Next Generation Sequencing equipment for synthetic DNA analysis
Abstract
The main focus of DNA sequencing has been on genomics, and this need has driven rapid improvements in sequencing rates and costs. The application of chemically- synthesized DNA as a material for artificial systems has also exploded in the last decade, giving rise to nanoscale structures, some with up to 10,000 components; dynamic systems for detection of rare alleles in blood, proximity recording of macromolecules, or DNA structure completion; and even systems that operate within living cells to record complex information or provide orthogonal gene expression control. Under ONR funding, we have developed the Primer Exchange Reaction (PER) and Auto-cycling Proximity Recording (APR) systems for conditionally generating DNA strands, autonomously and at isothermal conditions, in turn enabling the recording of spatial or temporal information for sequencing readout. Because these systems employ non-standard sequences and structures, however, they often require non-standard approaches to DNA preparation and sequencing protocols. For example, APR is extremely sensitive to information loss that naturally happens when DNA is amplified in sequencing prep. Though standard sequencing core protocols require amplification to 10,000-fold the material that will actually be sequenced, this is not strictly required for successful results. Independent control over machine operation would increase performance in these unusual applications, as well as decrease costs and lower barriers to use. For this we propose a new equipment resource, an Illumina MiSeq machine, to be shared between ~Molecular Robotics~ and ~Synthetic Biology~ platforms at the Wyss Institute that developed the synthetic DNA applications above. As capacity needs vary by application, an algorithm will be developed to share this resource across these programs, both between runs and especially within a single run (i.e., split 20 millions reads by 3 customers in arbitrary ratios, when appropriate). The equipment will be put to use immediately, either within the Wyss Institute, managed by the programs themselves, or housed in the Biopolymers Facility to ensure optimal maintenance while allowing direct access on a priority basis. APPROVED FOR PUBLIC RELEASE.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Aug 20, 2019
- Source ID
- N000141912532
Entities
People
- Peng Yin
Organizations
- Office of Naval Research
- President and Fellows of Harvard College
- United States Navy