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GeneDetect oligonucleotide gene probes  

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GeneDetect® oligonucleotide gene probes.

Click on one of the categories to your left to BROWSE or click on the search button on the Navigation Bar to SEARCH for a specific probe among the more than 4000 scientifically validated gene probes available from GeneDetect.

Introduction
Uses
How supplied
Labeling options
Costs
Discounts
Which labeling method is best for your application?
Correct storage and handling
The GeneDetect® oligonucleotide probe database

Introduction

"Gene Probe: A piece of DNA that binds specifically to a particular gene or part of a gene"

In measuring tissue gene expression, independent of the technique used, the sequence of the gene probe must be complementary to the nucleotide bases of the specific mRNA or DNA sequence of interest. Gene probes can be as small as 20-40 base pairs or be up to 1000bp long. GeneDetect® oligonucleotide gene probes are produced synthetically by an automated chemical synthesis using sequences derived from the GeneDetect® oligonucleotide probe database and are usually 40-50 nucleotides long. The majority of our probes are validated by prior publication in the scientific literature. Each online product description contains a link to published article(s) in PubMed/Medline that have used and characterized the probe. 

Dear GeneDetect, 
I just wanted to let you know that I had great success with your GreenStar DIG oligos. Until I worked with your oligos I spent 2 months on this project with very limited success. I will definitely be back in touch for future projects. Regards, Jeanette 

Jeanette M. Rheinhardt, B.S., HTL (ASCP)
Senior Scientist I, Pathology Biomarker Development, Localization and Confirmation, Novartis Institutes for Biomedical Sciences, Inc
250 Massachusetts Avenue, Room 4C-480, Cambridge, MA 02139

 

Uses of GeneDetect® oligonucleotide gene probes

GeneDetect® oligonucleotide gene probes can be used in any of the following techniques.

In situ hybridization
Dot/slot blotting (link coming soon)
Colony/plaque hybridization (link coming soon)
Northern blots (link coming soon)
Southern blots (link coming soon)

How supplied

GeneDetect® oligonucleotide gene probes are supplied lyophilized with 2500 pmoles (~35ug) of unlabeled probe per vial. All probes are cartridge purified to ensure product supplied is >95% full length meaning that you do not get a random mixture of half synthesized probes that could lead to increased background staining or cross hybridization to non-targeted genes. Probes are also available labeled with either biotin, FITC, rhodamine or digoxigenin (DIG, Licensed from Roche Diagnostics GmbH)§.
Read below to determine the labeling method that will most closely suit your needs.

When you purchase a standard probe pack you are   supplied with three single-stranded GeneDetect® oligonucleotide gene probes (labeled or unlabeled) in sufficient quantities that allow for many hybridization experiments to be performed. The figure to the right shows the typical purity obtained by cartridge-purifying your GeneDetect probes. Cartridge purification works well over a wide range of probes lengths.

A standard GeneDetect® oligonucleotide gene probe pack contains THREE oligonucleotides:

1. the antisense (complementary) probe to the gene of interest
2. its sense (control) companion and
3. a poly(dT) probe that allows you to confirm the quality of the mRNA in your sample.

You also receive full probe sequence information in the Product Specification Sheet, copies of up to three journal articles that have characterized and used the probe, protocols and relevant GenBank FASTA/BLAST printouts showing target specificity. You are also eligible for full technical support from our resident expert scientists via email to Scientific@GeneDetect.com to ensure successful use of the probe within your experiments. All technical support questions are answered within 24 hours.

Dear GeneDetect, 
The GreenStar Biotin hyperlabeled VEGF probes we purchased from you worked very well. We are very happy with the results. Thanks again for your kind help. We really enjoy your product. Sincerely 

Dr Wenyin Shi
University of Florida ARB R5-187, 1600 SW Archer Rd 
Gainesville, FL 32610 USA

 

Labeling options

In addition to supplying GeneDetect® oligonucleotide probes unlabeled, we can supply probes 5' labeled with one molecule of either biotin, FITC or rhodamine. You will need to specify the labeling required when making your order. 

