OligoArchitect™ Online v2.0

Open Design Tool

Glossary of Parameters (606 Kb PDF)

Exon Design Protocol (244 Kb PDF)

Improve your PCR and qPCR assays with Sigma’s OligoArchitect Online v2.0 design tool powered by the industry standard Beacon Designer™ (Premier Biosoft). Our design tool has been enhanced and now includes features to help achieve MIQE compliance.

v2.0 Enhancements
Feature	Description
Sequence Loading	Template sequences are retrieved from NCBI by accession number
Sequence View	Template sequences are displayed in GenBank-like format
Sequence Features (To Design Across Exon Splice Sites)	Template-sequence features, i.e. exon and SNP positions, are displayable
Search Range Setting (To Design Across Exon Splice Sites)	Designs can be confined to a selected range on the template sequence; in combination with the SNP function, designs can be performed across exon splice sites
Homology Searching (For MIQE Compliance)	BLAST search primers and probes against any database available at NCBI to avoid off-target amplification
Template Folding (For MIQE Compliance)	Fold the template sequence to check for secondary structures, which can prevent proper annealing of the primers / probes and thereby lower the yield
Alternative Designs	Up to 50 additional assay designs are possible
Multiplex Designs	Up to 5 different template sequences can be included in the same assay
Design Rating	Designs are rated on how closely they match the specified search properties

Specifications
Applications	Detection Chemistries
Traditional PCR Endpoint Genotyping Gene Expression Analysis Genomic Copy Number Determination Allele Discrimination SNP Detection Haplotyping Multiplexing	SYBR^® Green I Primers Dual-Labeled Probes¹

1 Also known as hydrolysis probes, which are used in the 5’ nuclease assay.

OligoArchitect online is easy to use: register or login, select either ‘SYBR Green’ or ‘Dual Labeled Probe,’ type in the name of your assay, enter your sequence, and click search. You can add or delete a SNP and select ‘Primer Parameters’ or ‘Probe Parameters’ if you wish to adjust the default settings (download the glossary (606 Kb PDF) to learn more about the various parameters).

All reported sequences, associated properties, and assay parameters are available for export to Excel and convenient email ordering.

If you need assistance, email: oligotechserv@sial.com.

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