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This is an ALISA protocol for protein concentration.



PBST 0.1% Tween_20

Coating Buffer

Carbonate/bicarbonate (pH 9.6) 100 ml
0.293 g NaHCO3 (anhydrous)
0.159 g Na2CO3 (anhydrous)

  • Use carbonate/bicarbonate to adjust pH to 9.6*

Blocking Buffer

2% Amersham ECL Advance Blocking Reagent in PBST

Phosphate/Citrate Buffer

50 mM citric acid and 100 mM sodium phosphate
0.74 g dibasic sodium phosphate (anhydrous)
1.3 g citric acid (anhydrous)
Dissolve in 50 ml water
*Adjust pH to 5.0*
*Add 40 μl fresh 30% H2O2 to 100 ml solution before use*

Other Reagents

Monoclonal 6E10
iQ SYBR Green Supermix



  • Dilute 6E10 (1mg/ml stock) 1:1000 in Coating Buffer to make the Coating Solution
  • Add 200ul Coating Solution to each well of a 96-well flat-bottom microtiter plate
  • Incubate at room temperature with shaking for 2 hours or overnight in the cold room


  • Dump Coating Solution into the sink
  • Add 200ul Blocking Buffer
  • Incubate at room temperature with shaking for at least two hours or overnight in the cold room

Incubation with protein preparation

  • Prepare the desired dilution series of the protein from 500nM using PBS as diluent
  • Add 100ul of each standard to the plate's wells in triplicate or quadruplicate
  • Add 100ul of PBS in triplicate or quadruplicate as a control
  • Incubate at room temperature for 1.5-2h

Aptamer Incubation

  • Dilute detecting aptamer (100 μM) 1:1000 in Blocking Buffer
  • Add 100ul of the aptamer solution to each well
  • Incubate at room temperature with shaking for 1-1.5h
  • Wash the plate with four 10min washes with 110ul PBST per well
  • Tap the plate dry on a pad of Kimwipes

Aptamer Recovery

  • Reverse the antibody-protein-aptamer sandwich by floating the microtiter plate in a 95 °C water bath and incubating for 10-15 minutes. This should irreversibly denature the capture antibody and target protein, the aptamer will be reversibly denatured.
  • Transfer 1 μL of each well to a plate suitable for qPCR (conical wells coated with silicon to avoid non-specific interaction with protein).
  • Add positive and negative PCR controls to the plate.
  • Add primers to each well to a final concentration 100-500 nM.
  • Add 12.5 μL iQ SYBR Green Supermix to each well.
  • Add H2O to a final volume of 25 μL.

Perform qPCR


  • Record the Ct values for all samples, standards and controls and compare to the positive control to estimate initial copy number.
  • Interpolate samples into the standard curve to estimate protein concentration.


A related protocol has been published: Yoshida Anal Bioanal Chem 2009