GreenStar*TM hyperlabeled probes are optimized for use with in situ hybridization.

GreenStar*TM hyperlabeled probes have 10 x label molecules added to the 3' end for enhanced sensitivity.  10 molecules of either biotin, FITC, rhodamine or digoxigenin (DIG)§ are attached to the 3' end of the probe. These labels are optimally spaced for enhanced detection of the probe using standard methods. 

Dear GeneDetect,
The GreenStar FITC probe that you synthesized for us last month is giving **wonderful** results and our lab staff and customers were extremely pleased and happy. Thanks for the good work and we will always give referrals to you.

Rebecca Caffrey, PhD
Regional Director of Business Development, Services
Asterand, Inc, 440 Burroughs, TechOne, suite 501, Detroit, MI 48202

 

On request we are also able to add to your GeneDetect® probe(s) the 3' TTTTTCg linker enabling oligonucleotide labeling with direct fluorescent 3DNA StarfishTM technology. StarfishTM is a trademark of Genisphere Inc, www.Genisphere.com. In this case you will also need to purchase the probe labeling kit from Genisphere Inc.



Summary of current probe labeling options that can be selected during probe purchase:

Label Amount of Probe supplied
Unlabeled 2500 pmoles or ~ 35µg
5' Biotin 5000 pmoles or ~ 70µg
5' FITC 5000 pmoles or ~ 70µg
5' rhodamine 5000 pmoles or ~ 70µg
3' GreenStar* Biotin 350 pmoles or ~ 5µg
3' GreenStar* FITC 350 pmoles or ~ 5µg
3' GreenStar* rhodamine 350 pmoles or ~ 5µg
3' GreenStar* DIG 350 pmoles or ~ 5µg
3' TTTTTCg linker 2500 pmoles or ~ 35µg

Costs

All prices are in US dollars. Shipping costs are not included in these prices. Prices are subject to change. Please add $139 per probe pack if you wish to have a custom probe prepared.

Label Cost per probe (USD)
Unlabeled $159
5' Biotin Unlabeled + $90 = $249
5' FITC Unlabeled + $90 = $249
5' rhodamine Unlabeled + $90 = $249
3' GreenStar* Biotin Unlabeled + $189 = $348
3' GreenStar* FITC Unlabeled + $189 = $348
3' GreenStar* rhodamine Unlabeled + $189 = $348
3' GreenStar* DIG Unlabeled + $189 = $348
3' TTTTTCg linker Unlabeled + $10 = $169

Discounts

We run various discounts, promotions and sales throughout the year. To see what is currently available for you to take advantage of click here or here.

Which labeling method is best for your application?

The type of labeled probe you choose will depend upon the final use you have in mind for your probe. The following table summarizes the different types of labeled probes available and their suitability for various applications.

Label Application Suitability 
High = ++++
5' label In situ hybridization ++
Dot/slot blotting ++++
Colony/plaque hyb. ++++
Northern blots ++++
Southern blots  ++++
GreenStar* In situ hybridization +++++++
Dot/slot blotting ++++
Colony/plaque hyb. ++++
Northern blots ++++
Southern blots  ++++


Dear GeneDetect,
I received the Surfactant B oligo probe Dec 15th and completed one experiment before I left for the holidays. Success!! The results were stunning on the first try. 

Mike Roosevelt, New York University
Dep't of Medical and Molecular Parasitology, 341 E 25th St 
OPH-507 New York, NY 10010

Correct storage and handling

Storage

Standard lyophilized oligonucleotides are stable for many years if they are stored frozen at -20°C. When in solution however, to prolong shelf life the oligonucleotide should be kept frozen at -20°C preferably as a "stock solution" with a final concentration not much less than 15m M (~ 200ng/ul of a 48mer probe) in TE buffer (Tris-EDTA 10 mM, 1mM) buffer at pH 7.5-8.0.

