DEL Hit Validation
On-DNA hit confirmation with full kinetic characterization
The off-DNA bottleneck
After DNA-encoded library (DEL) selection and next-generation sequencing (NGS) readout, DNA barcodes are decoded to identify enriched hits. But barcodes encode the building blocks used during synthesis, not the chemistry that actually happened. All products from the same synthesis step carry the same barcode. If the real binder is a side product — formed through an unintended reaction pathway — sequencing will never reveal it. The barcode points to the intended product, not to the molecule that actually bound the target during selection.
The conventional approach to validate DEL hits is off-DNA synthesis: rebuild the assumed hit from scratch using traditional medicinal chemistry. This means switching from aqueous, DNA-compatible conditions to organic solvents, a fundamentally different reaction environment that produces a different molecular mixture with different side products. The process takes 2–4 months per compound and consumes significant resources in synthetic chemistry, analytical characterization, assay development and money.
Critically, even when resynthesis succeeds, you cannot be certain that the molecule you are testing is the one that was enriched during selection. The original library synthesis may have produced reactive intermediates or unexpected adducts that contributed to target binding none of which will be present in the off-DNA version. The result: high attrition rates, wasted medicinal chemistry effort, and side-product binders lost forever.
Why off-DNA synthesis can fails
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1
Different chemistry route
Off-DNA synthesis uses organic solvents and different reaction conditions than the original library
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2
Different side-products
The resynthesized mixture contains different impurities; the original side-product binders are lost
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3
High false positive rate
You may be characterizing the wrong molecule entirely, wasting 2–4 months per compound
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See the MACS Matchmaker DEL workflow
From NGS readout to kinetic data
Four steps to validated DEL hits
Identify
NGS identifies enriched barcodes from DEL selection
Resynthesize
On-DNA resynthesis under original library conditions
Immobilize
DNA-directed immobilization on oligo sensorchip
Characterize
Full kinetic profiling (ka, kd, KD) on the MACS Matchmaker
The MACS Matchmaker solution
Resynthesize hits on-DNA under the same conditions as library synthesis. Validate binding directly on the oligo sensorchip.
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1
Chemistry
Same conditions
On-DNA resynthesis under original library conditions. Same side reactions, same molecular mixture as the screen.
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2
Discovery
Side-product recovery
Higher-quantity resynthesis enables MS identification of real binders that off-DNA resynthesis misses entirely.
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3
Kinetics
Full characterization
Complete ka, kd, KD determination in approximately 90 minutes per chip.
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4
Throughput
64 hits per chip
8×8 mologram array for parallel measurement. No sequential testing required.
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5
Speed
4 weeks, not 4 months
Reduce the validation bottleneck from months of off-DNA resynthesis to weeks.
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6
IP Protection
No sequence disclosure
DNA Ligation Kit protects proprietary sequences during immobilization on the oligo sensorchip.
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Validate your DEL hits
Download our poster on hit validation after DEL screening to learn how the MACS Matchmaker enables on-DNA compound characterization with full kinetic profiling — directly from your library synthesis, without off-DNA resynthesis.
Want to discuss your project? Contact us