DNA Backbone Research Articles

RNA-Templated Peptide Bond Formation Promotes L-Homochirality.

The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood. Herein, we show that an RNA-peptide world, in which peptides grow on RNAs constructed from D-ribose, leads to the self-selection of homo-L-peptides, which provides a possible explanation for the homo-D-ribose and homo-L-amino acid combination seen in nature.

RNA‐Vermittelte Peptidbindungen Fördern die L‐Homochiralität

AbstractDie Welt, in der wir leben, ist homochiral. Die Riboseeinheiten, die das Rückgrat von DNA und RNA bilden, sind alle D‐konfiguriert, und die kodierten Aminosäuren, aus denen die Proteine aller lebenden Arten bestehen, weisen an den α‐Kohlenstoffatomen eine L‐Konfiguration auf. Die Homochiralität der α‐Aminosäuren ist unerlässlich für die Faltung der Peptide in wohldefinierte und funktionelle 3D‐Strukturen und die Homochiralität der D‐Ribose ist entscheidend für die Ausbildung einer Helix und die Basenpaarung. Die Frage, warum die Natur nur kodierte L‐α‐Aminosäuren verwendet, ist nicht geklärt. Wir zeigen hier, dass eine RNA‐Peptid‐Welt, in der Peptide an aus D‐Ribose aufgebauten RNAs wachsen, zur Selbstselektion von homo‐L‐Peptiden führt, was eine mögliche Erklärung für die in der Natur beobachtete Kombination von homo‐D‐Ribose und homo‐L‐Aminosäuren liefert.

Abstract 3888: TOP1 mutations mediate cross resistance to ADCs in metastatic breast cancer

Abstract Background: Antibody-drug conjugates (ADCs) have improved survival for patients with metastatic breast cancer (MBC). In patients with HER2 negative MBC, two ADCs have FDA approval: sacituzumab govitecan (SG) and trastuzumab deruxtecan (T-DXd), both with topoisomerase-I (topo-I) inhibitor payloads. Given the many other ADCs in development, there is great interest in using ADC after ADC to maximize treatment benefit for patients. However, there is limited understanding regarding resistance mechanisms to ADCs and impact on ADC sequencing. We conducted a translational study to address this, and here we report the incidence of TOP1 mutations and clinical impact on ADC sequencing. Methods: All patients with MBC treated with ADCs at a large academic medical institution (Massachusetts General Hospital) who had comprehensive plasma-based genotyping (500 gene GuardantOMNI panel) were included. Since both SG and T-DXd have topo-I inhibitor-based payloads, we particularly focused on TOP1 mutations, variant allele frequency (VAF), and germline/somatic characterization. Incidence of TOP1 mutations in the ADC cohort was compared to The Cancer Genome Atlas (TCGA). Clinical “cross-resistance” was defined as progressive disease (PD) as best response to second ADC (ADC2) or treatment time on ADC2 of less than 60 days. Results: Based on comprehensive plasma-based genotyping we identified 4 distinct TOP1 mutations: S57C, R364H, W401C, G359E, at a frequency of 6.0% (4/67) at the time of disease progression on ADC compared to a frequency of 0.5% described in primary breast cancer in TCGA. Two of the amino acids found to be mutated are known to form direct interactions with the DNA backbone (G359) or the topoisomerase inhibitor itself (R364). For clinical resistance, one patient was briefly on ADC2 but stopped after 1 dose for toxicity; among the other 3 patients, two had cross-resistance to ADC after ADC, with both ADCs containing topo-I inhibitor payloads. Median duration on first ADC was 455 days compared to a median of 52 days for ADC2. Finally, one patient treated sequentially with 3 ADCs (all with topo-I inhibitor payloads) was found to have rising TOP1 VAF with progressive ADC treatments. Conclusion: This is the first report describing emergence of TOP1 mutations under selective pressure from ADCs and the impact on mediating cross-resistance to ADC after ADC with topo-I inhibitor payloads. Novel ADCs with alternative payloads may potentially be more effective when used sequentially after an ADC with a topo-I inhibitor. Further biomarker research is needed to optimize ADC sequencing for patients with TOP1 mutant MBC. Citation Format: Rachel Occhiogrosso Abelman, Haley Barnes, Arielle J. Medford, Annika Putur, Bogang Wu, Caroline Weipert, Geoffrey Fell, Laura M. Spring, Seth A. Wander, Beverly Moy, Andreas Varkaris, Dejan Juric, Leif Ellisen, Ryan Corcoran, Aditya Bardia. TOP1 mutations mediate cross resistance to ADCs in metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3888.

