DNA Engine® Multi-Bay Thermal Cyclers — Alpha™ Unit Reaction Modules



DNA Engine® Multi-Bay Thermal Cyclers — Alpha™ Unit Specifications
  Single-Block Alpha Units Dual-Block Alpha Units
Speed of ramping Up to 3°C/sec Up to 3°C/sec
Temperature range 0–105°C 0–105°C
Temperature accuracy ±0.3°C of programmed target at 90°C ±0.4°C of programmed target at 90°C; NIST-traceable
Temperature uniformity ±0.4°C well-to-well within 30 sec of arrival at 90°C ±0.5°C well-to-well within 30 sec of arrival at 90°C
Gradient range 30–105°C* N/A
Temperature differential range 1–24°C* N/A
Calculator accuracy ±0.4°C of actual well temperature N/A
* Gradient feature only available on 96-well single-block Alpha unit.
Alpha™ Unit Reaction Module Selection Guide

Alpha units are interchangeable reaction modules available in a variety of formats to accommodate standard tubes and plates, and high-density microplates.

Every thermal cycler in the DNA Engine® family (the DNA Engine, DNA Engine Dyad®, Dyad Disciple™, and DNA Engine Tetrad® 2 cyclers) accepts all interchangeable Alpha unit reaction modules. Changing an Alpha unit reaction module takes less than 10 seconds, with no tools required. The temperature accuracy specifications of Alpha blocks ensure consistent results experiment-to-experiment and cycler-to-cycler.

Three-Step Installation of Alpha Units

Use the table below to select the best Alpha unit(s) for your needs.

Alpha Unit Reaction Module Selection Guide
Reaction Module Comments Configuration Capacity Sample Volume Catalog #
Single-block Alpha unit Adjustable heated lids set manually*;
96-well unit is gradient capable
96-well 96 x 0.2 ml tubes, one 96-well plate 5–125 µl ALS-1296G
One 384-well plate
3–30 µl
Dual-block Alpha unit 2 independently controlled sample blocks with 2 manually set adjustable heated lids* 48/48-well

2 x 48 x 0.2 ml tubes

5–125 µl


* The amount of pressure is optimized by adjustment with a thumbwheel; the lid temperature is set with the thermal cycler software.

Thermal Gradient for Optimization

Optimize Reactions in a Single Experiment
Molecular biology laboratories routinely need to optimize incubation temperatures for thermal cycling reactions. Optimization is critical but not always easy to do. Even after calculating the Tm (melting temperature) of a primer, the annealing temperature often needs to be determined empirically. This involves repeating a reaction at many different temperatures. Similar time-consuming tests may also be required to optimize the denaturation temperature.

The thermal gradient feature on the 96-well block of the DNA Engine multi-bay cyclers allows you to optimize assays in a single experiment by using a range of temperatures simultaneously. At any step in a protocol, a temperature gradient of up to 25°C may be programmed across the reaction block.

Predictable and Reproducible Gradient Temperatures
The temperature gradients formed by Bio-Rad thermal cyclers take a nonlinear, yet highly reproducible shape that allows accurate prediction of the actual sample temperatures. Extensive validation of the gradient temperatures on multiple reaction blocks indicates that the nonlinear gradient is both predictable and reproducible.

Temperature values displayed for each of the 12 columns of the reaction module on a DNA Engine cycler. Traces plotting measured temperature from four cyclers have been superposed, showing the cycler-to-cycler consistency. Note that the size of each point is far smaller than the specified error (±0.4°C).

Precision (Dynamic) Ramping Ensures That the Time Spent at the Incubation Temperature Is the Same for Each Sample
Precision (dynamic) temperature ramping means that the temperature gradient is formed during ramping. This ensures that each sample well reaches set temperatures (including gradient and uniform set temperatures) at the same time, and thus that the incubation period is consistent across all samples in the experiment. This is critical for objective evaluation of the temperature and assay conditions.

Dynamic ramping in gradient mode. Four thermal cyclers were programmed to develop a 45–65°C gradient across 12 columns. Thermal measurements were taken with NIST-traceable, laser-trimmed thermistors from 48 wells (four wells/column) in each cycler. Mean temperature of each column in each cycler (48 total traces) is plotted. Note that the software adjusts ramp rates so that all samples reach the incubation temperature at the same time.

Gradient Calculator

The gradient calculator for DNA Engine thermal cyclers tells you the incubation temperature of each column.

Programming a gradient step lets you determine the optimal temperature for a specific assay or test a range of annealing or denaturation temperatures in a single thermal cycler run.

This virtual gradient calculator uses the same algorithm that predicts well temperatures for a gradient step in DNA Engine thermal cyclers. Enter the lowest temperature (>30°C) and the highest temperature (<105°C) you want to use, and the calculator will indicate the incubation temperature that will be used for each column. The temperature accuracy (±0.4°C) ensures that at the end of a single optimization protocol you will know the optimal temperature for your experiment.

Bio-Rad thermal cyclers use dynamic ramping, which means all wells reach their target temperature at the same time, so all samples stay at target for the same duration. Therefore, both the incubation time and temperature can be easily transferred from your optimization experiment to your standard protocol.

Note: Gradient is available when the cycler is outfitted with a 96-well reaction module.

