Bookmark and Share
BioAssay: AID 1436

Homologous Recombination_Rad51_DNA binding assay

Ionizing radiation (IR) and inter-strand cross-linking agents (ICL) induce DNA double-stranded breaks (DSB). DSB are the most harmful type of DNA damage, which cause genome instability, cancer, genetic diseases, and premature aging. The system of homologous recombination (HR) is responsible for repair of DSB repair in all organisms including humans. Therefore, HR acts primarily as a tumor more ..
 Tested Compounds
 Tested Compounds
 Tested Substances
 Tested Substances
 Related BioAssays
 Related BioAssays
AID: 1436
Data Source: PCMD (Rad51_DNA binding)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Screening Center Network
BioAssay Version:
Deposit Date: 2008-11-25
Modify Date: 2008-12-03

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 4
Related Experiments
1385Homologous recombination - Rad 51Screeningdepositor-specified cross reference: Rad51 HTS (AID 1385)
1435Homologous Recombination - Rad 51_Dose responseConfirmatorydepositor-specified cross reference
Project Title: A screen for modulators of human Rad51, a key DNA repair protein

Application Number: MH084119

Assay Submitter: Dr. Alex Mazin

Submitter Institution: Drexel University

Screening Center Name: Penn Center for Molecular Discovery (PCMD)

Principal Investigator of Screening Center: Scott Diamond

Ionizing radiation (IR) and inter-strand cross-linking agents (ICL) induce DNA double-stranded breaks (DSB). DSB are the most harmful type of DNA damage, which cause genome instability, cancer, genetic diseases, and premature aging. The system of homologous recombination (HR) is responsible for repair of DSB repair in all organisms including humans. Therefore, HR acts primarily as a tumor suppressor. However, HR may also protect cancer cells against IR and ICL that are commonly used in anti-cancer therapy. In addition, HR is required for cell proliferation, the function of which is essential for tumorigenesis. Consequently, we propose to specifically inhibit HR during anti-cancer therapy by targeting hRad51, a key HR protein. hRad 51 has a unique activity: it promotes a search for homologous DNA sequences and DNA strand exchange between homologous DNA molecules, a basic step of HR. However, the mechanism of DNA strand exchange remains unknown. Specific inhibitors and stimulators of proteins are especially useful in determining the mechanism of enzymatic reactions.
Our goal is to identify specific modulators (inhibitors and stimulators), which can be used as chemical probes for analysis of the hRad51 mechanism and for development of novel anti-cancer therapies.

DNA strand exchange of hRad51 with fluorescently-labeled DNA substrates. To measure the hRad51 protein DNA strand exchange activity, a fluorimetric assay based on FRET was developed. In this assay, dsDNA substrate was prepared by annealing two complementary ssDNA oligonucleotides (47-mers): one containing fluorescein, a donor fluorophore with the excitation maximum at 490 nm and the emission maximum at 521 nm, at the 5'-end, and another containing black hole quencher 1 (BHQ1), a nonfluorescent acceptor, at the 3'-end. Since direct transfer of energy decreases with the sixth power of the distance between the fluorophores, the annealing of two complementary oligonucleotides increased direct energy transfer from donor to acceptor and thereby quenched the photon emission from the donor fluorescein group. The expected result of DNA strand exchange was an increase in fluorescence because displacement of the fluorescein carrying ssDNA strand from the duplex containing the quencher results in separation of the fluorescein and quencher groups. DNA strand exchange was initiated by addition of the dsDNA substrate to the hRad51 nucleoprotein filament that was formed on the non-fluorescent ssDNA identical in sequence to the fluorescein-labeled oligonucleotide. Inhibitors would be picked up as compounds that inhibit this fluorescence.

