C5R CORP.

Amplify and recover DNA

Physical end-to-end experiments
Task space

Amplify sfGFP DNA by PCR, purify the product, and quantify the recovered DNA using a calibrated fluorescence assay.

Producing usable DNA requires more than completing a PCR cycle. Amplification and cleanup must preserve the product while limiting contamination, and measurements must distinguish recovered DNA from background signal.

Agents instruct a human to perform the initial aliquoting into plates, then program the Hamilton liquid handler for subsequent liquid-handling steps. They coordinate reaction setup, matched no-template controls, thermocycling, magnetic-bead cleanup, and quantification of at least four independently purified samples against a DNA standard curve. The task tests reliable execution across human and robotic work, with valid measurements and DNA signals clearly above the controls.

Scoring

Pass all execution checks and qualify all four sample wells under the control and quantitation requirements.

RESULTS

Amplify sfGFP DNA by PCR, purify the product, and quantify the recovered DNA using a calibrated fluorescence assay.
ModelPass@1Cost ($)Model/API inference cost only, averaged per task attempt. Lab and labor costs are not reported. Repeats are averaged using the same task and family weights as scores.
GPT–6 Astraxhigh0.0%$107.84
Claude Opus 5xhigh0.0%$213.86
GPT–5.6 Solxhigh0.0%$45.28
Claude Fable 5.1xhigh0.0%$159.40
Gemini 3.8 Flashhigh0.0%$15.73
Grok 4.6xhigh0.0%$51.95
0%50%100%

Run progress

Elapsed time from task receipt. Milestones use published annotations or the first matching recorded Facility action. A red × marks when a run stopped, at its last reached milestone.

Task receivedPCR cycling startedPCR cycling completedEluate collectedFluorescence assay readEnd of recorded run02h4h6h7.8hElapsed time / hoursGemini 3.8 Flash · Task received: 0m; 1/1 attemptsGemini 3.8 Flash · PCR cycling started: 2h 33m; 1/1 attemptsGemini 3.8 Flash · PCR cycling completed: 3h 19m; 1/1 attemptsGemini 3.8 Flash · Eluate collected: 4h 10m; 1/1 attemptsGemini 3.8 Flash · Fluorescence assay read: 4h 31m; 1/1 attemptsGemini 3.8 Flash · End of recorded run: 5h 08m; 1/1 attempts65.0 %Grok 4.6 · Task received: 0m; 1/1 attemptsGrok 4.6 · PCR cycling started: 4h 11m; 1/1 attemptsGrok 4.6 · PCR cycling completed: 4h 55m; 1/1 attemptsGrok 4.6 · Eluate collected: 5h 51m; 1/1 attemptsGrok 4.6 · Fluorescence assay read: 6h 08m; 1/1 attemptsGrok 4.6 · End of recorded run: 6h 21m; 1/1 attempts52.5 %GPT–6 Astra · Task received: 0m; 1/1 attemptsGPT–6 Astra · PCR cycling started: 1h 46m; 1/1 attemptsGPT–6 Astra · PCR cycling completed: 2h 41m; 1/1 attemptsGPT–6 Astra · Eluate collected: 4h 37m; 1/1 attemptsGPT–6 Astra · Fluorescence assay read: 6h 23m; 1/1 attemptsGPT–6 Astra · End of recorded run: 6h 39m; 1/1 attempts40.0 %Claude Fable 5.1 · Task received: 0m; 1/1 attemptsClaude Fable 5.1 · PCR cycling started: 2h 46m; 1/1 attemptsClaude Fable 5.1 · PCR cycling completed: 3h 35m; 1/1 attemptsClaude Fable 5.1 · Eluate collected: 4h 44m; 1/1 attemptsClaude Fable 5.1 · Fluorescence assay read: 6h 27m; 1/1 attemptsClaude Fable 5.1 · End of recorded run: 6h 39m; 1/1 attempts40.0 %Claude Opus 5 · Task received: 0m; 1/1 attemptsClaude Opus 5 · PCR cycling started: 5h 21m; 1/1 attemptsClaude Opus 5 · PCR cycling completed: 6h 10m; 1/1 attemptsClaude Opus 5 · Eluate collected: 7h 12m; 1/1 attemptsClaude Opus 5 · Fluorescence assay read: 7h 24m; 1/1 attemptsClaude Opus 5 · End of recorded run: 7h 48m; 1/1 attempts40.0 %GPT–5.6 Sol · Task received: 0m; 1/1 attemptsGPT–5.6 Sol · PCR cycling started: 2h 55m; 1/1 attemptsGPT–5.6 Sol · PCR cycling completed: 3h 50m; 1/1 attemptsGPT–5.6 Sol · Eluate collected: 4h 58m; 1/1 attemptsGPT–5.6 Sol · Fluorescence assay read: 5h 15m; 1/1 attemptsGPT–5.6 Sol · End of recorded run: 5h 29m; 1/1 attempts55.0 %

Model trajectories

Run grading

Fail
MeasurementRecorded resultOutcome
Score65.0 %× Fail

Pass condition: Pass all execution checks and qualify all four sample wells under the control and quantitation requirements.

