Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.

DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures. Moreover, the experimentally determined 3D structures of DNA molecules with exquisite functions remain scarce. These factors impede our comprehension and optimization of some important DNA aptamers. Here, we performed a streamlined solution NMR-based structural investigation on the 41-nt sgc8c, a prominent DNA aptamer used to target membrane protein tyrosine kinase 7, for cancer theranostics. We show that sgc8c prefolds into an intricate three-way junction (3WJ) structure stabilized by long-range tertiary interactions and extensive base-base stackings. Delineated by NMR chemical shift perturbations, site-directed mutagenesis, and 3D structural information, we identified essential nucleotides constituting the key functional elements of sgc8c that are centralized at the core of 3WJ. Leveraging the well-established structure-function relationship, we efficiently engineered two sgc8c variants by modifying the apical loop and introducing L-DNA base pairs to simultaneously enhance thermostability, biostability, and binding affinity for both protein and cell targets, a feat not previously attained despite extensive efforts. This work showcases a simplified NMR-based approach to comprehend and optimize sgc8c without acquiring the complex structure, and offers principles for the sophisticated structure-function organization of DNA molecules.

Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS.

An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature.

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.

Monodispersed and Monofunctionalized DNA-Caged Au Nano-Clusters with Enhanced Optical Properties for STED Imaging.

The performance of Stimulated Emission Depletion (STED) microscopy depends critically on the fluorescent probe. Ultrasmall Au nanoclusters (Au NCs) exhibit large Stokes shift, and good stimulated emission response, which are potentially useful for STED imaging. However, Au NCs are polydispersed in size, sensitive to the surrounding environment, and difficult to control surface functional group stoichiometry, which results in reduced density and high heterogeneity in the labeling of biological structures. Here, this limitation is overcome by developing a method to encapsulate ultrasmall Au NCs with DNA cages, which yielded monodispersed, and monofunctionalized Au NCs that are long-term stable. Moreover, the DNA-caging also greatly improved the fluorescence quantum yield and photostability of Au NCs. In STED imaging, the DNA-caged Au NCs yielded ≈40 nm spatial resolution and are able to resolve microtubule line shapes with good labeling density and homogeneity. In contrast, without caging, the Au NCs-DNA conjugates only achieved ≈55 nm resolution and yielded spotted, poorly resolved microtubule structures, due to the presence of aggregates. Overall, a method is developed to achieve precise surface functionalization and greatly improve the monodispersity, stability, as well as optical properties of Au NCs, providing a promising class of fluorescent probes for STED imaging.

Programmable manipulation of oligonucleotide-albumin interaction for elongated circulation time.

Oligonucleotide (ON) therapeutics are emerging as a new generation of medicine with tremendous potential, but their clinical translation is hampered by inferior stability and short circulation time in the human body. Here, we report a general approach to manipulating the interaction between ONs and albumin by modulating hydrophobicity. A series of DNA aptamer derivatives were designed and prepared by programmable synthesis as an ON library with a gradient of hydrophobic base 'F'. In vitro experiments revealed that the introduction of two F bases at both ends of ONs enhanced the biostability without sacrificing biological activities, while the binding affinity toward albumin was dramatically increased with Kd in the range of 100 nM to 1 µM. In vivo imaging confirmed the immediate formation of the aptamer-albumin complex after the injection, and the circulation time of the aptamer was dramatically elongated owing to the enhanced biostability and retarded renal excretion. The programmable incorporation of the F base provides a general approach to regulating albumin-binding affinity and enhancing the stability of aptamers in vivo, conferring aptamer therapeutics prolonged circulation time to meet clinical requirements.

Sequential Control of Cellular Interactions Using Dynamic DNA Displacement.

