C-LANA Counter Screen: DNA intercalators Measured in Biochemical System Using Plate Reader - 2117-02_Inhibitor_Dose_CherryPick_Activity_Set2
We wish to exclude "hits" which non-specifically inhibit C-LANA DNA binding by intercalating into DNA. Compound libraries contain many flat molecules which may intercalate into DNA. We modified and miniaturized an assay to counterscreen for DNA intercalators. Acridine orange fluoresces and intercalates into DNA, and this binding can be measured by fluorescence polarization (FP). DNA more ..
BioActive Compounds: 128
Keywords: DNA, intercalation, acridine orange
We wish to exclude "hits" which non-specifically inhibit C-LANA DNA binding by intercalating into DNA. Compound libraries contain many flat molecules which may intercalate into DNA. We modified and miniaturized an assay to counterscreen for DNA intercalators. Acridine orange fluoresces and intercalates into DNA, and this binding can be measured by fluorescence polarization (FP). DNA intercalators compete for acridine orange binding. Titration of DNA into a solution of 50 nM acridine orange results in a steep increase in FP signal followed by a plateau. This assay is specific since excess mitoxantrone, a DNA intercalator, strongly inhibits FP signal.
Expected Outcome: Since the primary assay involves DNA binding, the lead compounds will consist of DNA intercalators and other binders. The goal is to find compounds that are specific to the LANA DNA binding site and not general DNA intercalating compounds. Compounds that have an IC50 of greater than 30 uM will be of interest while any active compounds in this assay will be eliminated from contention due to their ability to bind DNA in a non-specific manner.
Compounds will be tested for their ability to bind DNA. Acridine orange is a DNA intercalator that binds independent of a specific DNA target sequence. 50 nM acridine orange (Invitrogen) and 6 ug/mL salmon sperm DNA (Invitrogen) are incubated with compounds for 30 minutes. Mitoxantrone, a known DNA intercalator, is used as the positive control at 10 uM. Fluorescence polarization is measured using a 480 nM excitation filter and 535 nM S and P emission filters with a D505 FP/D535 dichroic mirror. The S and P values are processed with the standard FP calculation formula (mP=1000*(S-G*P)/(S+G*P) where G is the G-factor and is approximately 1). The assay is formatted for 384 well plates and the reaction volume is 30 uL per well. Compounds are examined over a range of doses.
HEN assay Buffer: 10 mM HEPES, pH 7.5; 1 mM EDTA pH 7.5; 100 mM NaCl
500mL: 10 mL 1M HEPES, 20 mL 2.5M NaCl, 2 mL 0.5 M EDTA 468 mL water
Acridine orange: make 1 mM stock by dissolving 3 mg/mL in 10 mL water (Milli Q)
Salmon sperm DNA: stock is 10 mg/mL
ASSAY DEVELOPMENT SETUP:
6 ug/mL DNA, 50 nM Acridine orange (final concentrations in HEN buffer)
Dispense 30 uL per well to Corning non-binding 3575 black opaque 384 well plates, immediately add compound in 100 nL volume with a CyBio pinning apparatus and incubate at room temperature (in dark) for 20 minutes.
Read on the Perkin Elmer Envision plate reader using the 480 nM excitation filter, 535 S and P emission filters and D505fp/D535 dichroic mirror. Apply polarization calculation to determine mP values.
PRESENCE OF CONTROLS: Neutral control wells (NC; n=36) and positive control wells (PC; n=36) were included on every plate.
EXPECTED OUTCOME: Active compounds result in decreasing readout signal. Inactive compounds (i.e. non DNA intercalating) are desired for this project.
ACTIVE CONCENTRATION LIMIT:
For each sample, the highest valid tested concentration (Max_Concentration) was determined and the active concentration limit (AC_limit) was set to equal (10)(Max_Concentration).
The raw signals of the plate wells were normalized using the 'Stimulators minus neutral controls' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of -100.
Experimental wells values were scaled to this range.
PATTERN CORRECTION: No plate pattern correction algorithm from Genedata Condoseo (v.7.0.3) was applied.
MEASUREMENT USED TO DETERMINE ACTIVE CONCENTRATION (AC): AC50
AC values were calculated using the curve fitting strategies in Genedata Screener Condoseo (7.0.3).
AC values were calculated up to the active concentration limit described for each sample.
pAC was set to equal -1*log10(AC)
Activity_Outcome = 1 (inactive) when:
a) compound shows activity but in a direction opposite to the expected outcome
in these cases, values describing curve fitting parameters (Sinf, S0, Hill Slope, log_AC50, log_AC50_SE) are set to null
b) curve fit is constant where activity is > -30% and < 30% at all tested concentrations, or
c) AC > AC_limit
Activity_Outcome = 2 (active) when:
AC <= AC_limit
Activity_Outcome = 3 (inconclusive) when:
a) Curve fitting strategy resulted in a constant fit with activity >= -70% but <= -30%, or
b) The fit was deemed not valid due to poor fit quality.
If PUBCHEM_ACTIVITY_OUTCOME = 1 (inactive) or 3 (inconclusive),
then PUBCHEM_ACTIVITY_SCORE = 0
If PUBCHEM_ACTIVITY_OUTCOME = 2 (active)
then PUBCHEM_ACTIVITY_SCORE = (10)(pAC)
Scores relate to AC in this manner:
120 = 1 pM
90 = 1 nM
60 = 1 uM
30 = 1 mM
0 = 1 M
When the active concentration (AC) is calculated to be greater than the highest valid tested concentration (Max_Concentration), the PUBCHEM_ACTIVITY_SCORE is calculated using Max_Concentration as the basis.
When the active concentration (AC) is calculated to be less than the lowest tested concentration, the PUBCHEM_ACTIVITY_SCORE is calculated using the lowest tested concentration as the basis.
The individual dose data point columns ('Activity_at_xxuM') reported here represent the median of valid (unmasked) replicate observations at each concentration. These values are the inputs to a curve fitting algorithm.
All other data columns represent values which are derived during the curve fitting algorithm; this may sometimes include automatic further masking of some replicate data points.
Occasionally this results in perceived inconsistencies: for example, between the derived 'Maximal_Activity' and the apparent most active data point.
Categorized Comment - additional comments and annotations
Assay Format: Biochemical
Assay Format: Biochemical
Assay Type: Binding
* Activity Concentration. ** Test Concentration.
Data Table (Concise)