Biology subjects

Shih, W.

Publications and source records attributed to Shih, W..

12 recordsLinked to original sources

bioRxiv2026

OrthoSeq: A Design Workflow for Thermodynamically Orthogonal DNA Sequence-Pair Libraries

Programmable DNA hybridization underlies many technologies in DNA nanotechnology, fluorescence imaging, and synthetic DNA sequence assembly. A common design challenge is to generate large sequence libraries in which each strand binds strongly to its intended partner while avoiding cross-hybridization and self-folding. Here, we introduce OrthoSeq, a workflow for designing thermodynamically orthogonal DNA sequence-pair libraries under user-defined experimental conditions. OrthoSeq uses NUPACK to evaluate intended binding, cross-hybridization, and self-folding. Within OrthoSeq, candidate sequence pairs form vertices in a conflict graph, while pairwise cross-hybridization conflicts define the edges. Library selection is then formulated as an independent-set problem and addressed using search strategies tailored to the computational regime considered here, in which thermodynamic evaluations dominate the computational cost. In benchmark comparisons, these strategies identify larger sequence-pair libraries than the commonly employed sequential candidate-addition strategy under the same thermodynamic constraints and computational budget. We further show that sequence-level barcode libraries can serve as candidate pools for thermodynamic refinement with OrthoSeq. To support practical use, OrthoSeq provides a graphical user interface that implements the complete workflow. Altogether, OrthoSeq provides an application-agnostic framework for designing DNA sequence-pair libraries under explicit thermodynamic constraints.

bioinformatics↗

bioRxiv2026

A computational framework for designing micron-scale crisscross DNA megastructures

Crisscross polymerization enables the assembly of hundreds of unique DNA origami slats into micron-sized structures with nanoscale precision. To design these megastructures, thousands of handle sequences from a fixed library must be assigned to individual slats to encode the desired binding architecture. This complexity presents two major challenges: handles must be selected to minimize parasitic interactions that compete with desired assembly, and the fabrication of hundreds of unique slats creates a substantial logistical burden. Here, we develop a unified framework that standardizes the design and fabrication of crisscross megastructures. We use an evolutionary algorithm to optimize handle assignment and minimize parasitic binding between slats, paired with a graph-based algorithm that expands the handle library. Together, these algorithms enable the assembly of large, multi-layered megastructures that otherwise would be produced at negligible yields. We have released this framework as #-CAD, an open-source graphical application that integrates these algorithms, streamlines laboratory workflows, and makes crisscross DNA origami more broadly accessible.

synthetic biology↗

bioRxiv2025

Single-molecule Mechanostructural Fingerprinting of Nucleic Acid Conformations

Understanding the three-dimensional structure and mechanical response of biomolecules is key to uncovering their molecular mechanisms, particularly in contexts where force plays a regulatory role. Structural methods such as X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy provide high-resolution conformational data, while single-molecule force spectroscopy reveals mechanical properties--but these approaches are rarely integrated. A more comprehensive understanding of structure-function relationships, including non-equilibrium conformations and transitions under force, calls for methods capable of simultaneously resolving structural and mechanical properties at the single-molecule level. To meet this need, we present a DNA nanoswitch calipers platform capable of both measuring multiple intramolecular distances and mechanically unfolding individual biomolecules along defined axes. Using human telomeric DNA G-quadruplexes as a model system, we mapped distances between labeled sites to distinguish conformational states and performed directional unfolding to characterize mechanical stability along defined axes. This integrative approach revealed subtle conformational and mechanical differences, showcasing DNA nanoswitch calipers as a modular, broadly applicable approach for mechanostructural analysis of complex biomolecular systems.

biophysics↗

bioRxiv2024

Reusing excess staple oligonucleotides for economical production of DNA origami

DNA origami has enabled the development of responsive drug-delivery vehicles with precision features that were previously not attainable in bionanotechnology. To reduce the costs of creating therapeutics-scale amounts of DNA origami that need to bear costly modifications with high occupancy, we reused the excess staple oligonucleotides that are leftover from the folding process to fold additional origami. We determined that a DNA origami can be successfully folded with up to 80% cost savings by cyclic recovery and reuse of excess staple strands. We found evidence that higher quality staple strands are preferentially incorporated into origami, consistent with past reports, and therefore are preferentially depleted from the free-strand pool. The folding of DNA origami with staple strands that were reused up to eleven times was indistinguishable by our panel of assays versus a control folded with new strands, so long as the reused oligonucleotides were replenished each cycle with a small excess of fresh strands. We also observed a high degree of incorporation of guests on the DNA origami. By recovering, reusing, and replenishing excess staple oligonucleotides, it is possible to significantly lessen production costs to create well-formed origami, which is useful to allow more therapeutic designs to be tested.

