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Adding nucleotide pairs to a DNA alphabet not only increases the linear information density of DNA molecules, but also may increase the diversity of folds available to the molecular system. Reported here is an example of this. A single additional nucleotide, with the 5-nitro-6-aminopyridone ("Z") heterocycle, selected from an artificially expanded genetic information system (AEGIS), was incorporated at twelve sites into a DNA strand 23 nucleotides in length. With a fluor at its 5'-end and a quencher at its 3'-end, this molecule is shown by fluorescence quenching to fold in mildly alkaline (pH 8-9) conditions. This folded structure is quite stable, melting at Tm = 66.5 ℃ at pH 8.5. Spectroscopic, gel, and 2-dimensional NMR (800 MHz) analyses show that the structure is held together by "reverse" Z-:Z base pairs, which have been previously seen in a crystal structure of the free heterocycle, 5-nitro-6-aminopyridone. This, in turn, requires that the strands joined by Z-:Z reverse pairs be oriented in parallel. This, in turn, requires the fold to have a four stranded compact "down-up-down-up" fold. The structure does not form when various Zs are replaced or scrambled. Of two possible structures, we also considered the possibility of "intercalated" Z-:Z base pairs, a fold that resemble the i-motif of standard DNA where an analogous "down-up-down-up" fold is held together by C:C+ pairing at lower pH between parallel strands. An alternative model has a "down-up-down-up" fold without intercalation.

Lipid–oligonucleotide conjugates (LONs) are powerful molecular-engineering materials for various applications ranging from biosensors to biomedicine. Their unique amphiphilic structures enable the self-assembly and the conveyance of information with high fidelity. In particular, LONs present remarkable potential in measuring cellular mechanical forces and monitoring cell behaviors. LONs are also essential sensing tools for intracellular imaging and have been employed in developing cell-surface-anchored DNA nanostructures for biomimetic-engineering studies. When incorporating therapeutic oligonucleotides or small-molecule drugs, LONs hold promise for targeted therapy. Moreover, LONs mediate the controllable assembly and fusion of vesicles based on DNA-strand displacements, contributing to nanoreactor construction and macromolecule delivery. In this review, we will summarize the general synthesis strategies of LONs, provide some characterization analysis and emphasize recent advances in bioanalytical and biomedical applications. We will also consider the relevant challenges and suggest future directions for building better functional LONs in nanotechnology and materials-science applications.

Adoptive T cell immunotherapy, such as chimeric antigen receptor (CAR) T cell therapy, has proven to be highly efficient in the treatment of hematologic malignancies. However, it is challenged by complicated

Breast cancer is a significant public health issue that remains the second leading cause of cancer death among women. Current treatment strategies for breast cancer can contribute to severe side effects and insufficient efficacy. For example, chemotherapy, radiotherapy, and hormone receptor and HER2 targeted therapies can lead to healthy cell damage, a partial, delayed effect, and cardiac toxicity and acquired immune resistance, respectively. An emerging alternative targeted therapy approach is proteolysis targeting chimeras (PROTAC), which triggers proteasomal degradation of target proteins implicated in cancer. PROTAC provides precision targeting of low-affinity targets for robust, selective efficacy. However, wide-spread clinical use is limited due to instability and poor cell penetration in vivo. In order to enhance the efficacy of PROTAC, we introduce a novel extracellular vesicle (EV) transfection platform for highly efficient loading of PROTAC. This approach can enhance cellular delivery by utilizing EV’s in vivo properties, like high biocompatibility, long circulation times, and specific targeting. Microfluidic droplet-based electroporation (μDES) was developed and optimized for high- efficient EV transfection, which offers continuous flow transfection suited for scaling up and GMP manufacturing. We compared the drug loading efficiency to conventional transfection methods, including simple incubation, chemical transfection through lipofection, and conventional physical transfection through the Neon electrotransfection system (ThermoFisher). The resulting EVs were characterized by nanoparticle tracking analysis for size, concentration, and zeta potential, and by TEM for morphological determinations. PROTAC transfection efficiency was also measured through absorbance spectrometry. The resulting μDES PROTAC-loaded EVs showed little, or no, changes compared to the native EVs and Neon control group, while offering higher recovery and transfection rates. We also tested the in vitro therapeutic functionality of PROTAC loaded EVs for histone deacetylase 3 and 8 degradation in the breast cancer cell line MDA-MB-231 with western blot analysis. We demonstrated high degradation ability of µDES loaded EVs and, thus, significantly higher therapeutic function. We also plan to investigate biodistribution behavior of the therapeutic EVs in vivo. PROTAC delivery by EVs could enhance stability, biocompatibility, transportability, and targeting ability of the drug. This serves as a novel PROTAC drug delivery, formulation, and administrative strategy that fills an important gap in current PROTAC use. Citation Format: Nina Erwin, Xiaoshu Pan, Nikee Awasthee, Yufeng Xiao, Guangrong Zheng, Daiqing Liao, Mei He. Extracellular vesicle loading of proteolysis targeting chimeras for targeted therapeutic delivery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB002.