Intercellular interactions play a significant role in various complex biological processes, and their dysregulation promotes disease progression. To reveal the mechanisms of intercellular interactions without destroying basic life processes, it is necessary to mimic multicellular behaviors in vitro. However, the precise control of multicellular systems remains technically challenging owing to dynamic interactions. Here, we used DNA as a molecular lock and key to sequentially assemble and disassemble different cell clusters in a programmed way, regulating intercellular interactions. Tagging the surface of live cells with cholesterol-modified DNA enabled dynamical intercellular assemblies. By consecutively adding corresponding metaphorical locks (attaching DNA strands) and keys (detaching DNA strands), clusters of different cells could be sequentially formed. This strategy improved the capability of natural killer NK-92 cells to target tumor cells, improving the antitumor therapy efficacy. Our suggested approach allows dynamic regulation of intercellular interactions in complex cell systems and increases understanding of intercellular communication networks.

Controlled Self-Assembly of the Catalytic Core of Hydrolases Using DNA Scaffolds.

Precisely organizing functional molecules of the catalytic cores in natural enzymes to promote catalytic performance is a challenging goal in respect to artificial enzyme construction. In this work, we report a DNA-scaffolded mimicry of the catalytic cores of hydrolases, which showed a controllable and hierarchical acceleration of the hydrolysis of fluorescein diacetate (FDA). The results revealed that the efficiency of hydrolysis was greatly increased by the DNA-scaffold-induced proximity of catalytic amino acid residues (histidine and arginine) with up to 4-fold improvement relative to the free amino acids. In addition, DNA-scaffolded one-dimensional and two-dimensional assemblies of multiple catalytic cores could further accelerate the hydrolysis. This work demonstrated that the DNA-guided assembly could be used as a promising platform to build enzyme mimics in a programmable and hierarchical way.

Insulin-like Growth Factor 2-Tagged Aptamer Chimeras (ITACs) Modular Assembly for Targeted and Efficient Degradation of Two Membrane Proteins.

Overexpression of pathogenic membrane proteins drives abnormal proliferation and invasion of tumor cells. Various strategies to durably knockdown membrane proteins with heterobifunctional degraders have been successfully developed, including LYTAC, KineTAC, and AbTAC. However, challenges including complicated synthetic procedures and the inability to simultaneously degrade multiple pathogenic proteins still exist. Herein, we developed insulin-like growth factor 2 (IGF2)-tagged aptamer chimeras (ITACs) that link the cell-surface lysosome-targeting receptor IGF2R and membrane proteins of interest (POIs) based on specific recognition of aptamers to the POIs and high-affinity binding of IGF2 to IGF2R. We demonstrated that ITACs exhibit robust degradation efficiency of various membrane proteins in multiple cell lines. Furthermore, systematic studies revealed that a moderate cell-surface IGF2R level is responsible for the excellent degradation performance of ITACs. Importantly, we further established a modular assembly strategy that allows assembly of one IGF2 with two aptamers with precise stoichiometry (dITACs), enabling cooperative and simultaneous degradation of two membrane proteins. This work provides an efficient and facile target membrane protein degradation platform and will shed light on the treatment of diseases related to the overexpression of membrane proteins.

Leveraging DNA-Encoded Cell-Mimics for Environment-Adaptive Transmembrane Channel Release-Induced Cell Death.

The advancement of cell-mimic materials, which can forge sophisticated physicochemical dialogues with living cells, has unlocked a realm of intriguing prospects within the fields of synthetic biology and biomedical engineering. Inspired by the evolutionarily acquired ability of T lymphocytes to release perforin and generate transmembrane channels on targeted cells for killing, herein we present a pioneering DNA-encoded artificial T cell mimic model (ARTC) that accurately mimics T-cell-like behavior. ARTC responds to acidic conditions similar to those found in the tumor microenvironment and then selectively releases a G-rich DNA strand (LG4) embedded with C12 lipid and cholesterol molecules. Once released, LG4 effectively integrates into the membranes of neighboring live cells, behaving as an artificial transmembrane channel that selectively transports K+ ions and disrupts cellular homeostasis, ultimately inducing apoptosis. We hope that the emergence of ARTC will usher in new perspectives for revolutionizing future disease treatment and catalyzing the development of advanced biomedical technologies.

