1
|
Berezin CT, Peccoud S, Kar DM, Peccoud J. Cryptographic approaches to authenticating synthetic DNA sequences. Trends Biotechnol 2024; 42:1002-1016. [PMID: 38418329 PMCID: PMC11309913 DOI: 10.1016/j.tibtech.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In a bioeconomy that relies on synthetic DNA sequences, the ability to ensure their authenticity is critical. DNA watermarks can encode identifying data in short sequences and can be combined with error correction and encryption protocols to ensure that sequences are robust to errors and securely communicated. New digital signature techniques allow for public verification that a sequence has not been modified and can contain sufficient information for synthetic DNA to be self-documenting. In translating these techniques from bacteria to more complex genetically modified organisms (GMOs), special considerations must be made to allow for public verification of these products. We argue that these approaches should be widely implemented to assert authorship, increase the traceability, and detect the unauthorized use of synthetic DNA.
Collapse
Affiliation(s)
- Casey-Tyler Berezin
- Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Samuel Peccoud
- Department of Electrical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Diptendu M Kar
- Department of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Jean Peccoud
- Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, CO, USA; Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA; School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA; Department of Systems Engineering, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
2
|
Jones AA, Snow CD. Porous protein crystals: synthesis and applications. Chem Commun (Camb) 2024; 60:5790-5803. [PMID: 38756076 DOI: 10.1039/d4cc00183d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.
Collapse
Affiliation(s)
- Alec Arthur Jones
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
| | - Christopher D Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA
| |
Collapse
|
3
|
Wang D, Hedayati M, Stuart JD, Madruga LYC, Popat KC, Snow CD, Kipper MJ. Ligand Presentation Inside Protein Crystal Nanopores: Tunable Interfacial Adhesion Noncovalently Modulates Cell Attachment. MATERIALS TODAY. NANO 2023; 24:100432. [PMID: 38370345 PMCID: PMC10871713 DOI: 10.1016/j.mtnano.2023.100432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein crystals with sufficiently large solvent pores can non-covalently adsorb polymers in the pores. In principle, if these polymers contain cell adhesion ligands, the polymer-laden crystals could present ligands to cells with tunable adhesion strength. Moreover, porous protein crystals can store an internal ligand reservoir, so that the surface can be replenished. In this study, we demonstrate that poly(ethylene glycol) terminated with a cyclic cell adhesion ligand peptide (PEG-RGD) can be loaded into porous protein crystals by diffusion. Through atomic force microscopy (AFM), force-distance correlations of the mechanical interactions between activated AFM tips and protein crystals were precisely measured. The activation of AFM tips allows the tips to interact with PEG-RGD that was pre-loaded in the protein crystal nanopores, mimicking how a cell might attach to and pull on the ligand through integrin receptors. The AFM experiments also simultaneously reveal the detailed morphology of the buffer-immersed nanoporous protein crystal surface. We also show that porous protein crystals (without and with loaded PEG-RGD) serve as suitable substrates for attachment and spreading of adipose-derived stem cells. This strategy can be used to design surfaces that non-covalently present multiple different ligands to cells with tunable adhesive strength for each ligand, and with an internal reservoir to replenish the precisely defined crystalline surface.
Collapse
Affiliation(s)
- Dafu Wang
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Mohammadhasan Hedayati
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Julius D Stuart
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, FortCollins, CO 80523, U.S.A
| | - Liszt Y C Madruga
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Ketul C Popat
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, U.S.A
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, FortCollins, CO 80523, U.S.A
- School of Biomedical Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, U.S.A
| | - Matt J Kipper
- Department of Chemical and Biological Engineering, Colorado State University, 1370Campus Delivery, Fort Collins, CO 80523, U.S.A
- School of Advanced Materials Discovery, Colorado State University, 1617 Campus Delivery, Fort Collins, CO 80523, U.S.A
- School of Biomedical Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, U.S.A
| |
Collapse
|
4
|
Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLoS Pathog 2023; 19:e1011588. [PMID: 37651317 PMCID: PMC10470969 DOI: 10.1371/journal.ppat.1011588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
Collapse
Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Nathan D Grubaugh
- Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Courtney C Murdock
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
- Northeast Regional Center for Excellence in Vector-borne Diseases, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
5
|
Stuart JD, Wickenkamp NR, Davis KA, Meyer C, Kading RC, Snow CD. Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications. Int J Mol Sci 2023; 24:2549. [PMID: 36768872 PMCID: PMC9917336 DOI: 10.3390/ijms24032549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.
Collapse
Affiliation(s)
- Julius D Stuart
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Natalie R Wickenkamp
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kaleb A Davis
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Camden Meyer
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Rebekah C Kading
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Christopher D Snow
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|