Abstract 3363: LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo

Abstract Women harboring a mutation in the BRCA1 gene have a >7X increased risk of developing breast cancer and >35X increased risk of developing ovarian cancer in their lifetime compared to women lacking such mutations. While PARP1/2 inhibitors are efficacious in the BRCA mutant setting, this efficacy is limited and resistance develops readily. Additional therapeutic targets beyond PARP1/2 are needed to treat cancer patients with BRCA mutations. We performed CRISPR screens in 11 BRCA1/2 wild-type and 2 BRCA1 mutant cancer cell lines to identify targets that are synthetic lethal with BRCA1 mutations. In addition to USP1, PARP1 and POLQ, we identified the DNA ligase gene LIG1 as a novel target that when knocked out kills BRCA1 mutant cells selectively. Internal analysis of BRCA mutations in breast and ovarian cancer cell lines in the Project Achilles database further validated the hyperdependence of BRCA1 mutant cells on LIG1. Single-gene perturbation of LIG1 using CRISPRn, CRISPRi, and RNAi confirm the lethal effect of LIG1 inactivation in BRCA1 mutant cell lines, but not BRCA1/2 wild-type cell lines. This loss of viability could be rescued by complementing with an exogenous wild-type LIG1 cDNA, demonstrating the on-target nature of the genetic tools. Using a degradable DNA Ligase I fusion protein, we demonstrate a strong correlation between DNA Ligase I protein level and viability in BRCA1 mutant cells. Enzymatically inactive DNA Ligase I mutant protein (LIG1K568A) was unable to rescue the loss of viability caused by endogenous LIG1 depletion supporting the tractability of this target from a small molecule inhibitor perspective. These data were reproduced in vivo using BRCA1 mutant MDA-MB-436 derived tumors, in which tumor growth was inhibited >80% upon loss of LIG1.Mechanistically, DNA ligase I plays a critical role in DNA replication and damage repair by sealing nicks in the phosphodiester backbone of DNA. When these nicks are not repaired, they are marked by the addition of PAR chains. Consistent with this mechanism, we demonstrated that inactivation of LIG1 leads to increased PARylation. The induction of PARylation was proportional to the level of inactivation of LIG1 protein, supporting a correlation between LIG1 activity and DNA nick repair. Together, these data support DNA ligase I as a synthetic lethal target in the context of BRCA1 mutations. Citation Format: Lauren Martires, Leanne G. Ahronian, Charlotte Pratt, Nikitha Das, Xiaobin Zhang, Douglas A. Whittington, Hongxiang Zhang, Binzhang Shen, Jon Come, Patrick McCarren, Mu-Sen Liu, Chengyin Min, Tianshu Feng, Haris Jahic, Eric Brophy, Daniel Aird, Jannik N. Andersen, Alan Huang, Fang Li, William D. Mallender, Hilary E. Nicholson. LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3363.

Producing high-quantity and high-quality recombinant adeno-associated virus by low-cis triple transfection

Recombinant adeno-associated virus (rAAV)-based gene therapy is entering clinical and commercial stages at an unprecedented pace. Triple transfection of HEK293 cells is currently the most widely used platform for rAAV manufacturing. Here, we develop low-cis triple transfection that reduces the transgene plasmid usage by 10- to 100-fold, and overcomes several major limitations associated with standard triple transfection. This new method improves packaging of yield-inhibiting transgenes by up to 10-fold, and generates rAAV batches with reduced plasmid backbone contamination that otherwise cannot be eliminated in downstream processing. When tested in mice and compared with rAAV produced by standard triple transfection, low-cis rAAV shows comparable or superior potency, and results in diminished plasmid backbone DNA and RNA persistence in tissue. Mechanistically, low-cis triple transfection relies on the extensive replication of transgene cassette (i.e., ITR-flanked vector DNA) in HEK293 cells during production phase. This cost-effective method can be easily implemented and widely applicable to producing rAAV of high quantity, purity, and potency.

Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water.

Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.