  • ✓
    Thermocycling ran

    a cycling program reached a terminal state on the reaction plate

  • ✓
    PCR cleanup: product bound, washed and eluted on the magnet

    3 completed magnetic separations, 1 retried

  • ✓
    No-template controls carried through

    2 controls, assembled identically to the samples, reading 9,343 RFU against a 16,011 RFU blank standard (0.58x)

  • ✓
    Wells purified independently

    4 independent purifications

  • ×
    Absolute yield determined against a fluorescence standards curve

    the zero standard reads 16,011 RFU, at or above the 9,432 RFU of the lowest standard with DNA in it, so the curve has no working bottom: 0 ng/uL at 16,011 RFU, 25 ng/uL at 9,992 RFU, 50 ng/uL at 1,410,882 RFU, 100 ng/uL at 9,432 RFU

  • ×
    All 4 wells above 2x the control fluorescence

    2 of 4 wells over 2x the 9343 RFU control mean and over the 16011 RFU blank standard; sample mean 770802 RFU (82.5x)

Amplify and recover DNAGemini 3.8 Flash high
Run gradingFail
00:0000:01

Model activity

Model transcript

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Appendix

Equipment recorded in this task’s Facility actions, with materials specified by the task prompt.

Main equipment2 items
Hamilton Company

Hamilton Microlab STARlet — Autoload Workstation Base (ML STARlet)

HAMILTON:173021

Automated setup, liquid transfers and labware handling for PCR and cleanup.

BMG LABTECH

BMG LABTECH CLARIOstar Plus

BMG:CLARIOSTAR-PLUS

Read fluorescence from recovered DNA, controls and standards.

Supporting equipment6 items
ItemBrandSKURole
INHECO ODTC 96 Left On Deck Thermal Cycler (with ODTC Power & Control Unit)INHECO Industrial Heating and Cooling GmbHINHECO:8100100Thermocycle the reaction plate to amplify the sfGFP template.
Picus 2 Electronic Single Channel Pipette (5-120 uL)SartoriusSARTORIUS:LH-747041Transfer measured volumes of reagents and samples.
Picus 2 Electronic Single Channel Pipette (50-1000 uL)SartoriusSARTORIUS:LH-747081Transfer measured volumes of reagents and samples.
DLAB MX-E Economic Vortex Mixer, fixed 3000 rpm (sold ONiLAB-branded)DLAB ScientificDLAB:8031211000Mix reagent and sample solutions.
Picus 2 Electronic Single Channel Pipette (0.5-10 uL)SartoriusSARTORIUS:LH-747021Transfer measured volumes of reagents and samples.
Picus 2 Electronic Single Channel Pipette (100-5000 uL)SartoriusSARTORIUS:LH-747101Transfer measured volumes of reagents and samples.
Reagents10 items
ItemBrandSKURole
sfGFP T7 gBlock templateC5RC5R:T7-GBLOCK-TEMPLATEDNA template for sfGFP amplification.
Universal T7 promoter primer (forward)Integrated DNA TechnologiesIDT:universal-T7-FForward primer for amplification reactions and matched no-template controls.
Universal T7 terminator primer (reverse)Integrated DNA TechnologiesIDT:universal-T7-RReverse primer for amplification reactions and matched no-template controls.
Q5 High-Fidelity 2X Master MixNew England BiolabsNEB:M0492SPCR master mix for amplification reactions and matched no-template controls.
Monarch Mag PCR & DNA Cleanup Kit (5 µg)New England BiolabsNEB:T4130SMagnetic beads and binding, wash and elution buffers for independent DNA cleanup.
Qubit dsDNA BR Reagent, 200X in DMSOThermo Fisher ScientificKIT:THERMO-FISHER-Q32850-REAGENTFluorescent reagent for quantifying recovered double-stranded DNA.
Qubit dsDNA BR BufferThermo Fisher ScientificKIT:THERMO-FISHER-Q32850-BUFFERDilute the assay reagent and prepare sample and standard wells.
Qubit dsDNA BR Standard #1, 0 ng/µLThermo Fisher ScientificKIT:THERMO-FISHER-Q32850-STANDARD-1Zero-DNA standard for the same-plate calibration curve.
Qubit dsDNA BR Standard #2, 100 ng/µLThermo Fisher ScientificKIT:THERMO-FISHER-Q32850-STANDARD-2DNA stock standard for preparing the calibration concentrations.
Invitrogen nuclease-free water, not DEPC-treatedThermo Fisher ScientificTHERMO-FISHER:AM9932Prepare reactions and replace template in the no-template controls.