Metal "X" Frameworks (MXFs) constructed from metal ions and biomacromolecules ("X components") via coordination interactions show crystalline structures and diverse functionalities. Here, a series of MXFs composed of various metal ions (e.g., Zn

Stimuli-responsive biomaterials that contain logic gates hold great potential for detecting and responding to pathological markers as part of clinical therapies. However, a major barrier is the lack of a generalized system that can be used to easily assemble different ligand-responsive units to form programmable nanodevices for advanced biocomputation. Here we develop a programmable polymer library by including responsive units in building blocks with similar structure and reactivity. Using these polymers, we have developed a series of smart nanocarriers with hierarchical structures containing logic gates linked to self-immolative motifs. Designed with disease biomarkers as inputs, our logic devices showed site-specific release of multiple therapeutics (including kinase inhibitors, drugs and short interfering RNA) in vitro and in vivo. We expect that this 'plug and play' platform will be expanded towards smart biomaterial engineering for therapeutic delivery, precision medicine, tissue engineering and stem cell therapy.

The lack of blood-brain barrier (BBB) penetrating ability has hindered the delivery of many therapeutic agents for tauopathy treatment. In this study, we report the synthesis of a circular bifunctional aptamer to enhance the in vivo BBB penetration for better tauopathy therapy. The circular aptamer consists of one reported transferrin receptor (TfR) aptamer to facilitate TfR-aptamer recognition-induced transcytosis across BBB endothelial cells, and one Tau protein aptamer that we recently selected to inhibit Tau phosphorylation and other tauopathy-related pathological events in the brain. This novel circular Tau-TfR bifunctional aptamer displays significantly improved plasma stability and brain exposure, as well as the ability to disrupt tauopathy and improve traumatic brain injury (TBI)-induced cognitive/memory deficits in vivo, providing important proof-of-principle evidence that circular Tau-TfR aptamer can be further developed into diagnostic and therapeutic candidates for tauopathies.

Chemically engineering endogenous amino acids with a molecular tag is one of the most common routes of artificially functionalizing proteins for identification or cellular delivery. However, it is challenging to make conjugation efficient, facile and productive as well as avoiding a high chance of deactivation of the functional proteins. Here we present a new and straightforward design to specifically tether the distinct six polyhistidine tag, terminally expressed on protein cargoes and cellular membrane proteins by using bispecific circular aptamers (bc-apts). The anti-His tag aptamer on one end of the bc-apt can easily recognize the biorthogonal six polyhistidine tag (His tag) on functional proteins like EGFP or RNase A. Meanwhile, a cell-specific aptamer, sgc8, on the other end efficiently facilitates the targeted delivery of functional proteins, improving their overall bioactivity in the cellular milieu by around 4 fold. Therefore, the nuclease-resistant bc-apt is a promising molecular tethering reagent to enable the noncovalent crosslink between live diseased cells and His tag protein cargoes., A bispecific circular aptamer was utilized to tether a built-in His tag to specific cells to enhance the delivery of functional proteins.