A slightly alkaline buffer prevents possible depurination of the oligonucleotide. In an acid buffer A and G bases are eliminated, leading to oligonucleotide damage. While TE buffer is the preferred solution for oligonucleotide storage it is not necessarily the best solution for oligonucleotide use. TE buffer may interfere with various enzyme dependent reactions so the required amount of oligonucleotide probe should be removed from the stock solution and diluted in nuclease free distilled water for labeling or other procedures.

While oligonucleotides are very stable they are prone to BACTERIAL attack. Use autoclaved tips and tubes.

Storage versus (stability)

Dissolved at 25C (1 week to 3 months)
Lyophilized at 25C (2 months to 1 year)
Dissolved (<<15µM) at –20C (1 year to 3 years)
Dissolved (>15µM) at –20C (3 years+)
Lyophilized at –20C (indefinite)

5' or 3' labeled oligonucleotide probes should be kept away from air. Making sure the aliquot tube screw cap is on properly and that tubes are kept in properly closed ziplock bags should suffice. Fluorescent-labeled probes (FITC and rhodamine) should be shielded from light to prevent bleaching. Cover the tube in aluminum foil.

Repeated freeze-thawing can dramatically lower the shelf life of an oligonucleotide.

Dear GeneDetect,
You may remember that I ordered some Green Star FITC oligo probes from you last October. I am really happy with them and the signal that I have been getting with my sheep embryos has been excellent. In fact, I am so happy with them that I would like to order some more! 

Dr.Jane Taylor
Roslin Institute, Roslin, Midlothian, EH25 9PS

Handling

When you receive your GeneDetect® oligonucleotide gene probe it may be difficult to see the lyophilized oligonucleotide at the bottom of the tube. To resuspend the oligonucleotide please follow this procedure in a step wise fashion.

  1. Centrifuge the tube for a few seconds to ensure the oligonucleotide probe is fully collected at the bottom of the tube.
  2. Then carefully open the tube. Be aware that electrostatic charge build-up on standard laboratory gloves can cause DNA pellets to leave aliquot tubes. We suggest you hold the tube right at the bottom and slowly remove the cap.
  3. Add an appropriate amount of TE buffer or sterile nuclease free water, close the tube, allow to rehydrate for 2 minutes.
  4. Mix the tube by hand for a minute before using a vortex on the solution for 15 seconds. Re-centrifuge the solution. Aliquot and/or store the oligonucleotide probe.

The GeneDetect® oligonucleotide probe database

The GeneDetect® oligonucleotide probe database was created several years ago and is continually being updated. Presently it holds the "corrected" nucleotide sequences of over 4000 oligonucleotide gene probes referenced in peer-reviewed scientific journals to successfully detect tissue gene expression. Increasingly the sequences of proprietary probes designed in-house are being added to this database. Significantly, the sequences of all entries derived from the scientific literature are checked by our staff prior to inclusion since we have found a sequence error rate of approximately 4% in these sequences. Limited access to this database is provided free via this website.

  1. Use this website to search for a gene/mRNA whose expression you are interested in
  2. Find the corresponding GeneDetect® oligonucleotide gene probe
  3. Follow the hyperlink from the Product Description to the PubMed/Medline citation(s) of the original article(s) characterizing the Probe and tissue expression of the gene/mRNA.

Specific sequence information is available from this database. Please contact us for pricing via Sales@GeneDetect.com

§The use of digoxigenin technology to label nucleic acids is licensed under patents (EP 0 324 474, US 5.344.757, US 5.702.888, US 5.354.657, JP 1999884 and HK 1169) owned by Roche Diagnostics GmbH. For further information on products to label and detect digoxigenin-modified nucleic acids refer to www.roche-applied-science.com/dig/


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