Application Overview

IRDye end-labeled oligonucleotides and the Odyssey^® CLx Infrared Imaging System provide a safe and sensitive alternative to radioactive EMSA detection. 

• Easily adapt existing mobility shift assay protocols by replacing the radiolabeled oligonucleotides with IRDye® end-labeled oligonucleotides.

• IRDye fluorescent labels are stable, non-hazardous, and easy to use.

• Perform direct fluorescent detection in the wet gel, without waiting for gel drying or film exposures.

• Work more efficiently – go from binding reactions to results in less than two hours!

Advantages of Near-Infrared Fluorescent EMSA detection

Near-Infrared	Radioisotype
Easy access and disposal	Regulatory restrictions, disposal hassle and cost
Labeled oligos have extended stability	Short half-life of label
Non-hazardous	Hazardous
Wet gel imaged while still between gel plates	Gel drying and film/phoshor-screen exposure required
Fast, convenient detection of probe	Time-consuming, inconvenient detection
Gel can be replaced and run longer if needed	Gel run time cannot be extended
Results available in less than two hours	Experiment typically takes more than one day

Workflow

Technical Resources

• Urh, M et al.
  The Use of IR Fluorescent Technology for the Analysis of Signal Transduction and Protein-Nucleic Acid Interactions.
  Poster presentation, Advances in Genome Biology and Technology Conference (2002)

• Electrophoretic Mobility Shift Assay (EMSA) Using IRDye Oligonucleotides

• Odyssey Infrared EMSA Kit Instruction Manual

• Click here for a complete list of pack inserts

PubMed

Publishing with LI-COR data?

Shaik, SS et al.
Low intensity shear stress increases endothelial ELR+ CXC chemokine production via a focal adhesion kinase-p38{beta} MAPK-NF-{kappa}B pathway.
J Biol Chem. 284(9):5945-55 (2009)

Helmink, BA et al.
MRN complex function in the repair of chromosomal Rag-mediated DNA double-strand breaks.
J Exp Med. 206(3):669-79 (2009)

Steiner, S et al.
The role of phosphorylation in redox regulation of photosynthesis genes psaA and psbA during photosynthetic acclimation of mustard.
Mol Plant. 2(3):416-429 (2009)

Zhou, Q et al.
DNA-binding Domain within the Brh2 N Terminus Is the Primary Interaction Site for Association with DNA.
J Biol Chem. 284(13):8265-73 (2009)

Besse, F et al.
 Drosophila PTB promotes formation of high-order RNP particles and represses oskar translation.
Genes Dev. 23(2):195-207 (2009)

Wilson, BJ et al.
CUX1 transcription factor is a downstream effector of the proteinase-activated receptor 2 (PAR2).
J Biol Chem.284(1):36-45 (2009)

Emami, K et al.
 Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system.
J Biol Chem. 284(2):1086-96 (2009)

Feng, J et al.
Cardiac remodelling hinders activation of cyclooxygenase-2, diminishing protection by delayed pharmacological preconditioning: role of HIF1a and CREB.
Cardiovasc Res. 78(1):98–107 (2008)

Lu, P et al.
Structural basis of natural promoter recognition by a unique nuclear receptor HNF4alpha: diabetes gene product.
J Biol Chem. 283(48):33685-97 (2008)

Zhang, S et al.
Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein-DNA interactions.
Proc Natl Acad Sci USA. 105(11):4156-61 (2008)

Sharifi, N et al.
Effects of manganese superoxide dismutase silencing on androgen receptor function and gene regulation: implications for castration-resistant prostate cancer.
Clin Cancer Res. 14(19):6073-80 (2008)

Danno, H et al.
Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.
Proc Natl Acad Sci USA. 105(14):5408-13 (2008)

Berg, DT et al.
Smad6s regulates plasminogen activator inhibitor-1 through a protein kinase C-beta-dependent up-regulation of transforming growth factor-beta.
J Biol Chem. 280(15):14943-7 (2005)

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