Beacon Designer

Introduction

Beacon Designer helps design successful SYBR® Green, TaqMan®, LNA™ spiked TaqMan®, TaqMan® probes for MethyLight assays, molecular beacon for both standard and NASBA® assays and FRET assays by interpreting BLAST results for specificity and locating oligos avoiding template structures.

Optimal SYBR® Green Primer Design

Use Beacon Designer to design highly specific and efficient SYBR® Green primers. Specificity is assured by avoiding significant cross homologies identified by automatically interpreting BLAST search results. To assure efficient hybridization and high yield, the program avoids template secondary structures for locating primers. The template is folded by connecting to the Mfold server.

Dual Labeled Probe Design

Beacon Designer offers comprehensive support for designing TaqMan®, molecular beacon and FRET assays for studying differential gene expression or detecting SNPs using single template or multiplex reactions. You can even confirm SYBR® Green assay results by designing probes compatible with previously designed primer pairs for any of these techniques. Or simply evaluate partially or fully pre-designed assays using instant analysis capabilities of Beacon Designer.

Design Multiplex Assays

Beacon Designer uses innovative proprietary algorithms to design optimal primer-probe sets for single tube multiplex assays. You can choose the set best suited for your experimental needs from a list of alternates presented in variously sortable order. If you want to incorporate well-proven sets for some of the templates, or include reference or housekeeping genes for normalization purposes in the assay, Beacon Designer is equipped to fully support your needs.

LNA™, MethyLight & NASBA® Assays

Design the increasingly popular Locked Nucleic Acid (LNA™) substituted TaqMan® probes, which are more stable than standard probes. To study DNA methylation, Beacon Designer helps design primers and TaqMan® probes for MethyLight assays. MethyLight is a high throughput assay used to discriminate between methylated and unmethylated DNA. Nucleic acid sequence-based amplification (NASBA®) is a primer-dependent technology that can be used for the continuous amplification of nucleic acids in a single mixture at one temperature. You can now design molecular beacons for NASBA® assays for single template or multiplex reactions.

Intuitive Interface

All the information is displayed in a simple and succinct format. The program displays in a graphical format the locations of the primers and probes, all possible dimers, cross dimers, repeats and runs. You can generate an attractively formatted report for your lab notebook or for sharing notes with your colleagues.