Virtual Gradient Calculator

Temperature Control

High-Performance Technology for Unparalleled Results
The integrity of the DNA Engine family of thermal cyclers rests on the performance of Peltier heat pumps (thermoelectric modules, or TEs). Advanced hardware and software designs are used to reliably provide heating and cooling to every sample — regardless of position on the block, sample volume, or level of throughput. The practical result of these technologies is that PCR protocols can be quickly optimized, validated, and used with confidence in any DNA Engine family cycler.

Multizone Thermal Control
Multiple zones of thermal control across sample blocks enable the DNA Engine family of cyclers to deliver remarkable well-to-well temperature uniformity (±0.4°C). Precise Joule heaters adjust the temperature of perimeter wells — where thermal losses to radiative heat are the highest — independently of center wells. Sophisticated algorithms use readings from three sensors in a single-block Alpha unit to adjust four independently controlled thermal zones (left, right, inner, and outer), quickly bringing the sample block to uniformity even when samples are asymmetrically loaded.

Block vs. Calculated Temperature Control
The DNA Engine family of thermal cyclers offers two modes of controlling sample temperatures. With the simplest method, block temperature control mode, the instrument monitors the temperature of the block and precisely heats and cools as directed. When the temperature within a sample is measured, however, an almost asymptotic lag can be detected as heat is transferred from block to vessel to sample (upper panel, opposite).

As an alternative, cyclers in the DNA Engine family also offer a calculated temperature control mode. With this option, an algorithm that incorporates the sample volume and vessel type is used to calculate the temperature overshoot required to bring the sample to the programmed temperature rapidly (lower panel, opposite). Incubation periods are timed according to how long the samples, not the block, reside at target temperature. By removing some guesswork, calculated control can reduce both optimization time and overall run time. Calculated control is recommended for most applications.

Block assembly diagram of an Alpha unit. Precise Joule heaters adjust perimeter wells where thermal losses to radiative heat are the highest. Multiple sensors and independently controlled TEs compensate for asymmetrically loaded samples.

Block vs. calculated temperature control. Temperatures were ramped from 60–90°C using a 96-well Alpha unit on a DNA Engine cycler with 0.2 ml tubes and a 25 µl sample volume. The block temperature overshoot with calculated temperature control mode (bottom panel) results in the sample reaching the target temperature (vertical dashed line) approximately 5 sec earlier than with block temperature control mode.

Instrument Compatibility Chart

Instrument Compatibility of PCR Plastic Consumables


Thermal Cyclers
MJ Mini™ Gradient Thermal Cycler

T100™ Thermal Cycler

DNA Engine® Thermal Cycler Family

C1000 Touch™/S1000™ Thermal Cyclers
0.5 ml individual tubes   Deep well
module only
0.2 ml individual tubes
High-profile tube strips
Low-profile tube strips  
48- and 96-Well Plates
Hard-Shell® low-profile 96-well semi-skirted PCR plates      
Hard-Shell high-profile 96-well semi-skirted PCR plates  
Hard-Shell low-profile 96-well skirted PCR plates    
Multiplate™ high-profile unskirted PCR plates
Multiplate low-profile unskirted PCR plates  
iQ™ 96-well semi-skirted PCR plates  
384-Well Plates
Hard-Shell 384-well skirted PCR plates    
Domed cap strips
Optical flat cap strips
Adhesive Seals
Microseal® 'A' film  
Microseal 'B' adhesive seals  
Microseal ꞌCꞌ optical seals  
Microseal 'F' foil  
Heat Sealer and Heat Sealing Films and Foils
PX1™ PCR plate sealer  
Optically clear heat seal  
Pierceable foil heat seal  
Peelable foil heat seal  

Alpha unit reaction modules are available in several formats, including:

  • Gradient-enabled 96-well unit that allows simultaneous incubation at 8 different temperatures to optimize reactions in a single run
  • Dual 48/48-well unit that allows 2 independent experiments to run simultaneously
  • High-throughput 384-well unit

The DNA Engine Tetrad® 2 thermal cycler has been discontinued. Select Alpha unit reaction modules remain available for sale. Information about other Bio-Rad thermal cyclers is available.

96-Well Alpha Unit With Hot Bonnet Heated Lid
96-Well Alpha™ Unit with Hot Bonnet® Heated Lid

96-well reaction module for DNA Engine® thermal cyclers, holds one 96-well plate or 96 x 0.2 ml tubes

List Price:   $4,172.00
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384-Well High-Capacity Alpha™ Unit with Hot Bonnet® Heated Lid

384-well reaction module for DNA Engine® thermal cyclers, holds one 384-well microplate

List Price:   $4,476.00
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48/48 Dual Alpha™ Unit with Two Heated Lids

Reaction module for DNA Engine® thermal cyclers, includes 2 independent blocks, each holds 48 x 0.2 ml tubes

List Price:   $5,224.00
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Number Description Options
2592 Gradient Feature Flier: Maximize Your Optimization Power, Rev D Click to download
5277 Bio-Rad Thermal Cyclers Brochure, Rev G Click to download [ Add to Cart (Free) ]
5924 Stem Cell Basics for Life Science Researchers Brochure, Rev A Click to download [ Add to Cart (Free) ]