synthetic biology↗

bioRxiv2024

Cargo quantification of functionalized DNA origami for therapeutic application

In recent years, notable advances in nanotechnology-based drug delivery have emerged. A particularly promising platform in this field is DNA origami-based nanoparticles, which offer highly programmable surfaces, providing precise control over the nanoscale spacing and stoichiometry of various cargo. These versatile particles are finding diverse applications ranging from basic molecular biology to diagnostics and therapeutics. This growing interest creates the need for effective methods to quantify cargo on DNA origami nanoparticles. Our study consolidates several previously validated methods focusing on gel-based and fluorescence-based techniques, including multiplexed quantification of protein, peptide, and nucleic acid cargo on these nanoparticles. This work may serve as a valuable resource for groups researchers keen on utilizing DNA origami-based nanoparticles in therapeutic applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/609963v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1703793org.highwire.dtl.DTLVardef@50b368org.highwire.dtl.DTLVardef@327a3corg.highwire.dtl.DTLVardef@1f732b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

DNA origami vaccine (DoriVac) nanoparticles improve both humoral and cellular immune responses to infectious diseases

Current SARS-CoV-2 vaccines have demonstrated robust induction of neutralizing antibodies and CD4+ T cell activation, however CD8+ responses are variable, and the duration of immunity and protection against variants are limited. Here we repurposed our DNA origami vaccine nanotechnology, DoriVac, for targeting infectious viruses, namely SARS-CoV-2, HIV, and Ebola. The DNA origami nanoparticle, conjugated with infectious-disease-specific heptad repeat 2 (HR2) peptides, which act as highly conserved antigens, and CpG adjuvant at precise nanoscale spacing, induced neutralizing antibodies, Th1 CD4+ T cells, and CD8+ T cells in naive mice, with significant improvement over a bolus control. Pre-clinical studies using lymph-node-on-a-chip systems validated that DoriVac, when conjugated with antigenic peptides or proteins, induced promising cellular and humoral immune responses in human cells. Moreover, DoriVac bearing full-length SARS-CoV-2 spike protein achieved immune responses comparable to current mRNA vaccine platforms while potentially reducing storage constraints. These results suggest that DoriVac holds potential as a versatile, modular vaccine platform, capable of inducing both humoral and cellular immunities, underscoring its potential utility in addressing future pandemics.

immunology↗

bioRxiv2022

Perfusable Apparatus For Thick-tissue Creation And Growth (patch) Of Cardiac Tissue

Cardiac tissue engineering has been developed as a potential alternative treatment for heart failure. However, current 3D tissues are limited in size and thickness due to the lack of an effective vascularization method. We have developed a novel bioreactor system to create viable vascularized cardiac tissue from multicellular spheroids using a digital light processing (DLP) 3D bioprinting system. Spheroids were created from induced pluripotent stem cells (iPSC) and cardiac fibroblasts (FB) using special dimple plates for mass production. One centimeter cubic tissues were created from spheroids using a DLP 3D printed mold with vascular channels. The tissue was maintained in a perfusion chamber under regulated flow and pressure following differentiation to cardiac tissue and endothelialization. Mass production of large spheroids (35,000 / tissue, diameter of 395.99 um +/- 101.15 um) was achieved from 170 million iPSCs and 50 million FBs for the creation of 1cm3 cardiac tissue in a 3D printed mold with vascular channels. The cardiac tissues (n=5) were perfused for 20 days under stable pressure of 17.5 +/- 3.05 PSI and flow of 5000 uL/min +/- 1116.42 uL/min. On days 10 and 20, Alamar blue assays showed viability for all five tissues (Alamar blue intensity: Day 10 1.57 +/- 0.15. Day 20 2.21 +/- 0.19). Thick and viable cardiac tissues were created and maintained using a 3D printed vascularized mold and perfusion system for maturation and growth in vitro for 30 days. This technology will open new doors for viable in vitro cardiac tissue creation.

bioengineering↗

bioRxiv2022

Optimizing CpG spatial distribution with DNA origami for Th1-polarized therapeutic vaccination