Enzymatic Processing of DNA-Protein Crosslinks.

DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).

Modelling the Binding of Cytotoxic Dinuclear Copper Complexes to two Neighboring Phosphate Esters of DNA Using Glutarate: A Tetranuclear Metallo‐Macrocycle vs a Dinuclear Model

AbstractA family of dinuclear complexes was rationally designed to bind to two neighboring phosphate diesters of DNA by molecular recognition. Although these complexes bind strongly and irreversibly to DNA and induce apoptosis in cancer cells, a direct proof of the intended binding mode is missing. To mimic two neighboring phosphate diesters of DNA, we use here the dicarboxylate glutarate as a difunctional ligand. Starting from the acetate‐bound CuII2 complex, protonation results in the de‐coordination of acetate and allows the synthesis of the glutarate‐bound complex. Instead of bridging two CuII ions of one dinuclear complex, two glutarates bridge two dinuclear complexes resulting in a tetranuclear metallo‐macrocycle. The molecular structures of two different salts differ in the square‐pyramidal coordination to the CuII ions. The carboxylate stretching modes, the d‐d and the CT transtitions are not sensitive enough to resolve these differences. The exchange coupling is weakly antiferromagnetic between the CuII ions in the dinuclear subunits and negligible between the subunits via the glutarates. The consequences for suited ligands to model the binding to two neighboring phosphate diesters in the DNA backbone is discussed.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS).

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

Internal friction as a factor in the anomalous chain length dependence of DNA transcriptional dynamics.

Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τc for chain closure predicts-under the Wilemski-Fixman approximation for diffusion-controlled reactions-that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model.

Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems.

The DndABCDE systems catalysing the unusual phosphorothioate (PT) DNA backbone modification, and the DndFGH systems, which restrict invasive DNA, have enigmatic and paradoxical features. Using comparative genomics and sequence-structure analyses, we show that the DndABCDE module is commonly functionally decoupled from the DndFGH module. However, the modification gene-neighborhoods encode other nucleases, potentially acting as the actual restriction components or suicide effectors limiting propagation of the selfish elements. The modification module's core consists of a coevolving gene-pair encoding the DNA-scanning apparatus - a DndD/CxC-clade ABC ATPase and DndE with two ribbon-helix-helix (MetJ/Arc) DNA-binding domains. Diversification of DndE's DNA-binding interface suggests a multiplicity of target specificities. Additionally, many systems feature DNA cytosine methylase genes instead of PT modification, indicating the DndDE core can recruit other nucleobase modifications. We show that DndFGH is a distinct counter-invader system with several previously uncharacterized domains, including a nucleotide kinase. These likely trigger its restriction endonuclease domain in response to multiple stimuli, like nucleotides, while blocking protective modifications by invader methylases. Remarkably, different DndH variants contain a HerA/FtsK ATPase domain acquired from multiple sources, including cellular genome-segregation systems and mobile elements. Thus, we uncovered novel HerA/FtsK-dependent defense systems that might intercept invasive DNA during replication, conjugation, or packaging.

Molecular Ionization Dissociation Induced by Interatomic Coulombic Decay in an ArCH_{4}-Electron Collision System.

Interatomic Coulombic decay (ICD) is a significant fragmentation mechanism observed in weakly bound systems. It has been widely accepted that ICD-induced molecular fragmentation occurs through a two-step process, involving ICD as the first step and dissociative-electron attachment (DEA) as the second step. In this study, we conducted a fragmentation experiment of ArCH_{4} by electron impact, utilizing the coincident detection of one electron and two ions. In addition to the well-known decay pathway that induces pure ionization of CH_{4}, we observed a new channel where ICD triggers the ionization dissociation of CH_{4}, resulting in the cleavage of the C-H bond and the formation of the CH_{3}^{+} and H ion pair. The high efficiency of this channel, as indicated by the relative yield of the Ar^{+}/CH_{3}^{+} ion pair, agrees with the theoretical prediction [L. S. Cederbaum, J. Phys. Chem. Lett. 11, 8964 (2020).JPCLCD1948-718510.1021/acs.jpclett.0c02259; Y. C. Chiang et al., Phys. Rev. A 100, 052701 (2019).PLRAAN2469-992610.1103/PhysRevA.100.052701]. These results suggest that ICD can directly break covalent bonds with high efficiency, bypassing the need for DEA. This finding introduces a novel approach to enhance the fragmentation efficiency of molecules containing covalent bonds, such as DNA backbone.

