Primerize-2D

Primerize-2D automates primer design and organization to generate single-mutant and targeted multiple-mutant RNA libraries for multidimensional chemical mapping of RNA structure.

Key Features:

• Automated Primer Design: Produces primer sequences automatically for assembly of DNA templates used in in vitro transcription of RNA constructs.
• Library Targeting: Designs primers specifically for comprehensive single-mutant and targeted multiple-mutant libraries.
• Primer Sharing Across Constructs: Identifies and reuses shared primers across multiple constructs to reduce the number of distinct oligonucleotides required.
• Plate-aware Organization: Organizes primer placements across 96-well plate layouts to coordinate synthesis and assembly at scale.
• Support for PCR Assembly and In Vitro Transcription Workflows: Structures primer sets to address challenges in PCR assembly of DNA templates and downstream in vitro transcription.
• Experimental Validation Scale: Has been validated experimentally for RNA domains up to 300 nucleotides and libraries containing as many as 960 variants.

Scientific Applications:

• Multidimensional Chemical Mapping: Enables synthesis of mutant libraries used in multidimensional chemical approaches to probe RNA structure.
• RNA Structure-Function Studies: Facilitates generation of variants for systematic exploration of RNA structural elements and their functional effects.

Methodology:

Performs informatics-based optimization to automate primer design, identify shared primers across constructs, and organize primer placements across 96-well plates.