We have completed the HTS on ~200000 compounds (AID 1385). Hits identified were ordered from DPI and their dose-response was carried out (AID 1435). 19 compounds showed a good dose-response. To confirm selectivity of these compounds a DNA binding assay was carried out to rule out the effect of DNA intercalation by these compounds. Compounds that show a negative result in the DNA binding assay can be taken to be Rad51 inhibitors and further confirmatory tests will be carried out. Here we report results of the DNA binding assay.
ds DNA was provided by the assay provider. The fluorescence assay was carried out in 384-well black, low-volume plates from Corning (Cat # 3676). Ethidium bromide and buffer salts were from Sigma.
Compound was incubated with Ethidium bromide and DNA. Displacement of Ethidium bromide by the compound (if any) was determined by Fluorescence on Envision (Exc: 535 nm; Emm: 595 nm)
Dose response protocol
1.Serial dilute single compounds at in DMSO (16 two-fold dilutions from 2.5 mM to 75 nM)
2.Fill 384 well plate with 4 uL of water (nuclease-free) using Multidrop
3.Pin Tool compound into the plates using 384 pin-tool
4. Add 4 ul ds DNA
5. Add 2 ul Ethidium bromide
6.Read fluorescence on Envision reader (Ex: 535 nm; Em: 595 nm)
Data analysis
IC50 plates contained compounds in columns 3-22, controls (DMSO, no compound) in columns 1,2 and 23,24. Each column 3-22 contained 16 two-fold dilutions of a single compound, ranging in concentration from 85 uM to 2.5 nM. Percent activity was calculated for each dilution of each compound from the signal in fluorescence units (FU) and the mean of the plate controls and the mean of the plate blanks using the following equation:
% Activity = 100*((signal-blank mean)/(control mean-blank mean))
Dose response curves of percent activity were fit using XLfit equation 205 (four parameter logistic fit with maximum percent activity and minimum percent activity fixed at 100 and 0, respectively).
Activity scoring
IC50 scores were calculated as follows:
(1) Score = 5.75 x (pIC50-3), where pIC50 = -log(10) of Mean IC50 in mol/L
(2) For IC50 >85 uM (or highest concentration tested), Score = 0
Activity Score Range:
For active compound, Score = 14-8
For Inactive/Inconclusive compound, Score = 0
Activity Outcome
Compounds that gave a good dose-response in the Rad51 assay were tested for DNA binding. IC50 values were determined as described in protocol above.
Activity outcome is reported as follows:
(1) IC50 <85 uM in two or more IC50 determinations = active
(2) IC50 >85 uM (or highest concentration tested)= inactive
(3) IC50 >85 uM, but dose-response effect seen in curve = inconclusive
No. of compounds tested: 19
DNA binders: 4
Non-DNA binders: 12
Inconclusive: 3
This assay was submitted to the PCMD by Dr. Alex Mazin of Drexel University, assay development was done by Dr. Alex Mazin of Drexel University and Nuzhat Motlekar of UPenn, Dose response testing and data submission was done by Nuzhat Motlekar, of the University of Pennsylvania.
Please direct correspondence to Andrew Napper (
Result Definitions
Show more