Enforcing Local DNA Kinks by Sequence-Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study.

Bisacridinyl-bisarginyl porphyrin (BABAP) is a trisintercalating derivative of a tricationic porphyrin, formerly designed and synthesized in order to selectively target and photosensitize the ten-base pair palindromic sequence d(CGGGCGCCCG)2 . We resorted to the previously derived (Far et al., 2004) lowest energy-minimized (EM) structure of the BABAP complex with this sequence as a starting point. We performed polarizable molecular dynamics (MD) on this complex. It showed, over a 150 ns duration, the persistent binding of the Arg side-chain on each BABAP arm to the two G bases upstream from the central porphyrin intercalation site. We subsequently performed progressive shortenings of the connector chain linking the Arg-Gly backbone to the acridine, from n=6 methylenes to 4, followed by removal of the Gly backbone and further connector shortenings, from n=4 to n=1. These resulted into progressive deformations ('kinks') of the DNA backbone. In its most accented kinked structure, the DNA backbone was found to have a close overlap with that of DNA bound to Cre recombinase, with, at the level of one acridine intercalation site, negative roll and positive tilt values consistent with those experimentally found for this DNA at its own kinked dinucleotide sequence. Thus, in addition to their photosensitizing properties, some BABAP derivatives could induce sequence-selective, controlled DNA deformations, which are targets for cleavage by endonucleases or for repair enzymes.

Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers.

In recent years, DNA has emerged as a fascinating building material to engineer hydrogel due to its excellent programmability, which has gained considerable attention in biomedical applications. Understanding the structure-property relationship and underlying molecular determinants of DNA hydrogel is essential to precisely tailor its macroscopic properties at molecular level. In this review, the rational design principles of DNA molecular networks based on molecular dynamics of polymers on the temporal scale, which can be engineered via the backbone rigidity and crosslinking kinetics, are highlighted. By elucidating the underlying molecular mechanisms and theories, it is aimed to provide a comprehensive overview of how the tunable DNA backbone rigidity and the crosslinking kinetics lead to desirable macroscopic properties of DNA hydrogels, including mechanical properties, diffusive permeability, swelling behaviors, and dynamic features. Furthermore, it is also discussed how the tunable macroscopic properties make DNA hydrogels promising candidates for biomedical applications, such as cell culture, tissue engineering, bio-sensing, and drug delivery.

Connection number topological aspect for backbone DNA networks.

The present study investigates the complex topological characteristics of DNA networks, with a specific emphasis on the innovative metric known as Connection Number (CN) as a key factor in determining network structure. The Connection Number, represented as CN(v) for a vertex v, measures the count of unique paths that link v to every other vertex in the network. By employing rigorous mathematical modeling and analysis techniques, we are able to reveal the profound implications of CN (complex networks) in characterizing the structural robustness and dynamics of information flow within DNA networks. The study of how the theory of graphs and chemicals interact is known as chemical graph theory. This paper, computing the hyper Zagreb connection index, augmented connection index, inverse sum connection index, harmonic connection index, symmetric division connection index, geometric arithmetic connection index, and atom bond connectivity connection index, of two significant types of backbone DNA and Barycentric subdivision of backbone DNA networks. Direct method computation is used to produce these Connection-based topological descriptors.

Investigation of the impact of R273H and R273C mutations on the DNA binding domain of P53 protein through molecular dynamic simulation

The P53 protein, a cancer-associated transcriptional factor and tumor suppressor, houses a Zn2+ ion in its DNA-binding domain (DBD), essential for sequence-specific DNA binding. However, common mutations at position 273, specifically from Arginine to Histidine and Cysteine, lead to a loss of function as a tumor suppressor, also called DNA contact mutations. The mutant (MT) P53 structure cannot stabilize DNA due to inadequate interaction. To investigate the conformational changes, we performed a comparative molecular dynamic simulation (MDS) to study the effect of the P53-Wildtype (P53-WT) and the DNA contact mutations (R273H and R273C) on the DBD. Our research indicated that the DNA binding bases lose Hydrogen bonds (H bonds) when mutated to P53-R273H and P53-R273C during the simulation. We employed tools, such as PDIviz to highlight the contacts with DNA bases and backbone, major and minor grooves, and various pharmacophore forms of atoms. The contact maps for R273H and R273C were generated using the COZOID tool, which displayed changes in the frequency of the amino acids and DNA bases interaction in the DNA binding domain. These residues have diminished interactions, and the zinc-binding domain shows significant movements by Zn2+ ion binding to the phosphate group of the DNA, moving away from its binding sites. In conclusion, our research suggests that R273H and R273C each have unique stability and self-assembly properties. This understanding might assist researchers in better comprehending the function of the p53 protein and its importance in cancer. Communicated by Ramaswamy H. Sarma

