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Xpression Primer


Tagged Primer Design

Design Primers: Design thousands of primer pairs optimized for Gateway®, BD In-Fusion™, TOPO® and epitope systems or add functionally useful tags to design primers for any expression system.

Design Nested Primers: Design primers to successfully amplify ORFs with nested PCR. The outer primer is designed in the UTR in a region of no significant homology. The inner primer pair amplifies the PCR product generated by the outer primer pair.

Design Primers for Fusion Products: Designs primer for generating N and C terminal fusion products with functionally useful tags.

Lightning Speed: Processes three hundred 10kb sequences in approximately 2 minutes.

Maintain Reading Frame: Automatically maintain the reading frame of the ORF to be amplified when adding tags.

Avoid Termination Codon: Automatically checks for inframe termination codon.

High Throughput Primer Search

Algorithm: Calculates primer Tm using nearest neighbor thermodynamic algorithm.

Primer Rating: Uses statistical optimization techniques to output only the best rated primer pair.

Comprehensive Search Criteria: Primers are screened for their thermodynamic properties as well as secondary structures.

Uniform Conditions: Optimizes all primers in a single search run for uniform PCR cycling conditions.

Sequencing Primer Design

Design Primers: Sequencing primers are designed across amplicons with a user defined interval between forward primers. Reverse primers stagger on the opposing strands.

Design Primers for In vitro Expression Studies

Generate Precise Transcripts: Design primers to generate sense or antisense transcripts for in vitro expression studies.

Data and Database Management

Projects: Multiple projects can be created. Data of multiple experiments can be easily managed by creating separate project for each experiment.

Application Database: Maintains a local database for sequence information and search results.

Web Integration

Web Integration: Quickly retrieves batches of ORF sequences directly into the program from Entrez using accession numbers or GI numbers.


Input Formats: Supports sequences in GenBank, and FASTA formats. GenBank and FASTA formatted files can contain multiple sequences for batch loading.

View Output: Primer search results can be viewed and manipulated in any spreadsheet program like Microsoft Excel and Lotus123.

Load Output: Tab delimited format of the output file can be easily loaded into any database.

Extensive Assay Support for Tagged Primer design

Use the sophisticated algorithm of Xpression Primer to design thousands of tagged primers for expression cloning systems such as Gateway®, BD In-Fusion™, epitope and TOPO® Tools. You can choose to amplify an entire ORF or generate N terminal or C terminal fusion proteins. Xpression Primer ensures that the reading frame of the amplified ORF is conserved. To work with other expression systems, simply add functional tags of your choice and design tagged primers.

Successful Amplification with Nested PCR

To ensure the success of your PCR experiment, let Xpression Primer design nested tagged primers to amplify ORFs. You can locate the outer primers anywhere in the UTRs or in regions of no significant homology. Xpression Primer will BLAST your sequences, automatically interpret the results and design highly specific primers. The tagged inner primer pair amplifies the PCR product generated by the outer pair with little or no non-coding regions. You can also choose from a list of alternate primers to better meet specific experimental needs.


  • Tagged Primer Design
  • High Throughput Primer Search
  • Sequencing Primer Design
  • Design Primers for In vitro Expression Studies
  • Data and Database Management
  • Web Integration
  • Input/Output


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