Other Equipment Available

Agilent 2100 Bioanalyser

pipet in flask

The Agilent 2100 Bioanalyser is a microfluidics-based platform for sizing, quantification and quality control of DNA and RNA.

General Principle

After loading the sample on the Agilent chip of choice (see below), the sample moves through microchannels and sample components are electrophoretically separated. Smaller fragments migrate faster than the large ones. The fluorescent dye molecules intercalate into DNA or RNA strands. They are then detected by their fluorescence and translated into gel-like images (bands) and electropherograms (peaks).

General Information and Specifications

  • Faster than electrophoresis gels as it can analyze 11-12 samples in 30 minutes
  • Easy to use-load chip, press “start”, the instrument does the rest
  • Chip preparation takes less than 5 minutes
  • Ready-to-use assays and pre-packed reagent kits (see below)
  • High quality digital data
  • Minimal sample consumption (1 ul)
  • Quantification over a large linear dynamic range of PCR fragments from 25 to 12,000 bp
  • The Agilent assay kits can be used to analyzed, for example; PCR, RT-PCR, and restriction digests. They can also be used to do the sizing, quantification and quality control of DNA sequencing libraries.

DNA

  • For accurate determination of DNA concentration, the sample should have a 0.5 to 50 ng/ul concentration.
  • When analysis restriction digests, add EDTA or heat inactivate the restriction enzyme before loading the sample on the Agilent chip.
  • The maximum salt concentration that can be in the sample is 250 mM for KCl or NaCl and 15 mM for MgCl2.
  • Several assay kits are available for sizing and analysis of double-stranded DNA fragments:
  • Agilent DNA 1000 assay kit: detection of fragments between 25 to 1,000 bp.
  • Agilent DNA 7500 assay kit (currently available at GGF): detection of fragments between 100 to 7,500 bp.
  • Agilent DNA 12000 assay kit: detection of fragments between 100 to 12,000 bp.
  • Agilent High sensitivity DNA assay kit: detection of fragments between 50 to 7,000 bp.

RNA

  • For Eukaryote Total RNA, the RNA fragments detected are 18S and 28S.
  • For Prokaryote Total RNA, the RNA fragments detected are 16S and 23 S.
  • The integrity of the total RNA sample can also be determined. This should predict if an experiment such as RT-PCR or microarray will work.
  • RNA samples should be in deionized water and not more concentrated than specified below. Otherwise, the sample needs to be diluted in dH2O to the appropriate concentration. The Agilent Company clearly states that samples submitted in 50 mM Tris or 50 mM NaCl might influence the performance of the assay.
  • Two assay kits are currently available at GGF for analysis of RNA fragments:
  • RNA 6000 nano kit: For estimation of RNA concentration, total RNA in sample must be between 25-500 ng/ul and mRNA sample concentration between 25-250 ng/ul. The qualitative range is 5-500 ng/ul for total RNA and 25-250 ng/ul for mRNA.
  • RNA 6000 pico kit: For estimation of RNA concentration, total RNA in sample must be between 200-5,000 pg/ul and mRNA sample concentration between 500-5,000 pg/ul. The qualitative range is 50-5,000 pg/ul for total RNA and 250-5,000 pg/ul for mRNA.

 
For more applications, please see: http://www.chem.agilent.com/Library/brochures/5989-7725EN.pdf

Cost

  • $40 per chip for 1 to 12 samples
  • $35 per chip if it is part of an on-going project at GGF