Opentrons Thermocycler

Opentrons Thermocycler Module

Overview

The Opentrons Thermocycler Module automates PCR thermal cycling with precise, independent control of block temperature (4-99°C) and heated lid (37-110°C). Execute complex temperature profiles with automatic cycling, integrate with liquid handling for complete PCR setup automation, and use auto-sealing lids (GEN2) for walk-away workflows.

Core value: Fully automate PCR setup and cycling. Load samples, dispense reagents, seal plates (GEN2), run thermal profiles, and collect products—all without manual intervention.

When to Use

Use the Thermocycler skill when:

• Running PCR amplification protocols
• Performing qPCR or RT-PCR reactions
• Automating DNA/RNA thermal cycling workflows
• Executing multi-step temperature incubations
• Integrating thermal cycling with automated liquid handling
• Setting up high-throughput PCR screening

Don't use when:

• Simple temperature control needed (use Temperature Module for 4-95°C range)
• Shaking/mixing required during incubation (use Heater-Shaker Module)
• Temperature outside 4-99°C range (block) or 37-110°C (lid)

Quick Reference

Platform Compatibility

Both Opentrons Flex and OT-2

Module Generations

• GEN1 - Original thermocycler, compatible with both platforms
• GEN2 - Improved plate lift mechanism, auto-sealing lid support

API compatibility: Both generations support identical API methods

Deck Position

OT-2: Spans multiple deck slots (typically slots 7, 8, 10, 11)

Flex: Dedicated thermocycler position

Loading:

# No deck slot specified - thermocycler has fixed position
tc_mod = protocol.load_module("thermocyclerModuleV2")

Loading the Module

from opentrons import protocol_api

metadata = {'apiLevel': '2.19'}

def run(protocol: protocol_api.ProtocolContext):
    # Load Thermocycler Module (no location - fixed position)
    tc_mod = protocol.load_module("thermocyclerModuleV2")

    # Load PCR plate
    pcr_plate = tc_mod.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt")

Module versions:

• "thermocyclerModuleV1" - GEN1
• "thermocyclerModuleV2" - GEN2 (recommended)

Lid Control

Basic Lid Operations

# Open lid for pipette access
tc_mod.open_lid()

# Close lid for thermal cycling
tc_mod.close_lid()

Important for gripper (Flex):

• Always open lid before gripper operations
• Close lid only after plate is seated on thermocycler

Heated Lid

The heated lid prevents condensation during thermal cycling:

# Set lid temperature (blocks until reached)
tc_mod.set_lid_temperature(celsius=105)

# Run thermal profile
# ... cycling ...

# Turn off lid heater
tc_mod.deactivate_lid()

Lid temperature range: 37-110°C

Typical settings:

• Standard PCR: 105°C
• RT-PCR: 100-105°C
• Custom protocols: Match or exceed highest block temperature + 5-10°C

Note: Lid temperature is independent of block temperature and profiles.

Block Temperature Control

Basic Block Temperature

# Set block temperature and wait
tc_mod.set_block_temperature(
    temperature=95,
    hold_time_seconds=180,  # Hold for 3 minutes
    block_max_volume=50     # Volume in wells (µL)
)

# Block automatically maintains temperature for hold_time

Block temperature range: 4-99°C

Parameters:

• temperature - Target temperature in °C (required)
• hold_time_seconds - Duration to hold at temperature
• hold_time_minutes - Alternative duration in minutes
• block_max_volume - Sample volume in µL (default: 25µL)

Hold Time Behavior

With hold_time: Protocol waits at temperature for specified duration

# Wait 5 minutes at 95°C
tc_mod.set_block_temperature(
    temperature=95,
    hold_time_minutes=5,
    block_max_volume=50
)
# Protocol continues after 5 minutes

Without hold_time: Set temperature and continue immediately

# Set to 4°C and proceed (no hold)
tc_mod.set_block_temperature(temperature=4)

# Can perform other operations while maintaining 4°C

Block Max Volume

Specify sample volume for improved temperature accuracy:

# 50µL reactions
tc_mod.set_block_temperature(
    temperature=72,
    hold_time_minutes=10,
    block_max_volume=50  # Optimizes heating/cooling for 50µL
)

Default: 25µL if not specified

Why it matters: Algorithm adjusts for thermal mass of liquid to ensure accurate sample temperature.

