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LightCycler® Probe Design Software 2.0

Please note the LightCycler® 2.0 Instrument is no longer available for sale as of 18 December 2018. Contact your local sales representative for more information.

PCR Primer and Probe Design Software used with all LightCycler® Carousel-Based Instruments and LightCycler® 480 Instruments.

For general laboratory use.

Product No. Pack Size
04342054001 1 software package

To order these products, please contact your Roche order management team.

The LightCycler® Probe Design Software 2.0 is used to design primers and corresponding HybProbe and SimpleProbe probes, for use in quantitative or qualitative assays using the LightCycler® 480 Instrument or the LightCycler® Carousel-Based Systems.

This standalone software package provides a fully automated approach to design primers alone, primers and probes for monoplex reactions, as well as primers and probes for multiplex assays with up to four different templates in a single run. The designs can be performed for quantification analysis or mutation detection.

  • Easily import sequences and select design parameters for specific applications.
  • Automate analysis and scoring of selected probe sequences according to design parameters.
  • Obtain a ranked display of primer-probe research results.
  • Use advanced tools, such as cross-complementarity check or direct submission of probe sequences to NCBI BLAST.
  • Benefit from a detailed software manual that provides valuable hints and guidelines for optimized primer/probe design.

Note: The LightCycler® Probe Design Software 2.0 replaces LightCycler® Probe Design Software.

Free download of software here

Please refer to the Brochure for more information LightCycler® Probe Design Software 2.0 Operator's Manual

Use the LightCycler® Probe Design Software 2.0 to design primers and/or probes for simple qualitative analysis, gene expression analysis, or mutation detection on the LightCycler® 480 or LightCycler® Carousel-Based Systems in monoplex or multiplex assays with up to four different targets. LightCycler® Probe Design Software 2.0 automatically finds the optimal primers and probes for all real-time PCR applications, including multiplexing.

LightCycler® Probe Design Software 2.0 is optimized for designing:
  • Primer/probe sets for quantitative PCR.
  • Primer/probe sets for detecting mutations by melting curve analysis.
  • PCR primers for SYBR Green I assays.
  • SimpleProbe probes for genotyping.
  • Up to 4 different pairs of HybProbe probes for quantitative multiplex PCR and detecting mutations (requires the LightCycler® 2.0 Instrument).
The Sequence Tab Facilitates Import of Sequence Data and Selection of Design Parameters for Specific Applications

The areas on the right side of the Sequence Tab let you specify design parameters according to:

  • Experiment Type
    Specifies the type of primer or probe you want to design.
  • Sequence Information
    Defines the portion of the sequence you want to analyze. The options available depend on the type of primer or probe you specified in the Experiment Type section.
  • Experiment Settings
    Specifies design constraints, such as desired size of amplicon or melting temperature of a primer or probe.
    (You can also specify these experiment settings in a Settings dialog box, which opens when you click the Details button.)


The Primer/Probe Sets Tab Ranks the Primer/Probe Research Results

The designs generated by the software are shown in a ranked list, with the highest scoring designs at the top. By selecting a design, you can see the details of the design sequence directly below the ranked list. Information about the selected design is also displayed in text boxes at the bottom left of the screen. Reaction conditions and search parameters are summarized on the right.

After you have decided on a specific primer/probe set, you can prepare a more detailed analysis of the set using the Cross-Complementarity tool. This tool allows you to view the complementarities (including self-complementarities) between any two oligonucleotides in a selected design. On the graphic display, you can see the number, length, and location of the cross-complementarities at a glance. The tool also scores the cross-complementarities according to their number or their stability.


The Primer/Probe Sets Tab Ranks the Primer/Probe Research Results


The software automatically analyzes and scores each base in the sequence according to various criteria of your choice.

After sequence analysis, the Analysis tab presents the scores as a graph of score values (Y-axis) versus nucleotide positions (X- axis). Higher scores indicate more promising sites, lower scores indicate less desirable sites.

The shaded area is the area the software searched. This area contains potential primer/probe sites.


Primer/Probes for Multiplex Analysis

If you are analyzing multiple targets in one PCR, the design of primers/probes is the most critical step in the analysis, because any cross-complementarity between the multiple primer/probe pairs can lead to:

  • Formation of primer-dimers
  • Primer binding to a false target
  • Formation of by-products

The LightCycler® Probe Design Software 2.0 can optimize multiple primer/probe sets for multiplex reactions and analyze them for cross-complementarities. In addition, the software submits the probe sequences to the NBCI BLAST web site to check them for nonspecific binding.

For additional information, review the LightCycler® Probe Design Software 2.0 Operator's Manual

Product Specifications

OS Windows 2000 Windows XP Professional
CPU Pentium 4/750 Pentium 4/900 and higher
RAM 256 MB and higher 256 MB and higher
Display 1024 x 768
Printer Compatible with standard windows print module