Multiplexed and Quantitative Imaging of Live-Cell Membrane Proteins by a Precise and Controllable DNA-Encoded Amplification Reaction.

Amplifying DNA conjugated affinity ligands can improve the sensitivity and multiplicity of cell imaging and play a crucial role in comprehensively deciphering cellular heterogeneity and dynamic changes during development and disease. However, the development of one-step, controllable, and quantitative DNA amplification methods for multiplexed imaging of live-cell membrane proteins is challenging. Here, we introduce the template adhesion reaction (TAR) method for assembling amplifiable DNA sequences with different affinity ligands, such as aptamers or antibodies, for amplified and multiplexed imaging of live-cell membrane proteins with high quantitative fidelity. The precisely controllable TAR enables proportional amplification of membrane protein targets with variable abundances by modulating the concentration ratios of hairpin templates and primers, thus allowing sensitive visualization of multiple membrane proteins with enhanced signal-to-noise ratios (SNRs) without disturbing their original ratios. Using TAR, we achieved signal-enhanced imaging of six proteins on the same live-cell within 1-2 h. TAR represents an innovative and programmable molecular toolkit for multiplexed profiling of membrane proteins in live-cells.

Covalent LYTAC Enabled by DNA Aptamers for Immune Checkpoint Degradation Therapy.

Immune checkpoint blockade (ICB) therapy, while achieving tremendous clinical successes, still suffers from a low objective response rate in clinical cancer treatment. As a proof-of-concept study, we propose a new immune checkpoint degradation (ICD) therapy relying on lysosome-targeting chimera (LYTAC) to deplete immune checkpoint programmed death ligand-1 (PD-L1) on the tumor cell surface. Our designed chimeric aptamer on one side targets lysosome-trafficking receptor, and on the other side allows biorthogonal covalent-conjugation-reinforced specific binding of PD-L1. This covalent LYTAC is able to hijack PD-L1 for lysosomal degradation with greatly improved efficiency over its noncovalent counterpart in complex in vivo environment. Beyond abolishing the PD-1/PD-L1 axis associated immune resistance, we demonstrate for the first time that LYTAC-triggered PD-L1 degradation could directly cause immunogenic apoptosis of tumor cells to elicit tumor-specific immune responses, offering unparalleled advantages over ICB antibody therapy. Remarkably, ICD therapy with covalent LYTAC achieves comparable or higher antitumor efficacy while causing significantly less inflammatory injury compared to antibody-based ICB therapy. Moreover, covalent LYTAC can serve as a general platform for specifically degrading other membrane-associated proteins, making it a promising tool for future applications. Our work presents a novel molecular tool for effective LYTAC in complex environments, offering valuable insights in pushing DNA-based LYTAC drugs toward in vivo and clinical applications.

Association between 19 Allergens and Chronic Constipation in Adults: NHANES 2005-2006.

INTRODUCTION: There are increasing reports of a link between chronic constipation and allergies in children. However, similar epidemiological evidence is limited in the general adult population. Therefore, in this study, we attempted to assess the association between chronic constipation and allergy in adults aged ≥20 years in the USA. METHODS: We established a logistic regression model to test the relationship between chronic constipation and 19 specific immunoglobulin E (sIgE) types in adults aged ≥20 years using large-sample data from the National Health and Nutrition Examination Survey database (2005-2006). The weekly defecation times of the allergic and non-allergic groups were compared using the t test. RESULTS: We found that sIgE-sensitized participants had a 0.723 lower risk of chronic constipation than the general population (95% confidence interval (CI) = 0.566-0.923). There was a negative association between chronic constipation and sensitizations to peanut (odds ratio (OR) = 0.579, 95% CI = 0.381-0.935), egg (OR = 0.335, 95% CI = 0.134-0.838), dog (OR = 0.723, 95% CI = 0.522-0.965), and cockroach (OR = 0.540, 95% CI = 0.373-0.784). In addition, the frequency of defecation per week increased significantly in people allergic to peanuts and cockroaches (p < 0.05). DISCUSSION/CONCLUSION: The results of this study demonstrate an inverse relationship between sIgE sensitization and chronic constipation in adults. However, the specific association mechanism needs to be further studied.

