:
         1. Qubit 2µl is the most accurate reading.
         1. Both methods capable of determining concentration at this level with little difference.
         1. Readings:
|*Method*|*Measurements (ng/µl)*|*Average ng/µl*|*Standard Deviation*|
|Qubit 1µl | 121, 125, 127| 124.3| 3.05|
|Qubit 2µl | 125, 125, 124| 124.3| 0.57|
|!NanoDrop 1µl| 125.44, 128.5, 128.04|127.3|1.65|
|!NanoDrop 2µl| 128.82, 127.39 (-)¡|128.1|1.01|
¡measurement read -3.35ng/µl, but this graph showed this reading to be bad, and was removed from analysis. It is included in this section to highlight the potential for error in reading a sample with the !NanoDrop.

   * Accuracy of measurement across range of concentrations.
      1. 5 50% dilutions were made from the same Genomic DNA prep used in the previous experiment.
      1. Triplicate readings using 2µl for Qubit and 1µl for !NanoDrop were used based on previous findings with the following results:
         1. Qubit was significantly (p < 0.05 by ttest between groups of measurements) more accurate (closer to the expected value) for 4 of 5 measurements.
         1. !NanoDrop was non-signficantly (p = 0.058 by ttest) more accurate for 1 of 5 measurements. 
         1. !NanoDrop was unable to detect an expected DNA concentration of 3.9 ng/µl (average reading of -2.34 ng/µl). Should be noted that this is slightly outside the reported range of the instrument.
%ATTACHURL%/Serial_Dilution.jpg

   * Experiment still planned:
      * Spike excess salt and RNA into sample to see specific differences in !NanoDrop and Qubit

-- Main.DanielDeatherage - 20 Aug 2012
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
jpg	Bad_NanoDrop_output.jpg	r1	manage	68.0 K	2012-08-23 - 19:12	DanielDeatherage	Bad NanoDrop Graph
jpg	Good_NanoDrop_output.jpg	r1	manage	72.5 K	2012-08-23 - 19:12	DanielDeatherage	good Nanodrop Graph
jpg	Serial_Dilution.jpg	r1	manage	26.5 K	2012-08-23 - 17:00	DanielDeatherage	results graph of serial dilution experiment comparing Qubit and Nanodrop
Barrick Lab > ProtocolList > DNAConcentrationDetermination
Contributors to this topic
DanielDeatherage, JeffreyBarrick, KateElston, LindseyWolf, VictorLi, IsaacGifford, PengGeng, JuliePerreau
Topic revision: r9 - 2012-08-23 - 19:12:46 - Main.DanielDeatherage