Homology Path: The Ultimate Tool for Oligo DNA Assembly

Design your oligo assembly reactions quickly and efficiently with NinthBio’s Homology Path tool. From gene synthesis to protein engineering, this optimization tool streamlines the DNA assembly process, saving you time and money. Integrate it seamlessly within TeselaGen workflows and automate the entire process.

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NinthBio's Homology Path tool

NinthBio’s Homology Path tool is used to design oligo assembly reactions quickly and reliably. This algorithm creates a reaction design for the assembly of multiple single-stranded DNA (ssDNA) oligos into linear DNA molecules, sometimes called DNA fragments or gene fragments. In addition to the reaction design, the tool outputs a set of oligos to be synthesized, each of which contains a unique sequence that overlaps with the adjacent oligos to form a continuous sequence. In the context of building DNA variant libraries, the algorithm will identify regions of homology across a set of variant sequences and design oligos to maximally reuse them across all assembly reactions, within the constraints given by the user (e.g., both minimum and maximum oligo lengths, overlap melting temperatures).

“NinthBio leverages our understanding of DNA assembly chemistry and technology to empower our customers to build DNA more efficiently than ever before. Our state-of-the-art design algorithm, Homology Path, will analyze a set of variant sequences and find the homologous regions or the “path of homology” among the variants and design a minimum number of oligos such that individual oligos are maximally reused in the construction of the variant library,”

Steve Riedmuller

CEO and Founder of NinthBio

Applications Beyond Building Variant Libraries

Ninth Bio’s Homology Path design tool is most appropriate for applications that require the assembly of multiple oligos into a larger sequence, such as:

Gene synthesis: The tool can be used to design oligos for the assembly of synthetic genes that are too large or complex to be synthesized by traditional methods.
Site-directed mutagenesis: The tool can be used to design oligos for the introduction of point mutations into a target sequence.
CRISPR/Cas9 genome editing: The tool can be used to design oligos to make the donor DNA used in targeted genomic modifications, including insertions, deletions, and substitutions.
Protein engineering: The tool can be used to design oligos for the assembly of protein-coding sequences that have been optimized for expression, stability, or activity.
Broader synthetic biology: The tool can be used to design oligos for the assembly of genetic circuits or metabolic pathways that have been optimized for a specific application.

Ninth Bio's Homology Path design tool is useful for any application that requires the assembly of oligos into fragments, even when the sequence is too large or complex to be made as a fragment by DNA synthesis providers. This optimization tool reduces the cost of materials and the time required to obtain DNA fragments, making it a valuable tool for molecular biology researchers.

Integration within TeselaGen Workflows

Homology Path can be seamlessly integrated within larger TeselaGen workflows to execute assembly reactions. Oligo sequences generated by Homology Path can be fed into downstream DNA ordering tools. The reaction designs produced by the algorithm can be ingested by TeselaGen’s Inventory Check tool to determine if any designed oligos are already in house, and to inform users where DNA plates are in the freezer once they have been received. Reaction Planning and Worklist Planning tools allow users to automate the reaction setup by tracking required inputs and their quantities, including reagents such as enzyme master mixes, and generating worklist instructions for liquid handling robots.

Streamline the entire oligo DNA assembly process

The integration of the Homology Path design algorithm with TeselaGen’s LIMS software streamlines the entire oligo DNA assembly process, from design to execution, and eliminates the need for manual data entry and tracking. This automation increases the efficiency and reproducibility of molecular biology experiments and allows researchers to focus on the scientific aspects of their work rather than on the logistics of the experimental setup.

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