Multivalent presentation of ligands often enhances receptor activation and downstream signaling. DNA origami offers precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here we introduce a "square block" DNA origami platform to explore the importance of spacing of CpG oligonucleotides, which engage Toll-like receptors and thereby act as danger signals for dendritic cells. Through in vitro cell-culture studies and in vivo tumor-treatment models, we demonstrate that square blocks induce Th1 immune polarization when CpG is spaced at 3.5 nm. We observe that this DNA origami vaccine enhances DC activation, antigen cross-presentation, CD8 T cell activation, Th1-polarized CD4 activation and NK cell activation. The vaccine also synergizes effectively with anti-PD-L1 for improved cancer immunotherapy in melanoma and lymphoma models and induces long-term T cell memory. Our results suggest that DNA origami may serve as an advanced vaccine platform for controlling adjuvant spacing and co-delivering antigens. One Sentence SummaryThis study developed a DNA origami-based cancer vaccine (DoriVac) that co-delivers antigen and CpG immune adjuvant with an optimal nanospacing for Th1 immune polarization.

synthetic biology↗

bioRxiv2022

Multi-micron crisscross structures from combinatorially assembled DNA-origami slats

Living systems achieve robust self-assembly across length scales. Meanwhile, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes.However, erroneous and missing linkages restrict the number of unique origami that can be practically combined into a single supershape. We introduce crisscross polymerization of DNA-origami slats for strictly seed-dependent growth of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ~2000 strands that can be combinatorially assembled to yield any of ~1e48 distinct DNA origami slats, we realize five-gigadalton structures composed of >1000 uniquely addressable slats, and periodic structures incorporating >10,000 slats. Thus crisscross growth provides a generalizable route for prototyping and scalable production of devices integrating thousands of unique components that each are sophisticated and molecularly precise. One-sentence summaryCrisscross polymerization of DNA-origami slats can yield micron-scale structures with uniquely addressable nanoscale features.

synthetic biology↗

bioRxiv2019

Robust nucleation control via crisscross polymerization of DNA slats

Natural biomolecular assemblies such as actin filaments or microtubules polymerize in a nucleation-limited fashion1,2. The barrier to nucleation arises in part from chelate cooperativity, where stable capture of incoming monomers requires straddling multiple subunits on a filament end3. For programmable self-assembly from building blocks such as synthetic DNA4-23, it is likewise desirable to be able to suppress spontaneous nucleation24-31. However, existing approaches that exploit just a low level of cooperativity can limit spontaneous nucleation only for slow growth, near-equilibrium conditions32. Here we introduce ultracooperative assembly of ribbons densely woven from single-stranded DNA slats. An inbound "crisscross" slat snakes over and under six or more previously captured slats on a growing ribbon end, forming weak but specific half-duplex interactions with each. We demonstrate growth of crisscross ribbons with distinct widths and twists to lengths representing many thousands of slat additions. Strictly seed-initiated extension is attainable over a broad range of temperatures, divalent-cation concentrations, and free-slat concentrations, without unseeded ribbons arising even after a hundred hours to the limit of agarose-gel detection. We envision that crisscross assembly will be broadly enabling for all-or-nothing formation of microstructures with nanoscale features, algorithmic self-assembly, and signal amplification in diagnostic applications requiring extreme sensitivity.

synthetic biology↗

bioRxiv2019

Cell-free transcriptional regulation via nucleic-acid-based transcription factors

Cells execute complex transcriptional programs by deploying distinct protein regulatory assemblies that interact with cis-regulatory elements throughout the genome. Using concepts from DNA nanotechnology, we synthetically recapitulated this feature in cell-free gene networks actuated by T7 RNA polymerase (RNAP). Our approach involves engineering nucleic-acid hybridization interactions between a T7 RNAP site-specifically functionalized with single-stranded DNA (ssDNA), templates displaying cis-regulatory ssDNA domains, and auxiliary nucleic-acid assemblies acting as artificial transcription factors (TFs). By relying on nucleic-acid hybridization, de novo regulatory assemblies can be computationally designed to emulate features of protein-based TFs, such as cooperativity and combinatorial binding, while offering unique advantages such as programmability, chemical stability, and scalability. We illustrate the use of nucleic-acid TFs to implement transcriptional logic, cascading, feedback, and multiplexing. This framework will enable rapid prototyping of increasingly complex in vitro genetic devices for applications such as portable diagnostics, bio-analysis, and the design of adaptive materials.

synthetic biology↗

bioRxiv2019

Rapid and scalable in vitro production of single-stranded DNA

We present a rapid, scalable, user-friendly method for in vitro production of high-purity single-stranded DNA (ssDNA) ranging from 89-3315 nucleotides in length. PCR with a forward primer bearing a methanol-responsive polymer generates a tagged amplicon that enables selective precipitation of the modified strand under denaturing conditions. We demonstrate that the recovered ssDNA can be used for CRISPR/Cas9 homology-directed repair in human cells, DNA-origami folding, and fluorescent in situ hybridization.

molecular biology↗