DNAzymeBuilder

DNAzymeBuilder assembles and recommends DNA- and RNA-cleaving DNAzymes for specified nucleotide substrates to enable site-specific cleavage reactions.

Key Features:

• Internal database: Contains entries for RNA- and DNA-cleaving DNAzymes with optimal reaction conditions, kinetic parameters, types of cleavage reactions catalyzed, recognition sequences, specific cleavage sites, and special design features.
• Sequence-based recommendation: Processes an input nucleotide sequence to generate a curated list of suitable DNAzymes capable of the desired cleavage reaction.
• Automated assembly: Automates the assembly of DNAzyme constructs for selected targets.
• Output metrics: Provides expected yield, potential reaction products, and optimal reaction conditions for each recommended DNAzyme.
• DNAzyme properties: Focuses on DNA- and RNA-cleaving DNAzymes characterized by robust catalytic activity, chemical stability, cost-effectiveness, and ease of synthesis relative to ribozymes and protein enzymes.

Scientific Applications:

• Site-specific cleavage design: Selection and design of DNAzymes for site-specific cleavage of DNA or RNA substrates in vitro.
• Experimental integration: Integration of DNAzymes into experimental workflows where chemical stability, cost-efficiency, or synthetic accessibility are required.
• Reaction optimization: Guiding experimental planning through selection of optimal reaction conditions and prediction of expected yields and products.

Methodology:

Queries an internal DNAzyme database with the input nucleotide sequence to identify compatible RNA- and DNA-cleaving DNAzymes, automates assembly of recommended constructs, and reports expected yields, potential products, and optimal reaction conditions.