Kun Wang

Dynamic DNA nanomachines are programmable devices capable of executing certain controlled movements, structural reconfigurations, and functional tasks. Over the past few decades, extensive advancements have been made in designing DNA-based molecular systems driven by strand displacement, catalytic reactions, enzymatic processes, chemical or physical stimuli. The development of DNA nanotechnology has further enabled the construction of highly precise and complex DNA nanomachines. Herein, we review dynamic DNA nanomachines from a motion-to-function perspective, emphasizing how programmable movement, structural reconfiguration, or autonomous operation can be converted into biomedical output. Structural platforms, driving mechanisms, biomedical functions, and translational barriers are discussed. Particularly, we focus on the systems in which DNA dynamics directly contribute to biosensing, bioimaging, therapeutic activation, cell regulation, and molecular decision-making. This framework distinguishes dynamic DNA nanomachines from static DNA nanostructures, which also highlights the design requirements needed to move these systems toward practical biomedical applications.

DNA nanotechnology offers unique opportunities for creating various accurate and responsive nanostructures. Nevertheless, large-scale conformational changes with high geometric precision and efficiency remain major challenges. Herein we report a topologically engineered DNA origami that undergoes a dramatic transformation from a flexible, shape-indeterminate polygon into a fixed sharply angled rhombus. The DNA quadrilateral nanostructure is first built from a six-helix bundle backbone incorporating three hinge regions to confer mechanical flexibility. Sticky ends at opposing corners are designed as programmable docking domains. A facile catalytic hairpin assembly (CHA) circuit triggered by target miRNA generates duplex lockers that bridge these docking domains, collapsing the DNA quadrilateral into a locked conformation of sharply angled rhombus. Such geometry brings adjacent Cy3−Cy5 couples within the Förster distance. Fluorescence spectra are thus analyzed, which provide a quantitative readout of target miRNA information. A generalizable strategy is established for linking molecular recognition to large-scale DNA nanostructural reconfiguration.

Many new structures, machines, active materials, and devices have been produced in the rapidly growing field of DNA nanotechnology. However, the thermodynamics of complex DNA assemblies remains not well understood. Here, we treat the assembly, melting, and activation of more complex structures where interactions are generally cooperative. We abandon a rigorous theory involving a complex landscape in favor of a two-state (open-close) scenario with effective concentration and entropy effects. We test our model with self-replication of DNA origami motifs of increasing sizes and with FRET on a single DNA pair held in proximity, and it predicts melting temperatures to ~2°C where there is a 50°C shift arising from cooperativity. The model is especially useful for designing interactions between large objects programmed to open and close and is readily adaptable to assembly and activation in systems other than DNA.

Autonomous molecular machines capable of converting chemical energy into mechanical motion are foundational components for synthetic nanoscale systems. Inspired by biological motors, we report the construction of a tunable, RNA-fueled DNA origami engine that drives the cyclic movement of a 500 nm-diameter particle at the microscale. The engine operates via sequential RNA–DNA hybridization and enzymatic cleavage by RNase H, enabling reversible switching between folded and unfolded conformations without external intervention. By modulating RNA and enzyme concentrations and controlling temperature, we achieve tunable switching kinetics, with transition periods as short as ~10 s. Kinetic modeling reveals that the folding pathway is governed by both productive RNA binding and the enzymatic clearance of misfolded intermediates, while unfolding is primarily controlled by RNase H activity. Since the RNA fuel binds specifically to the DNA strands, each engine is addressable simply by changing the sequences. This work demonstrates a programmable, self-resetting molecular actuator and offers a blueprint for building more complex nanomechanical systems with forces and energies comparable to molecular motors.

Hydrogen-bonded organic frameworks (HOFs) are emerging porous materials. Herein, we prepare HOFs (PFC-1) and develop a facile pH-responsive fluorescent system, since they contain organic ligands with acid-base sensitive groups (H₄TBAPy). Upon the addition of alkali, the carboxyl groups undergo deprotonation, and intramolecular charge transfer (ICT) is inhibited, which induces hydrogen bond reconstruction, widens the band gap, and enhances the restricted intramolecular motion (RIM) effect. These changes result in blue shift and significant enhancement of fluorescence emission. We also employ HOFs as excellent pH indicators to analyze histamine and protamine concentrations. The fluorescent system is further applied to monitor food spoilage, since PFC-1 materials exhibit a distinct fluorescent color change upon the generation of biogenic amines. This study thus provides a promising example for designing pH-responsive HOFs, laying a solid foundation for their further applications in food safety, environmental monitoring, and biomedical sensing fields.