Personalized DNA Vaccine Immunogenic Against Melanoma.

A personalized neoantigen vaccine built around a DNA backbone, EVX-02, elicited robust and lasting T-cell responses in patients with melanoma after surgery. The first-in-human data, presented at the Society for Immunotherapy of Cancer Annual Meeting, have inspired a next-generation DNA vaccine candidate, EVX-03, that includes an additional payload and a more sophisticated antigen-selection process.

Role of Neutrophil Extracellular Traps in Health and Disease Pathophysiology: Recent Insights and Advances

Neutrophils are the principal trouper of the innate immune system. Activated neutrophils undergo a noble cell death termed NETosis and release a mesh-like structure called neutrophil extracellular traps (NETs) as a part of their defensive strategy against microbial pathogen attack. This web-like architecture includes a DNA backbone embedded with antimicrobial proteins like myeloperoxidase (MPO), neutrophil elastase (NE), histones and deploys in the entrapment and clearance of encountered pathogens. Thus NETs play an inevitable beneficial role in the host’s protection. However, recent accumulated evidence shows that dysregulated and enhanced NET formation has various pathological aspects including the promotion of sepsis, pulmonary, cardiovascular, hepatic, nephrological, thrombotic, autoimmune, pregnancy, and cancer diseases, and the list is increasing gradually. In this review, we summarize the NET-mediated pathophysiology of different diseases and focus on some updated potential therapeutic approaches against NETs.

Tailoring high-energy self-powered sensing system by Walker-mediated CRISPR/Cas12a cascade signal amplification and hybridization chain reaction for ultrasensitive microRNA detection

MicroRNAs (miRNAs) are important cancer-associated biomarkers for early detection. However, accurately measuring miRNAs is challenging due to their low abundance and high homogeneity in human serum. CRISPR technology can greatly improve the specificity and sensitivity of detection in biosensor construction. In this study, we develop a remarkably responsive self-powered biosensing platform for detecting microRNA-21 (miRNA-21) using hybridization chain reaction (HCR) and CRISPR/Cas12a amplification cascade mediated by 3D DNA walkers. Carbon-coated molybdenum disulfide nanotubes with a large surface area and excellent conductivity are fabricated on flexible carbon paper as the anode and cathode for biological fuel cell construction. Glucose oxidase is loaded onto the anode surface, while serving as the biological cathode, it initiated HCR, generating abundant double-stranded DNA. The negatively charged DNA backbone captures electron acceptors [Ru(NH3)6]3+ through electrostatic adsorption, resulting in a significant open circuit voltage (EOCV) signal. Through CRISPR/Cas12a amplification cascade mediated by 3D DNA walkers, a smaller EOCV is produced, enabling sensitive target detection. The method exhibits a detection range spanning from 0.0001 to 10,000 pM and capable of detecting as low as 19.0 aM (S/N = 3). This highly selective and sensitive method provides an effective approach for accurately detecting tumor markers in clinical applications.

Probing Mitotic Chromosome Mechanics Using Optical Tweezers.

During mitosis, cells compact their DNA into rodlike shapes, four orders of magnitude shorter than the DNA backbone contour length. We describe an experimental protocol to isolate and study these intricate mitotic chromosomes using optical tweezers. We touch upon the technical details of the required optical tweezers and microfluidics setup, including advanced force calibration procedures to accurately measure the high forces the chromosomes withstand. The procedure used to isolate mitotic chromosomes, including biotinylation of the telomeric ends to facilitate trapping them in optical tweezers, is described in detail. Finally, we provide a protocol for carrying out optical tweezers experiments on the isolated mitotic chromosomes.