Rationale: A cascade, or domino, reaction consists of two, or more, consecutive reactions such that subsequent reactions occur only if some chemical functionality has first been established in the prior step. However, while construction of predesigned and desired molecular domino reactors in a tailored manner is a valuable endeavor, it is still challenging. Methods: To address this challenge, we herein report an aptamer-based photodynamic domino reactor built through automated modular synthesis. The engineering of this reactor takes advantage of the well-established solid-phase synthesis platform to incorporate a photosensitizer into G-quadruplex/ hemin DNAzyme at the molecular level. Results: As a proof of concept, our photodynamic domino reactor, termed AS1411/hemin- pyrochlorophyll A, achieves in vivo photodynamic domino reaction for efficient cancer treatment by using a high concentration of hydrogen peroxide (H2O2) in the tumor microenvironment (TME) to produce O2, followed by consecutive generation of singlet oxygen (1O2) using the pre-produced O2. More specifically, phosphoramidite PA (pyrochlorophyll A) is coupled to aptamer AS1411 to form AS1411-PA ApDC able to simultaneously perform in vivo targeted imaging and photodynamic therapy (PDT). The insertion of hemin into the AS1411 G-quadruplex was demonstrated to alleviate tumor hypoxia by decomposition of H2O2 to produce O2. This was followed by the generation of 1O2 by PA to trigger cascading amplified PDT. Conclusion: Therefore, this study provides a general strategy for building an aptamer-based molecular domino reactor through automated modular synthesis. By proof of concept, we further demonstrate a novel method of achieving enhanced PDT, as well as alleviating TME hypoxia at the molecular level.

In recent years, cancer immunotherapy has been observed in numerous preclinical and clinical studies for showing benefits. However, due to the unpredictable outcomes and low response rates, novel targeting delivery approaches and modulators are needed for being effective to more broader patient populations and cancer types. Compared to synthetic biomaterials, extracellular vesicles (EVs) specifically open a new avenue for improving the efficacy of cancer immunotherapy by offering targeted and site-specific immunity modulation. In this review, the molecular understanding of EV cargos and surface receptors, which underpin cell targeting specificity and precisely modulating immunogenicity, are discussed. Unique properties of EVs are reviewed in terms of their surface markers, intravesicular contents, intrinsic immunity modulatory functions, and pharmacodynamic behavior in vivo with tumor tissue models, highlighting key indications of improved precision cancer immunotherapy. Novel molecular engineered strategies for reprogramming and directing cancer immunotherapeutics, and their unique challenges are also discussed to illuminate EV's future potential as a cancer immunotherapeutic biomaterial.

Summary Compared with conventional chemotherapy and radiotherapy, targeted molecular therapy, e.g., antibody-drug conjugates or aptamer-drug conjugates, can specifically identify overexpressed natural receptors on the cancer cell, perform targeted release of anticancer drugs, and achieve targeted killing of tumor cells. However, many natural receptors are also expressed on non-cancer cells, thereby diverting the targeting molecules to healthy cells. By generating artificial cell surface receptors specific to diseased cells, aptamer-drug conjugates can identify these artificial receptors, improve therapeutic efficacy, and decrease the minimum effective dosage. In this study, we use high K+ and high H2O2 of the tumor microenvironment (TME) to produce polydopamine only on living cancer cell membrane. Owing to the significant reactivity of polydopamine with amino groups, e.g., the amino group of proteins, polydopamine can deposit on tumor cells and act as “artificial receptors” for targeted delivery of anticancer drugs with amino groups, in other words, amino-containing drugs and protein drugs., Graphical Abstract, Highlights • Polydopamine (PDA) generation catalyzed using G-quadruplex DNAzyme • TME high K+ and H2O2 employed to produce PDA only on cancerous cells membrane • PDA generated and deposited on cancerous cells and acted as artificial receptors • PDA artificial receptors facilitated targeted delivery of drugs with amino groups, Drug Delivery System; Cancer; Biomaterials