Temperature Profiles

Automate repeated temperature cycles for PCR:

Defining a Profile

# PCR profile: Denature → Anneal → Extend
pcr_profile = [
    {"temperature": 95, "hold_time_seconds": 30},  # Denaturation
    {"temperature": 57, "hold_time_seconds": 30},  # Annealing
    {"temperature": 72, "hold_time_seconds": 60}   # Extension
]

Profile structure: List of dictionaries with temperature and hold_time_seconds

Executing a Profile

# Run profile for 30 cycles
tc_mod.execute_profile(
    steps=pcr_profile,
    repetitions=30,
    block_max_volume=50
)

Parameters:

• steps - List of temperature steps (required)
• repetitions - Number of times to repeat profile (required)
• block_max_volume - Sample volume in µL

Complete PCR Protocol

# Setup
tc_mod = protocol.load_module("thermocyclerModuleV2")
pcr_plate = tc_mod.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt")

# Open lid for loading
tc_mod.open_lid()

# Pipette PCR reagents (not shown)
# ... add template, primers, polymerase, etc. ...

# Close lid and set lid temperature
tc_mod.close_lid()
tc_mod.set_lid_temperature(105)

# Initial denaturation
tc_mod.set_block_temperature(
    temperature=95,
    hold_time_seconds=180,  # 3 minutes
    block_max_volume=50
)

# PCR cycling
pcr_profile = [
    {"temperature": 95, "hold_time_seconds": 30},
    {"temperature": 57, "hold_time_seconds": 30},
    {"temperature": 72, "hold_time_seconds": 60}
]

tc_mod.execute_profile(steps=pcr_profile, repetitions=30, block_max_volume=50)

# Final extension
tc_mod.set_block_temperature(
    temperature=72,
    hold_time_minutes=5,
    block_max_volume=50
)

# Hold at 4°C
tc_mod.set_block_temperature(temperature=4)

# Cleanup
tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

Auto-Sealing Lids (GEN2)

Opentrons Flex GEN2 Thermocycler supports auto-sealing lids for walk-away protocols:

Auto-Sealing Lid Labware

# Load auto-sealing lid and riser
auto_seal_lid = protocol.load_labware(
    "opentrons_tough_pcr_auto_sealing_lid",
    location="lid_stack_location"
)

riser = protocol.load_labware(
    "opentrons_flex_deck_riser",
    location="deck_location"
)

Lid Stack Management

# Stack up to 5 auto-sealing lids
lid_stack = tc_mod.load_lid_stack(
    "opentrons_tough_pcr_auto_sealing_lid",
    quantity=5
)

# Move lid with gripper
protocol.move_lid(
    lid=lid_stack,
    new_location=pcr_plate,
    use_gripper=True
)

Important: Do not affix rubber seal to internal Thermocycler lid when using auto-sealing lids.

Complete Workflow with Auto-Sealing

# Load module and labware
tc_mod = protocol.load_module("thermocyclerModuleV2")
pcr_plate = tc_mod.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt")

