Navigation Links
Quantitation of DNA for Automated Sequencing Using the VersaFluor Fluorometer

Wenda Ribeiro and Margaret Saha, Department of Biology, College of William and Mary, Williamsburg, Virginia 23187


Introduction
DNA sequence analysis is an integral part of genetic research. Recently, the use of automated sequencers has become increasingly more common in small research laboratory settings. However, the success of automated long read sequencing reactions require precise picomolar concentrations of DNA. We have successfully employed the VersaFluor fluorometer (Bio-Rad) to accurately and routinely quantify DNA for sequencing with the LiCor 4200 automated sequencer.


Materials and Methods
A genomic clone for xHif (Xenopus hypoxia inducible factor) was isolated by a homology screen of a Xenopus muscle genomic library using a 32P-dCTP labeled mouse probe (a gift of Steven McKnight). Phage DNA was isolated using a standard protocol, digested with EcoRI and HindIII and run on a 1.2% agarose gel (Figure 1). Bands corresponding to insert DNA were excised and the DNA isolated on glass milk. The DNA fragments were subcloned into BlueScript SK+ (Stratagene) and transformed into DH5a cells. Plasmid DNA was isolated using anion exchange chromatography. A λZap (Stratagene) cDNA clone for Xenopus xHif was also isolated using a homology screen of a tadpole library. Rescued plasmid DNA was obtained using the manufacturers instructions and was subsequently transformed into DH5α cells. Plasmid DNA was isolated using anion exchange chromatography.

Quantitation of the DNA was achieved using the Fluorescent DNA Quantitation Kit (Bio-Rad) with a 360 nm excitation filter and a 460 nm emission filter. The standard curve was established for quantification of DNA concentrations ranging from 1005,000 g/ml by plotting seven points of varying DNA concentrations made by serial dilution of control calf thymus DNA. All dilutions were made in 2 ml of 1 g/ml Hoechst 33258 dye and included 0 ng DNA as a blank and 10,000 ng DNA as the upper range. The values were recorded in relative fluorescence units (RFUs) and were plotted on a graph with the x axis = DNA concentration (ng) and the y axis = RFU (Figure 2). The slope of the line was determined to be 1.0.

By employing the equation y = mx+b, we established the value of b to be equal to 0. Therefore, by setting the upper range value at 10,000 RFU using 10 l of 1 mg/ml calf thymus DNA and using 2 l of the sample DNA in 2 ml of the 1 g/ml Hoechst dye, the RFU reading is equal to ng/ml for our sample. We are then able to calculate the volume of DNA needed to obtain a 250 femtamolar concentration per reaction.


Results and Discussion
Using the Excel II sequencing kit (Epicenter) and quantifying our DNA with the VersaFluor fluorometer, we have been able to achieve highly readable and reproducible sequencing runs of up to 1,200 bp with the LiCor 4200 automated sequencer. This has enabled us to sequence the entire 2.2 Kb cDNA for Xenopus hypoxia inducible factor, xHIF, in several runs, and will allow us to sequence our genomic clone easily and efficiently.

The correct concentration of DNA in each reaction is the key to obtaining good reads on the LiCor 4200. This entails precise quantitation of the DNA. The VersaFluor fluorometer has proven to be easy to calibrate and provides excellent and reproducible results.

This work is supported by National Institute of Health Grant 1815HD32080 and National Science Foundation Grant 1BN9553176.


back to top
'"/>

Source:


Page: All 1 2 3

Related biology technology :

1. Quantitation of Cabergoline at Extremely Low Plasma Concentrations with a Triple Quadrupole Mass Spectrometer
2. Bioanalytical Method Intraday Validation for the Quantitation of Paroxetine in Bovine Plasma using the TSQ Quantum Mass Spectrometer
3. Quantitation of the Protein MIA as a Marker for Chondrocytes in Research Samples
4. Comparison of Different Methods of mRNA Quantitation
5. Quantitation of RNA for Hybridization Blots Using the VersaFluor Fluorometer
6. Quantitation of Lymphangiogenesis Using the iCycler iQ Real-Time PCR Detection System and Scorpions Detection System, Rev A
7. Quantitation of GAD67 Gene Expression in Prefrontal Cortex of Schizophrenia Patients Using the iCycler iQ Detection System and Molecular Beacons, Rev A
8. Benchmark Plus Microplate Reader: Quantitation of Protein Concentration Using Two Different Colorimetric Assay Kits, Rev A
9. A Robust LC/MS/MS Method for the Quantitation of Very Long Chain Fatty Acids for Research into the Characterization of Peroxisomal Disorders
10. A new LC/MS/MS Research Method for Rapid Quantitation of Five Immunosuppressant Drugs, including Mycophenolic Acid (MPA)
11. Separation and Quantitation of R and S Enantiomers using Normal Phase Chromatography on an API 3000 LC/MS/MS System
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:2/11/2016)... CRUZ, Calif. , Feb. 11, 2016  Dovetail ... applications to its beta program for a planned metagenomic ... will present the company,s metagenomic genome assembly method in ... Advances in Genome Biology & Technology conference in ... assembly of these highly complex datasets is difficult. Using ...
(Date:2/11/2016)... ... February 11, 2016 , ... Global Stem Cells ... in Quito, Ecuador. The new facility will provide advanced protocols and state-of-the-art techniques ... the world. , The new GSCG clinic is headed by four prominent ...
(Date:2/10/2016)... is introducing a hybrid membership model which will provide ... joining or renewing through an organizational purchasing model. For ... employee in any size association or AMC office can ... benefits.   John H. Graham, IV , ... organizations of any size and their employees to gain ...
(Date:2/10/2016)... ... February 10, 2016 , ... Benchmark Research, a fully-integrated network ... two long-standing principal investigators (PI) to the roles of Chief Medical Officer, Clinical ... Dr. Laurence Chu, a Benchmark Research PI in the Austin office, will assume ...
Breaking Biology Technology:
(Date:2/11/2016)... , Feb. 11, 2016  Vigilant Solutions announces today that ... are being used by Lee,s Summit ... recent location and arrest of a homicide suspect. ... covers around 65 square miles and is home to ... Department has a single mobile license plate reader system and ...
(Date:2/8/2016)... , February 8, 2016 ... payment platform which presents innovation for clients, comfort ... feature called VoiceKey. --> Worldcore ... presents innovation for clients, comfort and unbeatable security, ... --> Worldcore is the ...
(Date:2/3/2016)... , February 3, 2016 ... market research report "Automated Fingerprint Identification System Market by ... Search), Application (Banking & Finance, Government, Healthcare, and Transportation) ... MarketsandMarkets, the market is expected to be worth USD ... 21.0% between 2015 and 2020. The transformation and technology ...
Breaking Biology News(10 mins):