Photoresponsive materials are emerging as ideal carriers for precise controlled drug delivery owing to their high spatiotemporal selectivity. However, drawbacks such as slow release kinetics, inherent toxicity, and lack of targeting ability hinder their translation into clinical use. We herein constructed a new DNA aptamer-grafted photoresponsive hyperbranched polymer, which can self-assemble into nanoparticles, thereby achieving biocompatibility and target specificity, as well as light-controllable release behavior. Upon UV-irradiation, rapid release induced by disassembly was observed for Nile Red-loaded nanoparticles. Further in vitro cell studies confirmed this delivery system’s specific binding and internalization performance arising from the DNA aptamer corona. The DOX-loaded nanoassembly exhibited selective phototriggered cytotoxicity towards cancer cells, indicating its promising therapeutic effect as a “smart” drug delivery system.

Tau proteins are proteins that stabilize micro-tubules, but their hyperphosphorylation can result in the formation of protein aggregates and, over time, neuro-degeneration. This phenomenon, termed tauopathy, is pathologically involved in several neurodegenerative disorders. DNA aptamers are single-stranded oligonucleotides capable of specific binding to target molecules. Using tau epitopes predisposed for phosphorylation, we identified six distinct aptamers that bind to tau at two phosphorylatable epitopes (Thr-231 and Ser-202) and to full-length Tau441 proteins with nanomolar affinity. In addition, several of these aptamers also inhibit tau phosphorylation (IT4, IT5, IT6) and tau oligomerization (IT3, IT4, IT5, IT6). This is the first report to identify tau epitope-specific aptamers. Such tau aptamers can be used to detect tau in biofluids and uncover the mechanism of tauopathy. They can be further developed into novel therapeutic agents in mitigating tauopathy-associated neurodegenerative disorders.

Aptamers that recognize specific cells in a complex environment have emerged as invaluable molecular tools in bioanalysis and in the development of targeted therapeutics. The selective recognition of aptamers, however, can be compromised by the coexistence of target receptors on both target cells and other cells. To address this problem, we constructed a structure-switchable aptamer (SW-Apt) with reconfigurable binding affinity in accordance with the microenvironment of target cells. The SW-Apt makes use of i-motifs, which are quadruplex structures that form in sequences rich in cytosine. More specifically, we report the design of single-stranded, pH-responsive i-motif-modified aptamers able to bind specifically with target cells by exploiting their pH. Here, the i-motif serves as a structural domain to either facilitate the binding ability of aptamers to target cells or suppress the binding ability of aptamers to nontarget cell based on the pH of the cellular microenvironment. SW-Apt exhibited high binding ability with target cells at acidic pH, while no obvious binding was observed at physiological pH. The i-motif-induced structure-switching was verified with Förster resonance energy transfer and circular dichroism spectroscopy. Notably, SW-Apt exhibits high specificity in serum and excellent stability, likely attributed to the folded quadruplex i-motif structure. This study provides a simple and efficient strategy to chemically modulate aptamer binding ability and thus improve aptamer binding specificity to target cells, irrespective of the coexistence of identical receptors on target and nontarget cells.

The specific binding ability of DNA-lipid micelles (DLMs) can be increased by the introduction of an aptamer. However, supramolecular micellar structures based on self-assemblies of amphiphilic DLMs are expected to demonstrate low stability when interacting with cell membranes under certain conditions, which could lead to a reduction in selectivity for targeting cancer cells. We herein report a straightforward cross-linking strategy that relies on a methacrylamide branch to link aptamer and lipid segments. By an efficient photoinduced polymerization process, covalently linked aptamer-lipid units help stabilize the micelle structure and enhance aptamer probe stability, further improving the targeting ability of the resulting nanoassembly. Besides the development of a facile cross-linking method, this study clarifies the relationship between aptamer-lipid concentration and the corresponding binding ability.

