Method for detecting transcription factor-protein interactions

Abstract

A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation in part of application Ser. Nos. 09 / 877,738, 09 / 877,243, 09 / 877,403, and 09 / 877,705, each filed on Jun. 8, 2001, each of which are incorporated herein by reference.FIELD OF THE INVENTION[0002]The present invention relates to methods for detecting activated transcription factors in a cell sample. More specifically, the invention relates to methods for detecting interactions between activated transcription factors in a cell sample and compositions, kits, and uses arising there from.DESCRIPTION OF RELATED ART[0003]All living organisms use nucleic acids (DNA and RNA) to encode the genes which make up the genome for that organism. Each gene encodes a protein that may be produced by the organism through expression of the gene.[0004]It is important to note that the mere presence of a gene in a cell does not communicate the functionality of that gene to the cell. Rather, it is only when the gene is expressed and...

AI Technical Summary

Benefits of technology

The present invention provides methods and kits for isolating DNA probes that bind to activated transcription factors. These methods involve contacting a biological sample with a library of double stranded DNA probes, and separating the probes that form complexes with the activated transcription factors from non-complexed probes. The isolated probes can then be identified using an agarose gel separation and a hybridization array. The methods, arrays, and kits can be used for detecting activated transcription factors in biological samples.

Problems solved by technology

A difficulty arises in needing to generate antibodies to each protein to be detected.

Unfortunately, it tends to be difficult to isolate a sufficient amount of protein to obtain a reliable sequence.

A further difficulty associated with quantifying gene expression by measuring an amount of protein gene product in a cell is that protein expression is an indirect measure of gene expression.

As a result, it is hard to determine whether protein expression changes over time due to cells being exposed to different stimuli.

One of the difficulties associated with measuring gene expression by measuring transcription factors is that one must measure the subset of transcription factors which are “activated.” Certain post-transcriptional modifications occur which render transcription factors “active” in the sense that they are capable of binding to DNA.

This method is impractical for detecting multiple different activated transcription factors due to difficulties associated with developing numerous different antibodies having the requisite bind specificities.

Since individual gel shift assays must be performed for each activated transcription factor—DNA complex, this method is currently impractical for measuring multiple different activated transcription factors at the same time.

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