Unbiased amplification of single stranded DNA oligos across versatile application spaces

The National Institutes of Health National Human Genome Research Institute awarded $484,634 to Dnali Data Technologies, Inc. on September 1, 2026, under the Human Genome Research program (CFDA 93.172) to develop and commercialize a platform for unbiased amplification of single-stranded DNA oligonucleotides.

Current methods for producing and amplifying single-stranded DNA are inefficient, biased, and fail to maintain sequence fidelity or representation, particularly for long templates, very short oligonucleotides, or diverse oligonucleotide pools. The project will integrate microfluidic engineering and biochemical innovations to address these limitations. Aim I will employ laminar flow in microfluidic devices to enhance efficiency by improving reagent distribution and minimizing inhibitory byproducts. Aim II will screen biochemical conditions and strand-displacing polymerases to identify optimal protocols for high-yield amplification of 200 nucleotide single-stranded DNA. Aim III will map performance characteristics across challenging application spaces, including very short and long single-stranded DNA and highly diverse oligonucleotide pools, benchmarking bias and fidelity using high-throughput sequencing. If successful, the project will deliver the first broadly applicable method for unbiased single-stranded DNA amplification, enabling more reliable, scalable, and cost-effective access to single-stranded DNA for biomedical researchers, diagnostic developers, and synthetic biology companies.

Performance of work occurs in Cary, North Carolina. The period of performance runs from September 1, 2026, through August 31, 2027. This is a project grant, a form of assistance.

Abstract

Single-stranded DNA (ssdna) oligonucleotides are foundational reagents across genomics, diagnostics, biotechnology, and synthetic biology. They are used in applications ranging from next-generation sequencing to gene editing and DNA nanotechnology. However, current methods for producing and amplifying ssdna are in- efficient, biased, and not generalizable. Most existing amplification techniques were developed for double- stranded DNA and fail to maintain sequence fidelity or representation when applied to ssdna, particularly for long templates, very short oligos, or diverse oligo pools. These limitations constrain research, increase costs, and reduce the accessibility of ssdna-dependent technologies. This project will develop and commercialize a platform for unbiased amplification of ssdna oligonucleotides. The approach integrates engineering and biochemical innovations to overcome the shortcomings of existing methods. Aim i will employ laminar flow in microfluidic devices to enhance efficiency by improving reagent DIS- tribution and minimizing inhibitory byproducts. Aim II will systematically screen biochemical conditions and strand-displacing polymerases to identify optimal protocols for high-yield amplification of 200 NT ssdna, a REP- resentative length relevant to many synthetic biology and diagnostic applications. Aim III will map performance characteristics across challenging application spaces, specifically very short and long ssdna (200NT) and highly diverse oligo pools, benchmarking bias and fidelity using high-throughput sequencing. If successful, this project will deliver the first broadly applicable method for unbiased ssdna amplification. The technology will directly benefit biomedical researchers, diagnostic developers, and synthetic biology companies by enabling more reliable, scalable, and cost-effective access to ssdna. Longer term, this innovation has the potential to expand the oligonucleotide market by unlocking applications that are currently impractical due to amplification bias, including large-scale DNA standards for sequencing, equitable oligo pool representation for synthetic biology, and robust production of DNA scaffolds for nanotechnology. By bridging a critical technologi- CAL GAP, this work will accelerate discovery, reduce barriers to commercialization, and support the rapidly EX- panding DNA-based economy.