# Load auto-sealing lids
lid_stack = tc_mod.load_lid_stack(
    "opentrons_tough_pcr_auto_sealing_lid",
    quantity=3
)

# Setup samples
tc_mod.open_lid()
# ... pipette reagents ...

# Apply auto-sealing lid with gripper
protocol.move_lid(lid_stack, pcr_plate, use_gripper=True)

# Close thermocycler lid
tc_mod.close_lid()

# Run PCR
# ... thermal cycling ...

# Open for retrieval
tc_mod.open_lid()

Common Patterns

Standard PCR

# Standard Taq PCR protocol
tc_mod.close_lid()
tc_mod.set_lid_temperature(105)

# Initial denaturation
tc_mod.set_block_temperature(95, hold_time_minutes=3, block_max_volume=50)

# Cycling
standard_pcr = [
    {"temperature": 95, "hold_time_seconds": 30},
    {"temperature": 55, "hold_time_seconds": 30},
    {"temperature": 72, "hold_time_seconds": 60}
]
tc_mod.execute_profile(steps=standard_pcr, repetitions=35, block_max_volume=50)

# Final extension
tc_mod.set_block_temperature(72, hold_time_minutes=10, block_max_volume=50)

# Hold at 4°C
tc_mod.set_block_temperature(4)

tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

Gradient PCR (Multiple Annealing Temperatures)

# Test multiple annealing temperatures in columns
annealing_temps = [52, 54, 56, 58, 60, 62, 64, 66]  # 8 temperatures

for i, temp in enumerate(annealing_temps):
    protocol.comment(f"Column {i+1}: {temp}°C annealing")

    # Pipette samples into column (example)
    # pipette.transfer(50, master_mix, pcr_plate.columns()[i])

    # Run gradient PCR for this column
    gradient_profile = [
        {"temperature": 95, "hold_time_seconds": 30},
        {"temperature": temp, "hold_time_seconds": 30},  # Variable annealing
        {"temperature": 72, "hold_time_seconds": 60}
    ]

    tc_mod.execute_profile(steps=gradient_profile, repetitions=30, block_max_volume=50)

Note: This example is simplified. True gradient PCR requires hardware that supports simultaneous temperature gradients across the block.

Two-Step PCR (No Extension)

# Two-step PCR (denature + anneal/extend combined)
tc_mod.close_lid()
tc_mod.set_lid_temperature(105)

tc_mod.set_block_temperature(95, hold_time_minutes=3, block_max_volume=25)

two_step = [
    {"temperature": 95, "hold_time_seconds": 15},
    {"temperature": 60, "hold_time_seconds": 60}  # Combined anneal/extend
]

tc_mod.execute_profile(steps=two_step, repetitions=40, block_max_volume=25)

tc_mod.set_block_temperature(4)
tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

RT-PCR (Reverse Transcription + PCR)

# Reverse transcription + PCR
tc_mod.close_lid()
tc_mod.set_lid_temperature(100)

# Reverse transcription
tc_mod.set_block_temperature(42, hold_time_minutes=30, block_max_volume=20)

# RT inactivation
tc_mod.set_block_temperature(85, hold_time_minutes=5, block_max_volume=20)

# Cool for PCR enzyme addition (if needed)
tc_mod.set_block_temperature(4)
tc_mod.open_lid()

# Add PCR enzymes
# pipette.transfer(...)

tc_mod.close_lid()
tc_mod.set_lid_temperature(105)

# PCR cycling
tc_mod.set_block_temperature(95, hold_time_minutes=2, block_max_volume=25)

rt_pcr_profile = [
    {"temperature": 95, "hold_time_seconds": 15},
    {"temperature": 60, "hold_time_seconds": 30},
    {"temperature": 72, "hold_time_seconds": 30}
]

tc_mod.execute_profile(steps=rt_pcr_profile, repetitions=40, block_max_volume=25)

tc_mod.set_block_temperature(4)
tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

Touchdown PCR

# Touchdown PCR - decreasing annealing temperature
tc_mod.close_lid()
tc_mod.set_lid_temperature(105)
tc_mod.set_block_temperature(95, hold_time_minutes=3, block_max_volume=50)