The use of aptamers in bioanalytical and biomedical applications exploits their ability to recognize cell surface protein receptors. Targeted therapeutics and theranostics come to mind in this regard. However, protein receptors occur on both cancer and normal cells; as such, aptamers are now taxed with identifying high vs. low levels of protein expression. Inspired by the flexible template mechanism and elegant control of natural nucleic acid-based structures, we report an allosteric regulation strategy for constructing a structure-switching aptamer for enhanced target cell recognition by engineering aptamers with DNA intercalated motifs (i-motifs) responsive to the microenvironment, such as pH. Structure-switching sensitivity can be readily tuned by manipulating i-motif sequences. However, structure-switching sensitivity is difficult to estimate, making it equally difficult to effectively screen modified aptamers with the desired sensitivity. To address this problem, we selected a fluorescent probe capable of detecting G-quadruplex in complicated biological media., The authors have successfully developed allosterically regulated, and binding switchable aptamers from conventional G-quadruplex aptamer that can be readily, economically built, and can achieve more precise recognition of target cells according to the cellular microenvironment.

Photodynamic therapy (PDT) is an effective and noninvasive therapeutic strategy employing light-triggered singlet oxygen (SO) and reactive oxygen species (ROS) to kill lesional cells. However, for effective in vivo delivery of PDT agent into the cancer cells, various biological obstacles including blood circulation and condense extracellular matrix (ECM) in the tumor microenvironment (TME) need to be overcome. Furthermore, the enormous challenge in design of smart drug delivery systems is meeting the difference, even contradictory required functions, in different steps of the complicated delivery process. To this end, we present that TME-activatable circular pyrochlorophyll A (PA)-aptamer-PEG (PA-Apt-CHO-PEG) nanostructures, which combine the advantages of PEG and aptamer, would be able to realize efficient in vivo imaging and PDT. Upon intravenous (i.v.) injection, PA-Apt-CHO-PEG shows "stealth-like" long circulation in blood compartments without specific recognition capacity, but once inside solid tumor, PA-Apt-CHO-PEG nanostructures are cleaved and then form PA-Apt Aptamer-drug conjugations (ApDCs) in situ, allowing deep penetration into the solid tumor and specific recognition of cancer cells, both merits, considering anticipated future clinical translation of ApDCs.

The DNA strand displacement reaction has had sustained scientific interest in building complicated nucleic acid-based networks. However, extending the fundamental mechanism to more diverse biomolecules in a complex environment remains challenging. Aptamers bind with targeted biomolecules with high affinity and selectivity, thus offering a promising route to link the powers of nucleic acid with diverse cues. Here, we describe three methods that allow facile and efficient displacement reaction of aptamers from the living cell surface using complement DNA (cDNA), toehold-labeled cDNA (tcDNA), and single-stranded binding protein (SSB). The kinetics of the DNA strand displacement reaction is severely affected by complex physicochemical properties of the natural membrane. Toehold-mediated and SSB-mediated aptamer displacement exhibited significantly enhanced kinetics, and they completely removed the aptamer quickly to avoid a false signal caused by aptamer internalization. Because of its simplicity, aptamer displacement enabled detection of membrane protein post-translation and improved selection efficiency of cell-SELEX.

Inspired by this elegant system of cellular adaptivity, we herein report the rational design of a dynamic artificial adaptive system able to sense and respond to environmental stresses in a unique sense-and-respond mode. Utilizing DNA nanotechnology, we constructed an artificial signal feedback network and anchored it to the surface membrane of a model giant membrane vesicle (GMV) protocell. Such a system would need to both senses incoming stimuli and emit a feedback response to eliminate the stimuli. To accomplish this mechanistically, our DNA-based artificial signal system, hereinafter termed DASsys, was equipped with a DNA trigger-induced DNA polymer formation and dissociation machinery. Thus, through a sequential cascade of stimulus-induced DNA strand displacement, DASsys could effectively sense and respond to incoming stimuli. Then, by eliminating the stimulus, the membrane surface would return to its initial state, realizing the formation of a cyclical feedback mechanism. Overall, our strategy opens up a route to the construction of artificial signaling system capable of maintaining homeostasis in the cellular micromilieu, and addresses important emerging challenges in bioinspired engineering.

