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.