# High stringency cycles (65°C → 55°C, -1°C per cycle)
for temp in range(65, 54, -1):
    touchdown_profile = [
        {"temperature": 95, "hold_time_seconds": 30},
        {"temperature": temp, "hold_time_seconds": 30},
        {"temperature": 72, "hold_time_seconds": 60}
    ]
    tc_mod.execute_profile(steps=touchdown_profile, repetitions=1, block_max_volume=50)

# Lower stringency cycles (55°C for remaining)
standard_profile = [
    {"temperature": 95, "hold_time_seconds": 30},
    {"temperature": 55, "hold_time_seconds": 30},
    {"temperature": 72, "hold_time_seconds": 60}
]
tc_mod.execute_profile(steps=standard_profile, repetitions=25, block_max_volume=50)

tc_mod.set_block_temperature(72, hold_time_minutes=10, block_max_volume=50)
tc_mod.set_block_temperature(4)
tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

Integration with Liquid Handling

Automated PCR Setup

# Complete automated PCR setup
tc_mod = protocol.load_module("thermocyclerModuleV2")
pcr_plate = tc_mod.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt")
pipette = protocol.load_instrument("flex_1channel_1000", "left")

# Reagents
master_mix = protocol.load_labware("opentrons_24_tuberack_nest_1.5ml_snapcap", "C1")
template_plate = protocol.load_labware("biorad_96_wellplate_200ul_pcr", "C2")

# Open thermocycler
tc_mod.open_lid()

# Distribute master mix
pipette.distribute(
    volume=45,
    source=master_mix["A1"],
    dest=pcr_plate.wells(),
    new_tip="once"
)

# Add template DNA
pipette.transfer(
    volume=5,
    source=template_plate.wells(),
    dest=pcr_plate.wells(),
    mix_after=(3, 25),
    new_tip="always"
)

# Run PCR
tc_mod.close_lid()
tc_mod.set_lid_temperature(105)
tc_mod.set_block_temperature(95, hold_time_minutes=3, block_max_volume=50)

pcr_profile = [
    {"temperature": 95, "hold_time_seconds": 30},
    {"temperature": 58, "hold_time_seconds": 30},
    {"temperature": 72, "hold_time_seconds": 60}
]

tc_mod.execute_profile(steps=pcr_profile, repetitions=30, block_max_volume=50)
tc_mod.set_block_temperature(72, hold_time_minutes=5, block_max_volume=50)
tc_mod.set_block_temperature(4)

tc_mod.deactivate_lid()
tc_mod.deactivate_block()
tc_mod.open_lid()

Integration with Gripper (Flex)

# Prepare samples off-deck, move to thermocycler
sample_plate = protocol.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt", "C2")

# Setup samples
# ... pipetting ...

# Move to thermocycler with gripper
tc_mod.open_lid()
protocol.move_labware(sample_plate, tc_mod, use_gripper=True)

# Run PCR
tc_mod.close_lid()
# ... thermal cycling ...

# Retrieve plate
tc_mod.open_lid()
protocol.move_labware(sample_plate, "C2", use_gripper=True)

GEN2 Improvements

Plate lift mechanism:

• Press button for 3 seconds with lid open to activate
• Raises plate for easier manual or gripper removal
• Improves plate access and prevents damage

Auto-sealing lid support:

• Use Opentrons Tough PCR Auto-sealing Lids
• Stack up to 5 lids
• Automated lid placement with gripper

Best Practices

1. Set lid temperature before cycling - Prevents condensation
2. Use block_max_volume parameter - Improves temperature accuracy
3. Deactivate block and lid at protocol end - Prevents equipment running indefinitely
4. Open lid before gripper operations - Required for plate movement
5. Use profiles for repeated cycles - More efficient than individual set_block_temperature calls
6. Cool to 4°C at end - Preserves samples until retrieval
7. Plan for thermal equilibration - Allow extra time for large temperature changes
8. Test profiles with simulation - Verify timing before running on hardware
9. Document profile parameters - Include reasoning in protocol comments
10. Consider enzyme specifications - Match temperatures to polymerase requirements

Common Mistakes

❌ Not setting lid temperature:

tc_mod.close_lid()
tc_mod.execute_profile(...)  # Condensation risk - no lid heating

✅ Correct:

tc_mod.close_lid()
tc_mod.set_lid_temperature(105)
tc_mod.execute_profile(...)