Stimuli-responsive biomaterials that contain logic gates hold great potential for detecting and responding to pathological markers as part of clinical therapies. However, a major barrier is the lack of a generalized system that can be used to easily assemble different ligand-responsive units to form programmable nanodevices for advanced biocomputation. Here we develop a programmable polymer library by including responsive units in building blocks with similar structure and reactivity. Using these polymers, we have developed a series of smart nanocarriers with hierarchical structures containing logic gates linked to self-immolative motifs. Designed with disease biomarkers as inputs, our logic devices showed site-specific release of multiple therapeutics (including kinase inhibitors, drugs and short interfering RNA) in vitro and in vivo. We expect that this 'plug and play' platform will be expanded towards smart biomaterial engineering for therapeutic delivery, precision medicine, tissue engineering and stem cell therapy.

Circular bivalent aptamers (cb-apt) comprise an emerging class of chemically engineered aptamers with substantially improved stability and molecular recognition ability. Its therapeutic application, however, is challenged by the lack of functional modules to control the interactions of cb-apt with therapeutics. We present the design of a β-cyclodextrin-modified cb-apt (cb-apt-βCD) and its supramolecular interaction with molecular therapeutics via host−guest chemistry for targeted intra-cellular delivery. The supramolecular ensemble exhibits high serum stability and enhanced intracellular delivery efficiency compared to a monomeric aptamer. The cb-apt-βCD ensemble delivers green fluorescent protein into targeted cells with efficiency as high as 80%, or cytotoxic saporin to efficiently inhibit tumor cell growth. The strategy of conjugating βCD to cb-apt, and subsequently modulating the supramolecular chemistry of cb-apt-βCD, provides a general platform to expand and diversify the function of aptamers, enabling new biological and therapeutic applications.

Familial mutations in C99 can increase the total level of the soluble Aβ peptides produced by proteolysis, as well as the Aβ42/Aβ40 ratio, both of which are linked to the progression of Alzheimer’s disease. We show that the extracellular sequence of C99 forms β-sheet structure upon interaction with membrane bilayers. Mutations that disrupt this structure result in a significant increase in Aβ production and, in specific cases, result in an increase in the amount of Aβ42 relative to Aβ40. Fourier transform infrared and solid-state NMR spectroscopic studies reveal a central β-hairpin within the extracellular sequence comprising Y10-E11-V12 and L17-V18-F19 connected by a loop involving H13-H14-Q15. These results suggest how familial mutations in the extracellular sequence influence C99 processing and provide a structural basis for the development of small molecule modulators that would reduce Aβ production.

In this work, a surface-confined peptide network that can exhibit distinct structural features under protease cleavage and electrochemical treatment is developed as a highly sensitive biosensor for clinical detection of kallikrein 6 (KLK6). KLK6 is a serine protease of the tissue-remodeling process determining the development of hepatocellular carcinoma (HCC). The peptide network, immobilized on the electrode surface by a Au-S bond, loses its integrity upon KLK6 cleavage and is removed from the electrode by electrochemical desorption of thiol groups, while the network without protease cleavage can remain attached by a few intact Au-S bonds. In this manner, distinct conductivity of the electrode surface in the presence/absence of protease can result in a large signal-to-background ratio, enabling KLK6 detection in clinical samples. The detected KLK6 abundance can manifest the correlation between up-regulated KLK6 activity and the progress of HCC. These results suggest a potential future use of this peptide network as a biosensor to provide diagnostic information for better administration of HCC.

We report a new method to study stoichiometry of protein post-translational modification (PTM) via manipulating small-molecule labels. Such labels can simultaneously bind with all the modified amino acids in a target protein, resulting in a large signal. However, if the small-molecule labels are previously attached with a macromolecule comparable to the target protein in size, binding of one such label will prevent subsequent binding of more labels of its kind; thus, only one of the modified amino acids in the target protein can be bound with the label, resulting in a small signal. Therefore, the stoichiometric number of PTM can be determined by a ratio of the two signals. The proposed method can analyze nitration of several essential regulatory proteins of cellular life, all of which are found to have an integer stoichiometric number indicating regulated site-specific nitration. These results validate the efficacy of our method to provide detailed information on PTMs with biological significance.