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
2Mean IC50*FloatμM
3# of IC50 determinationsFloat
6IC50#1 Hill slopeFloat
7IC50#1 Signal at 85 uM (85μM**)FloatFU
8IC50#1 Signal at 42.5 uM (42.5μM**)FloatFU
9IC50#1 Signal at 21.25 uM (21.25μM**)FloatFU
10IC50#1 Signal at 10.625 uM (10.625μM**)FloatFU
11IC50#1 Signal at 5.3125 uM (5.3125μM**)FloatFU
12IC50#1 Signal at 2.656 uM (2.656μM**)FloatFU
13IC50#1 Signal at 1.32 uM (1.32μM**)FloatFU
14IC50#1 Signal at 0.66 uM (0.66μM**)FloatFU
15IC50#1 Signal at 0.33 uM (0.33μM**)FloatFU
16IC50#1 Signal at 0.166 uM (0.166μM**)FloatFU
17IC50#1 Signal at 0.083 uM (0.083μM**)FloatFU
18IC50#1 Signal at 0.041 uM (0.041μM**)FloatFU
19IC50#1 Signal at 0.020 uM (0.02μM**)FloatFU
20IC50#1 Signal at 0.0103 uM (0.01μM**)FloatFU
21IC50#1 Signal at 0.005 uM (0.005μM**)FloatFU
22IC50#1 Signal at 0.0025 uM (0.0025μM**)FloatFU
23IC50#1 Signal at 0.00125 uM (0.00125μM**)FloatFU
24IC50#1 number of control wellsInteger
25IC50#1 control meanFloatFU
26IC50#1 control standard deviationFloatFU
27IC50#1 control percent CVFloat%
30IC50#2 hill slopeFloat
31IC50#2 signal at 85 uM (85μM**)FloatFU
32IC50#2 signal at 42.5 uM (42.5μM**)FloatFU
33IC50#2 signal at 21.25 uM (21.25μM**)FloatFU
34IC50#2 signal at 10.625 uM (10.625μM**)FloatFU
35IC50#2 signal at 5.3125 uM (5.3125μM**)FloatFU
36IC50#2 signal at 2.656 uM (2.656μM**)FloatFU
37IC50#2 signal at 1.32 uM (1.32μM**)FloatFU
38IC50#2 signal at 0.66 uM (0.66μM**)FloatFU
39IC50#2 signal at 0.33 uM (0.33μM**)FloatFU
40IC50#2 signal at 0.166 uM (0.166μM**)FloatFU
41IC50#2 signal at 0.083 uM (0.083μM**)FloatFU
42IC50#2 signal at 0.041 uM (0.041μM**)FloatFU
43IC50#2 signal at 0.020 uM (0.02μM**)FloatFU
44IC50#2 signal at 0.010 uM (0.01μM**)FloatFU
45IC50#2 signal at 0.005 uM (0.005μM**)FloatFU
46IC50#2 signal at 0.0025 uM (0.0025μM**)FloatFU
47IC50#2 signal at 0.00125 uM (0.00125μM**)FloatFU
48IC50#2 number of control wellsInteger
49IC50#2 control meanFloatFU
50IC50#2 control standard deviationFloatFU
51IC50#2 control percent CVFloat%
54IC50#3 hill slopeFloat
55IC50#3 signal at 85 uM (85μM**)FloatFU
56IC50#3 signal at 42.5 uM (42.5μM**)FloatFU
57IC50#3 signal at 21.25 uM (21.25μM**)FloatFU
58IC50#3 signal at 10.625 uM (10.625μM**)FloatFU
59IC50#3 signal at 5.3125 uM (5.3125μM**)FloatFU
60IC50#3 signal at 2.656 uM (2.656μM**)FloatFU
61IC50#3 signal at 1.32 uM (1.32μM**)FloatFU
62IC50#3 signal at 0.66 uM (0.66μM**)FloatFU
63IC50#3 signal at 0.33 uM (0.33μM**)FloatFU
64IC50#3 signal at 0.166 uM (0.166μM**)FloatFU
65IC50#3 signal at 0.083 uM (0.083μM**)FloatFU
66IC50#3 signal at 0.041 uM (0.041μM**)FloatFU
67IC50#3 signal at 0.020 uM (0.02μM**)FloatFU
68IC50#3 signal at 0.010 uM (0.01μM**)FloatFU
69IC50#3 signal at 0.005 uM (0.005μM**)FloatFU
70IC50#3 signal at 0.0025 uM (0.0025μM**)FloatFU
71IC50#3 signal at 0.00125 uM (0.00125μM**)FloatFU
72IC50#3 number of control wellsInteger
73IC50#3 control meanFloatFU
74IC50#3 control standard deviationFloatFU
75IC50#3 control percent CVFloat%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: MH084119

Data Table (Concise)
Data Table ( Complete ):     View Active Data    View All Data