What are the risk factors for recurrent UTI with repeated ESBL-producing Enterobacteriaceae? A retrospective cohort study.

INTRODUCTION: A previous study has shown that two-thirds of patients with urinary tract infections (UTIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae experience recurrence with the same bacteria on subsequent UTI episodes. However, little is known about which patients suffer from UTI due to ESBL-producing Enterobacteriaceae repeatedly. This study aimed to investigate the risk factors for recurrent UTI due to repeated ESBL-producing organism infections. METHODS: This retrospective, single-center, observational cohort study screened all patients with UTI caused by ESBL-producing strains between January 2012 and April 2019. Among the patients who were followed up, patients who experienced UTI recurrence were enrolled and divided into two groups: ESBL recurrence group and non-ESBL recurrence group. Multivariable Cox proportional hazards regression analyses were performed to evaluate the association between patient characteristics and the development of recurrent UTI caused by ESBL-producing Enterobacteriaceae. RESULTS: A total of 330 patients were followed up after the diagnosis of UTI caused by ESBL-producing organisms. Among the patients, 115 (34.8%) experienced UTI recurrence, and 71 (61.7%) of them experienced subsequent recurrent UTI due to ESBL-producing organisms. Patient's age (hazard ratio [HR], 1.02; 95% confidence interval [CI], 1.00-1.04; P = 0.046) and recurrent UTI history (HR, 1.69; 95% CI, 1.05-2.72; P = 0.031) were significantly associated with an increased risk of recurrence with ESBL-producing Enterobacteriaceae. CONCLUSION: These findings showed that a history of previous frequent UTI recurrence is the risk factor for recurrence of UTI due to repeated ESBL producing Enterobacteriaceae infections.

FINDER: A Fluidly Confined CRISPR-Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification.

The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant in biological studies, personalized medicine, and biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a fluidly confined CRISPR-based DNA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. Benefiting from the spatial confinement effect for improved local concentration, and membrane fluidity for higher collision efficiency, the activity of CRISPR-Cas12a was, for the first time, found to be significantly enhanced on living cell membranes. This new phenomenon was then combined with multiple aptamer-based DNA logic gate for cell recognition, thus a FINDER system capable of accurate, rapid and sensitive cancer cell identification was constructed. The FINDER rapidly identified target cells in only 20 min, and achieved over 80 % recognition efficiency with only 0.1 % of target cells presented in clinical blood samples, indicating its potential application in biological studies, personalized medicine, and biomedical engineering.

Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China.

The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.

Targeting Pathogenic DNA and RNA Repeats: A Conceptual Therapeutic Way for Repeat Expansion Diseases.

Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.

Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury.

Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.

[Human urine-derived stem cell-derived exosomes improve diabetic erectile dysfunction in rats].