❌ Gripper movement with closed lid:

protocol.move_labware(plate, tc_mod, use_gripper=True)  # Error: lid closed

✅ Correct:

tc_mod.open_lid()
protocol.move_labware(plate, tc_mod, use_gripper=True)

❌ Not deactivating modules:

tc_mod.execute_profile(...)
# Protocol ends - thermocycler still heating!

✅ Correct:

tc_mod.execute_profile(...)
tc_mod.deactivate_lid()
tc_mod.deactivate_block()

❌ Wrong profile structure:

# Missing hold_time_seconds
bad_profile = [
    {"temperature": 95},
    {"temperature": 55}
]
tc_mod.execute_profile(steps=bad_profile, repetitions=30)  # Error

✅ Correct:

good_profile = [
    {"temperature": 95, "hold_time_seconds": 30},
    {"temperature": 55, "hold_time_seconds": 30}
]
tc_mod.execute_profile(steps=good_profile, repetitions=30)

Troubleshooting

Module not reaching temperature:

• Verify temperature is within range (4-99°C block, 37-110°C lid)
• Check ambient temperature for low-temp targets
• Allow sufficient time for thermal equilibration

Condensation in wells:

• Ensure lid temperature is set and reached before cycling
• Set lid temperature ≥ highest block temperature + 5-10°C
• Verify lid is properly closed

Profile not executing:

• Check profile structure (list of dicts with temperature and hold_time_seconds)
• Verify repetitions parameter is provided
• Ensure block_max_volume matches sample volume

Plate removal difficulty (GEN1):

• Wait for block to cool below 60°C
• Use plate lift mechanism (GEN2)
• Ensure lid is fully open

Gripper errors:

• Verify lid is open before movement
• Check plate is compatible PCR labware
• Ensure thermocycler position is clear

Integration with Other Modules

With Temperature Module (Pre-cooling)

temp_mod = protocol.load_module("temperature module gen2", "D1")
tc_mod = protocol.load_module("thermocyclerModuleV2")

# Pre-cool samples on temperature module
temp_mod.set_temperature(4)
protocol.move_labware(sample_plate, temp_mod, use_gripper=True)
protocol.delay(minutes=5)

# Transfer to thermocycler
tc_mod.open_lid()
protocol.move_labware(sample_plate, tc_mod, use_gripper=True)

# Run PCR
tc_mod.close_lid()
# ... thermal cycling ...

With Magnetic Module (PCR Cleanup)

# After PCR, perform magnetic bead cleanup
tc_mod.set_block_temperature(4)
tc_mod.open_lid()

mag_block = protocol.load_module("magneticBlockV1", "D2")

# Move PCR product to magnetic block
protocol.move_labware(pcr_plate, mag_block, use_gripper=True)

# Cleanup workflow
# ... magnetic bead purification ...

API Version Requirements

• Minimum API version: 2.0 (thermocycler support)
• GEN2 features: API 2.13+
• Auto-sealing lids: API 2.15+
• Recommended: 2.19+ for full feature support

Additional Resources

• Thermocycler Documentation: https://docs.opentrons.com/v2/modules/thermocycler.html
• PCR Protocol Library: https://protocols.opentrons.com/
• Opentrons Support: https://support.opentrons.com/

Related Skills

• opentrons - Main Opentrons Python API skill
• opentrons-temperature-module - Simple temperature control (4-95°C)
• opentrons-gripper - Automated labware movement (Flex)
• opentrons-magnetic-block - Magnetic bead separation for PCR cleanup