Gene Expression Analysis
Looking for a way to simplify and improve traditional genome and gene expression analysis methods?  Dynabeads® serve as an irresistibly easy-to-use magnetic solid-support. As the reactions can be performed in very small volumes, you only need a small starting sample for your analysis.

Application examples

Applications include: Differential display, 5’RACE, S1 nuclease mapping, DNase footprinting, purification of RNA/DNA binding proteins, and subtractive hybridization for isolation of tumor specific alterations and identification of toxin genes in pathogens.

Streptavidin-Coupled Dynabeads® or Dynabeads® Oligo (dT)25 are used in many gene expression profiling methods, e.g. based on representational cloning and sequencing of cDNAs from libraries. Double stranded DNA sequences longer than 2 kb are effectively immobilized with the Dynabeads® kilobaseBINDER™ Kit.

Streptavidin-coupled Dynabeads® used in a RTPCR/ECL assay provide a practical and sensitive approach for detection of various metastatic cancers in tissues and blood. The beads have also been cited in numerous published articles on the SAGE® technology and in a related method published by S. Brenner et al.

Why choose streptavidin-coupled Dynabeads® for genome or gene expression analysis?

  • Rapid and convenient magnetic solid-phase handling
  • Fast reaction kinetics
  • Less non-specific binding and more thorough washing
  • Isolate pure and homogeneous transcription factors in 30 minutes
  • Well suited for protein isolation
  • Enrich DNA and RNA binding proteins up to 20,000 fold
  • DNA coupled to Dynabeads® via the streptavidin-biotin association can be re-used at least ten times

Related References

Reverse transcription PCR
Jost R et al, (2007) Biotechniques 43: 206-211. Magnetic quantitative reverse transcription PCR: A high-throughput method for mRNA extraction and quantitative reverse transcription PCR.

DNA/RNA binding protein isolation
Mehta A et al. (1998). A sequence-specific RNA binding protein complements Apobec-1 to edit apolipo protein B mRNA. Mol. Cel. Biol. 18(8):4426-4432.
Biroccio A. et al. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. J. Virol. 76(8):3688-3696.
Nordhoff E. et al. (1999). Rapid identification of DNA-binding proteins by mass spectrometry. Nat. Biotechnol. 17: 884-888.
Brodsky AS. and Silver A. (2002). A microbead based system for identifying and characterizing RNA-protein interactions by flow cytometry. Mol. Cel. Proteomics 1(12):922-929.

Solid-phase DNase footprinting

Fletcher TM. et al. (2002). Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition. Mol. Cel. Biol. 20(17): 6466-6475.

Solid-phase S1 nuclease mapping

Dziembowski A. et al. (2001). Analysis of 3’ and 5’ ends of RNA by solid-phase S1 nuclease mapping. Anal. Biochem. 294:87-89.

Subtractive hybridization

Hansen-Hagge TE. et al. (2001). Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation mediated subtraction (Limes). Nucl. Acids Res. 29(4):e20.
Pradel N. et al. (2002). Genomic subtraction to identify and characterize sequences of Shiga toxin-producing Escherichia coli O91:H21. Appl. Env. Microbiol. 68(5):2316-2325.
 Laveder P. et al. (2002). A two-step strategy for constructing specifically self-subtracted cDNA libraries. Nucleic Acids Res. 30(9): e38

Differential display

Kornmann B. et al. (2001). Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Res. 29(11). e51
Brenner S. et al. (2000). In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs. PNAS. 97(4): 1665-1670.

Limes

Hansen-Hagge TE. et al. (2001). Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation mediated subtraction (Limes). Nucl. Acids Res. 29(4):e20.

5’RACE

Schramm G. et al. (2000).A simple and reliable 5’-RACE approach. Nucl. Acids Res. 28(22):e96

SAGE®

 Velculescu VE. et al. (1995). Serial analysis of gene expression. Science. 270(5235): 484-487.

TOGA

Sutcliffe JG. et al. (2000). TOGA: An automated parsing technology for analyzing expression of nearly all genes. PNAS. 97(5): 1976-1981.

RAGE

 Wang A. et al. (1999). Rapid analysis of gene expression (RAGE) facilitates universal expression profiling. Nucleic Acids Res. 27(23): 4609-4618.

Double stranded DNA fragments > 2 kB

Fletcher TM. et al. (2002). Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition. Mol. Cel. Biol. 20(17): 6466-6475.
Heald R. et al. (1996) Self-organization of microtubules into bipolar spindles around artificial chromosomes in Xenopus egg extracts. Nature 382:420-425.

S1 nuclease mapping

Lindblad-Toh K. et al. (2000). Large-scale discovery and genotyping of single nucleotide polymorphisms in the mouse. Nature Genetics. 24:381-386.

RTPCR/ECL

 Miyashiro I. et al. (2001). Molecular strategy for detecting metastatic cancers with use of multiple tumor-specific MAGE-A genes. Clin. Chem. 47(3):505-512.