To further activate devices based on DNA nanotechnology, we introduce an approach that notably enhances both the speed and force of DNA powered machines and artificial hinge machine. A microheater, with millisecond response, heats or recools DNA origami constructs, hybridizing or dehybridizing sticky ends. Because anything within 20 micrometers of the heater equilibrates to a programmed temperature change in milliseconds, sticky ends of a compound DNA origami machine can open and close synchronously and operate cooperatively, in phase, additively increasing the drive force compared to single pair of sticky ends DNA machine (the six-helix bundle DNA origami hinge machine). In our demonstrations, we fold and unfold two square origami with 10 pairs of complementary sticky ends to drive a bead on the end of a rod like origami to speeds exceeding 30 micrometers per second. Our device envisions the creation of complex, synchronized DNA machines.

The invention of DNA nanotechnology has enabled molecular computation as a promising substitute for traditional semiconductors which are limited to two-dimensional architectures and by heating problems resulting from densification. Current studies of logic gates achieved using DNA molecules are predominately focused on two-state operations (AND, OR, etc.); however, realizing tri-state logic (high impedance Z) in DNA computation is understudied. Here we actively fold DNA origami chain-like hinged rods to induce conformational changes that return tri-state logic signals. We use rigid six helix-bundle (6HB) DNA origami to self-assemble a linear trimer chain as a circuit platform with functional single-stranded (ss) DNA near each semi-flexible hinge. The presence or absence of ssDNA enable and input strands allows hybridization to take place at the hinges, activating one fold (0) or two folds (1) from the straight linear geometry (defined as High-Z) of the trimer chain. We design two different tri-state logic gate platforms, buffer and inverter, with corresponding enable/input ssDNA to unambiguously return tri-state signals, characterized by Atomic Force Microscopy (AFM) and/or agarose gel electrophoresis (GEL). Our work on tri-state logic significantly enhances DNA computation beyond the current two-state Boolean logic with both research and industrial applications, including cellular treatments and living matter utilizing the biocompatibility of DNA molecules.

Acute Myeloid Leukemia (AML) is a clonal hematopoietic neoplasm, accounting for ~80% of acute leukemia cases in adults. The poor clinical outcome of AML patients (~27% five-year overall survival) is largely due to the inefficiency and toxicity of standard therapies. In the past decade, immunotherapies or cellular therapies (CAR-T/TCR-T cells) have achieved FDA approvals in certain types of solid tumors and leukemia, but currently there is no approved immunotherapy in AML. One potential reason is that AML actively inhibits antigen presentation (AP) to reduce its immunogenicity, thus dampening the efficacies of immunotherapies. This growing consensus is supported by the clinical evidence that AML exhibits low levels of AP machinery at diagnosis and even lower when relapsed from conventional chemotherapies. Besides, better outcomes could be achieved when combining immune checkpoint blockade with neo-antigens-inducing hypomethylating agents, highlighting the importance of AP in AML. We thus hypothesize that targeting tumor-endogenous AP suppressors will enhance AML immunogenicity and benefit immunotherapies. Recent studies have suggested that autophagy or soluble protein PCSK9 can mediate MHC-I degradation or disrupt MHC-I recycling, respectively. Transcription/epigenetic repressors TRAF3 and EZH2, as well as thymidylate synthase, were identified as MHC-I inhibitors. However, their specificity in MHC-I modulation and precise roles in regulating tumor antigenic peptide-MHC-I complexes (pMHC-I) are still unclear. Hence, there is an increasing need to identify AML-specific AP regulation mechanisms. To map such mechanisms, we performed pMHC-I-guided CRISPR screens in both human and mouse AML cell lines. Through these screens, we constructed positive and negative regulatory networks of pMHC-I modulation and compared the role of these novel regulators in the simultaneous modulation of MHC-I expression. This is the first-in-class systematic identification of AP regulators in AML. Among these negative AP regulators, we are particularly interested in the interferon regulatory factor 2 binding protein 2 (IRF2BP2), an AML-specific transcriptional regulator that is highly expressed in AML compared with normal hematopoietic stem and progenitor cells (HSPCs). Notably, IRF2BP2 expression negatively correlates with major histocompatibility complex class I (MHC-I) expression, interferon (IFN) response signatures, and T cell activity in AML patients. Ablation of IRF2BP2 enhanced AP in AML and facilitated T cell-mediated elimination of AML. Moreover, IRF2BP2 depletion synergized with IFN treatment to further boost AP at both transcriptional and protein levels. Our findings reveal a new class of tumor-associated immune-evasion mechanisms that target AP, with potential application as therapeutic targets for next-generation cancer immunotherapies. Citation Format: Xufeng Chen, Qiao Lu, Hua Zhou, Jia Liu, Bettina Nadorp, Audrey Lasry, Zhengxi Sun, Jiangyan Zhang, Michael Cammer, Kun Wang, Zoe Ciantra, Jia You, Qianjin Guo, Hongbing Zhang, Debrup Sengupta, Ahmad Boukhris, Cheng Liu, Peter Cresswell, Patricia L. M. Dahia, Jun Wang, Iannis Aifantis. Targeting MHC-I antigen presentation for cancer immune evasion in acute myeloid leukemia [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A10.