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ODN Decoys  

Transcription Factor oligodeoxynucleotide decoys (ODN decoys).

Use our GeneDetect« transcription factor decoys to inhibit specific transcription factors in cell culture. 

Complete list of Transcription Factor decoy Products.

Introduction
Transcription factor ODN decoy approach
Advantages and disadvantages of the ODN decoy approach for studying cellular gene expression
ODN Decoys available from GeneDetect.com
How are these decoys used?
Controls
References

Introduction

Cells can respond to stimuli (normal or pathological) by changing the levels of expression of specific genes. The cellular proteins that regulate changes in gene expression are called transcription factors. Transcription factors are generally nuclear and can either be constitutively expressed within the cell (present under basal conditions, for example CREB) or themselves inducible (for example AP-1).

These transcription factor proteins bind specific sequences found in the promoter regions of genes (target genes) whose expression they then regulate (switch on or off). These binding sequences are generally 6-10 base pairs in length and are occasionally found in multiple copies within the promoter regions of target genes.

Although the transcription factor protein-DNA interaction is sequence-specific, the binding site for one given transcription factor may vary by several base pairs within different target genes. Therefore when we describe the specific DNA binding sequence for a transcription factor we refer to the non-variable part of the binding sequence, that is, the transcription factor consensus sequence. For example, the AP-1 transcription factor made up of Fos and Jun proteins binds to the TGACTCA consensus sequence. In comparison the consensus sequence for the Smad transcription factor family which mediate TGF-b, activin and BMP induced changes in gene expression is CAGACA.

Fig. 1. 

Transcription factor ODN decoy approach.

The basic theory behind the transcription factor ODN decoy approach involves flooding the cell with competing synthetic, transcription factor-specific consensus sequences. These synthetic decoys "compete" for binding of the transcription factor with consensus sequences in target genes. If delivered into the cell in sufficient concentrations these "decoys" thus have the potential to attenuate the binding of the transcription factor to promoter regions of target genes and thus attenuate the function of the transcription factor to regulate the expression of its target gene(s). Transfected at high concentrations these decoys have been reported in the literature to completely block transcription factor function. Clearly they represent powerful research tools for studying gene regulation both in vitro and also more recently in vivo (for Reviews see Moshita et al., 1998, Mann and Dzau, 2000).

Fig. 2.

Advantages and disadvantages of the ODN decoy approach for studying cellular gene expression.

Advantages.

  1. ODN decoys offer a means of specifically inhibiting transcription factor function in living cells.
  2. Inexpensive compared to other more classical methods of investigating gene expression such as chloramphenicol acetyltransferase and luciferase constructs in promoter-reporter gene transfection experiments.
  3. Allows for investigation of both endogenous and pathological gene regulation
  4. Proven to be highly effective and selective within in vitro experiments.
  5. Easy to use.

Disadvantages.

  1. An emerging technology that has not yet been fully characterized
  2. Issues of decoy synthesis. High levels of purity and stability required.
  3. Transfection issues. Which method is best. How to optimize transfection.
  4. Issue of controls. What controls are needed.

ODN Decoys available from GeneDetect.com

Click here for a full listing.

We have designed ODN decoys to over 45 common transcription factors. Our decoys are double-stranded synthetic phosphorothioate deoyxynucleotides which range in length from 20-28 base pairs. The transcription factor consensus sequence occurs within the middle of the decoy sequence and is flanked by carefully selected base-pairs that allow for "optimized" transcription factor binding. These ODN decoys are also available labeled so that you are able to optimize your specific transfection technique by imaging the passage of the decoy into the cell (for example by fluorescence microscopy). Our ODN decoys are purified by HPLC and assessed by gel electrophoresis to ensure that >99% of decoy supplied represents full length, double stranded, functional decoy. As a control, matching mutant decoys are available for each transcription factor. Mutant decoys have the same flanking sequences but contain a disrupted consensus sequence in comparison with the (wild type) ODN decoy.

How are these decoys used?

