GeneGenie

GeneGenie designs synthetic genes and oligonucleotide cohorts for self-assembly and construction of variant libraries for directed evolution by optimizing codon usage and oligonucleotide properties to improve expression in selected host organisms.

Key Features:

• Oligonucleotide cohort design and self-assembly: Designs cohorts of oligonucleotides for self-assembly of synthetic genes and constructs.
• Overlapping melting temperature optimization: Optimizes overlapping melting temperatures among oligomers to minimize misannealing during assembly.
• Codon usage optimization: Optimizes codon usage tailored to a selected host organism to enhance gene expression.
• Variant codon specification and degenerate codon handling: Allows specification of variant codons and generates equimolar codon mixtures such as TNT → TAT, TCT, TGT, TTT encoding Tyr, Ser, Cys, and Phe.
• Forward and reverse cloning sequence specification: Supports specification of forward and reverse cloning sequences to facilitate downstream ligation.
• Variant library construction: Constructs variant libraries for mutagenesis and directed evolution experiments.

Scientific Applications:

• Directed evolution and mutagenesis: Supports design and construction of variant libraries for directed evolution and mutagenesis studies.
• Expression optimization across hosts: Enables design of gene sequences optimized for expression across various host organisms via codon optimization and oligo Tm control.
• Synthetic biology and genetic engineering: Applicable to workflows requiring custom gene constructs and cloning for synthetic biology and genetic engineering.
• Protein variant generation (GFP example): Has been applied to generate variant libraries of enhanced green fluorescent protein (GFP) to produce functional protein variants.

Methodology:

Design of oligonucleotide cohorts; calculation and optimization of overlapping melting temperatures among oligomers to reduce misannealing; codon optimization for selected host organisms; enumeration of variant/degenerate codons into equimolar codon mixtures (e.g., TNT → TAT,TCT,TGT,TTT); specification of forward and reverse cloning sequences.