Methods and kits for identifying and quantifying RNAs and DNAs associated with RNA and DNA binding proteins

Abstract

Methods and kits for identifying RNAs and DNAs associated with an RNA or DNA binding protein via a detector specific for the binding protein or protein bound thereto which is linked to an oligonucleotide capable of directing the synthesis of cDNA copies of RNA or DNA that are in close proximity to or in the vicinity of the bound detector are provided.

Description

FIELD OF THE INVENTION [0001] A new methodology has now been developed for the identification and / or quantification of RNAs which associate with RNA binding proteins and DNAs which associate with DNA binding proteins. This methodology utilizes detectors specific to selected RNA or DNA binding proteins or proteins bound to these the RNA or DNA binding proteins to direct the synthesis of cDNA copies of RNAs or DNAs that are in close proximity to or in the vicinity of the detector via a selected oligonucleotide linked to the detector. Examples of detectors specific to selected RNA or DNA binding proteins include, but are not limited to, antibodies, single chain FVs (ScFVs), complementarity determining regions (CDRs) and other molecules that can interact with RNA or DNA binding proteins. Identification of RNAs associated with RNA binding proteins or DNAs associated with DNA binding proteins is useful in identifying and designing therapeutic agents which alternatively regulate the functi...

AI Technical Summary

Benefits of technology

The present invention provides methods for identifying and quantifying RNAs or DNAs associated with a RNA or DNA binding protein, as well as the cis-acting element of RNAs associated with a selected RNA or DNA binding protein. These methods involve adding a detector specific for the RNA or DNA binding protein to cells, which binds to the protein and directs the synthesis of cDNAs of RNAs or DNAs in close proximity to the detector. The cDNAs or aRNAs are then used as probes to screen for RNAs or DNAs that bind to the detector. The invention can be used with fixed cells or live cells and provides tools for identifying and characterizing the interactions between RNA or DNA binding proteins and their cognate RNAs or DNAs.

Problems solved by technology

Characterization of RNA binding proteins has been difficult.

However, these assays suffer from a lack of sensitivity and specificity that often result in erroneous results.

Images