The majority of experiments to date have used transcription factor ODN decoys to examine gene regulation in cultured primary cells and cell lines. The most important variables involved in determining whether or not your ODN decoy performs its required function include (a) the combination of cell type/cell density and transfection reagent used (b) the time cells are incubated with ODN decoy and (c) the concentration of ODN decoy used.

A. The combination of cell type/cell density and transfection reagent used.

While some investigators have achieved success by simply adding naked ODN decoys directly into the cell culture media, the most common method of in vitro ODN decoy transfection is to mix the ODN decoy with a cationic lipid to form a liposome complex before adding the ODN decoy/liposome mixture directly to the media. To aid transfection therefore we recommend mixing of your ODN decoy with an effective liposome-based carrier substance. One transfection reagent we have had good success with in our laboratories is the OligofectAMINE reagent. This is a proprietary formulation available from Invitrogen that is designed to optimize transfection of phosphorothioate ODNs into eukaryotic cells. Stable complexes are formed between the lipid and the ODN permitting efficient delivery of the ODN into mammalian cells. This product represents an improvement over the Lipofectin reagent in respect to transfection of ODNs. Please follow the manufacturers guidelines for use of this product. Product sheets are available via their website. Other transfection reagents we have had previous success with include FuGene 6 from Roche Diagnostics and Superfect Transfection Reagent from Qiagen.

Obviously certain cell types are more susceptible to transfection than others and certain liposome "carriers" perform better with certain cell types. Therefore an amount of trial and error may be required to optimize transfection under your specific conditions. It is therefore helpful to have a way of measuring the kinetics and efficiency of transfection of your ODN decoy. One way of doing this is to use either biotin or fluorescently labeled ODN decoys. After incubation of ODN decoys with your cells you can assess transfection efficiency by fluorescent microscopy or biotin detection. With successful transfection you should expect to see a strong nuclear signal with weaker but noticeable signal in the cytoplasm in 60-90% of your cells.

We have noticed that the transfection efficiency of ODN decoys and indeed ODNs in general (for example antisense ODNs) is much more sensitive to cell density than that of plasmid DNA. Therefore we recommend that a standard seeding protocol be maintained from experiment to experiment and that cell density be varied, if required, to optimize transfection efficiency.

B. The time cells are incubated with ODN decoy.

The time of incubation of cells with ODN decoys is critical. While there is no standard time of incubation due to the many other variables that can affect the incubation time required (including but not limited to ODN decoy concentration, cell type and transfection reagent used) an incubation time of 8hrs (minimum) to 24-28 hrs (maximum without re-addition of ODN decoy) is suggested. Significant ODN decoy degradation has been reported to occur after incubation periods of longer than 24 hrs. Obviously frequent re-addition of ODN decoy could be used to provide continuous blockade of transcription factor functionality beyond 24 hrs if required.

C. The concentration of ODN decoy used.

Within the recent literature ODN decoy concentrations of up to 5mM appear to be well tolerated and highly effective in most cell types with little or no observable effect on cell viability. With the newer transfection reagents (such as OligofectAMINE) a final ODN decoy concentration within the range of 0.1-2ÁM will be sufficient to block transcription factor activity without inducing non-specific cellular toxicity.

Controls.

To confirm that the effects of the ODN decoy are due to a consensus sequence-specific inhibition of transcription factor functionality rather than a non-specific effect of the ODN decoy on cell viability or functioning we recommend using our matching mutant ODN decoys as controls in each experiment. Mutant decoys have the same flanking sequences but contain a disrupted consensus sequence that does not bind transcription factor.

References

Morishita, R., Higaki, J., Tomita N. and Ogihara T. (1998) Application of transcription factor "decoy" strategy as means of gene therapy and study of gene expression in cardiovascular disease. Circ Res 82, 1023-1028.

Mann, M.J. and Dzau, V.J. (2000) Therapeutic applications of transcription factor decoy oligonucleotides. J. Clin. Invest. 106, 1071-1075.

 

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