Objective: To investigate the improving effect of human urine-derived stem cell-derived exosomes (USC-Exo) on the endothelial function and erectile function of male rats with diabetic ED (DED) and explore their action mechanism. METHODS: USC-Exo were extracted from the culture medium of USC by ultracentrifugation and identified. Cavernous sinus endothelial cells (CCEC) were collected from SD male rats and cultured in endothelial cell growth medium-2 (EGM-2) (the normal control group), EGM-2 + L-glucose at 25 mM (the high glucose group), EGM-2 + L-glucose at 25 mmol/L) + USC-Exo at 10 µg/ml (the Exo group), and EGM-2 + L-glucose at 25 mmol/L + USC-Exo at 10 µg/ml) + 3-methyladenine at 2 mmol/L (the 3-MA group), respectively. Changes of the autophagic flux in the CCECs transfected with mRFP-GFP-LC3 adenovirus were detected under the fluorescence microscope. The proliferation and tube-forming ability of the cells were assessed by CCK8 and Matrigel assays, respectively. DED was induced by intraperitoneal injection of streptozotocin in 10 of the rats, which were equally and randomly divided into a DED and an Exo group, and another 5 normal male rats were taken as controls. The rats in the normal and DED groups were injected intracavernously with 100 µl of PBS, and those in the Exo group with 100 µl of USC-Exo at the concentration of 1 µg/µl. Four weeks after treatment, the maximum intracavernous pressure (ICPmax) and mean arterial pressure (MAP) were measured, the endothelial marker CD31 detected by immunofluorescence assay, the expressions of the CD31, Beclin1 and LC3 I/II proteins examined by Western blot, and the number of autophagosomes in the cavernous endothelial cells determined under the transmission electron microscope. RESULTS: USC-Exo significantly increased the number of autophagosomes in the CCEC in the high glucose group compared with that in the normal controls (39.5 ± 6.2 vs 12.5 ± 5.4, P < 0.05). The expression of Beclin1 and proliferation of the CCEC were significantly higher in the Exo than in the high glucose group (P < 0.05). The autophagy inhibitor 3-MA evidently reversed the increasing effect of USC-Exo on the proliferation of the CCEC. The tube-forming ability of the CCEC was significantly increased in the Exo group compared with that in the high glucose group (15.3 ± 3.2 vs 6.3 ± 2.1, P < 0.05), which was also reversed in the 3-MA group. Both ICPmax and the ICPmax/MAP ratio were significantly higher in the Exo than in the DED group (ï¼»86.6 ± 12.6ï¼½ vs ï¼»37.9 ± 10.9ï¼½ mmHg, P < 0.05; 89.3 ± 14.1 vs 41.7 ± 11.5, P < 0.05), and so were the expressions of CD31, Beclin1 and LC3 I/II (P< 0.05) and the number of autophagosomes in the cavernosal endothelial cells (3.7 ± 0.6 vs 1.0 ± 1.0, P < 0.05). CONCLUSIONS: USC-Exo can significantly improve the endothelial and erectile functions of DED rats by increasing the autophagy of cavernosal endothelial cells.

Photo-Facilitated Detection and Sequencing of 5-Formylcytidine RNA.

5-Formylcytidine (f5 C) is one of the epigenetic nucleotides in tRNA. Despite the evident importance of f5 C in gene expression regulation, little is known about its exact amount and position. To capture this information, we developed a modification-specific functionalization with a semi-stabilized ylide. The chemical labelling exhibited a high selectivity towards f5 C and allowed distinction from similar 5-formyluridine. We realized a detection strategy based on the fluorescence signal of the cyclization product 4,5-pyridin-2-amine-cytidine paC, which exhibited a high quantum yield. The results clearly identified f5 C with a limit of detection at 0.58 nM. This method altered the hydrogen bonding activities of f5 C and modulated its reverse transcription signature in its sequencing profile. We showed that f5 C can be detected from tRNA segments with a single-base resolution. Taken together, this approach is a sensitive, antibody-free, and applicable detection and sequencing method for f5 C-containing RNA.

Logical Analysis of Multiple Single-Nucleotide-Polymorphisms with Programmable DNA Molecular Computation for Clinical Diagnostics.

Analyzing complex single-nucleotide-polymorphism (SNP) combinations in the genome is important for research and clinical applications, given that different SNP combinations can generate different phenotypic consequences. Recent works have shown that DNA-based molecular computing is powerful for simultaneously sensing and analyzing complex molecular information. Here, we designed a switching circuit-based DNA computational scheme that can integrate the sensing of multiple SNPs and simultaneously perform logical analysis of the detected SNP information to directly report clinical outcomes. As a demonstration, we successfully achieved automatic and accurate identification of 21 different blood group genotypes from 83 clinical blood samples with 100 % accuracy compared to sequencing data in a more rapid manner (3 hours). Our method enables a new mode of automatic and logical sensing and analyzing subtle molecular information for clinical diagnosis, as well as guiding personalized medication.