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The assembly of pH‐responsive DNA‐based, phase‐separated microdroplets (MDs) coacervates, consisting of frameworks composed of Y‐shaped nucleic acid modules crosslinked by pH‐responsive strands, is introduced. The phase‐separated MDs reveal dynamic pH‐stimulated switchable or oscillatory transient depletion and reformation. In one system, a photoisomerizable merocyanine/spiropyran photoacid is used for the light‐induced pH switchable modulation of the reaction medium between the values pH=6.0–4.4. The dynamic transient photochemically‐induced switchable depletion/reformation of phase‐separated MDs, follows the rhythm of pH changes in solution. In a second system, the Landolt oscillatory reaction mixture pH 7.5→4.2→7.5 is applied to stimulate the oscillatory depletion/reformation of the MDs. The autonomous dynamic oscillation of the assembly/disassembly of the MDs follows the oscillating pH rhythm of the reaction medium. [ABSTRACT FROM AUTHOR]

The adhesion of circulating tumor cells (CTCs) to the endothelial lumen and their extravasation to surrounding tissues are crucial in the seeding of metastases and remain the most complex events of the metastatic cascade to study. Integrins expressed on CTCs are major regulators of the extravasation process. This knowledge is primarily derived from animal models and biomimetic systems based on artificial endothelial layers, but these methods have ethical or technical limitations. We present a versatile microfluidic device to study cancer cell extravasation that mimics the endothelial barrier by using a porous membrane functionalized with DNA origami nanostructures (DONs) that display nanoscale patterns of adhesion peptides to circulating cancer cells. The device simulates physiological flow conditions and allows direct visualization of cell transmigration through microchannel pores using 3D confocal imaging. Using this system, we studied integrin‐specific adhesion in the absence of other adhesive events. Specifically, we show that the transmigration ability of the metastatic cancer cell line MDA‐MB‐231 is influenced by the type, distance, and density of adhesion peptides present on the DONs. Furthermore, studies with mixed ligand systems indicate that integrins binding to RGD (arginine‐glycine‐aspartic acid) and IDS (isoleucine‐aspartic acid‐serine) did not synergistically enhance the extravasation process of MDA‐MB‐231 cells. [ABSTRACT FROM AUTHOR]

Studying the direct effects of DNA irradiation is essential for understanding the impact of radiation on biological systems. Gas‐phase interactions are especially well suited to uncover the molecular mechanisms underlying these direct effects. Only relatively recently, isolated DNA oligonucleotides were irradiated by ionizing particles such as VUV or X‐ray photons or ion beams, and ionic products were analyzed by mass spectrometry. This article provides a comprehensive review of primarily experimental investigations in this field over the past decade, emphasizing the description of processes such as ionization, fragmentation, charge and hydrogen transfer triggered by photoabsorption or ion collision, and the recent progress made thanks to specific atomic photoabsorption. Then, we outline ongoing experimental developments notably involving ion‐mobility spectrometry, crossed beams or time‐resolved measurements. The discussion extends to potential research directions for the future. [ABSTRACT FROM AUTHOR]

Despite the expected direct effects of radiation on DNA through its direct interaction with the biomolecule, research indicates that radiation also interacts with the DNA’s environment, resulting in indirect effects. Therefore, in this study, we explored the feasibility of using the quartz tuning fork (QTF) sensor system in biomedical applications, specifically in detecting DNA damage caused by low doses of gamma radiation, directly and indirectly. We differentiated between direct and indirect damage by analyzing the fork’s resonance frequency changes. This experiment was divided into three stages: before, during, and after irradiation. Each stage involved samples of pure DNA and DNA in a 60-µL aqueous solution, evaluated under identical conditions. Before irradiation, we measured frequency shifts (Δf) over a 20-min period, resulting in values of 19.34, 20.25, and 7.6 Hz for water, DNA, and DNA in water, respectively. Subsequently, the samples were irradiated with cesium-137 for the specified duration, resulting in frequency shifts of ∼ 39.21, 28.37, and 41.23 Hz for the same conditions. Our investigations showed an increase in Δf from 20.25 to 28.3 Hz at doses ranging from 7.5 to 30 µGy for pure DNA. Interestingly, DNA in aqueous solution exhibited hypersensitivity to radiation, with frequency shifts ranging from 7.6 to 41.23 Hz. Furthermore, we observed a significant difference in frequency shift after irradiation between pure DNA and DNA in water, with shifts of ∼ 70.75–98.45 Hz and 56.32–79.28 Hz for DNA and DNA in water, respectively. This result indicates a significant increase in DNA damage in aqueous environments, driven by the generation of active hydroxyl radicals (OH−), resulting in base damage and an associated increase in strand breaks. Consequently, our research indicates a lack of substantial direct impact on DNA repair owing to the absence of a conducive postirradiation environment. Therefore, QTF is a valuable biomarker for radiation sensitivity and is promising for future applications as a mass-sensitive biosensor.

The formation and dissociation of duplexes or higher order structures from nucleic acid strands is a fundamental process with widespread applications in biochemistry and nanotechnology. Here, we introduce a simple experimental system—a diffusiophoretic trap—for the non‐equilibrium self‐assembly of nucleic acid structures that uses an electrolyte gradient as the driving force. DNA strands can be concentrated up to hundredfold by a diffusiophoretic trapping force that is caused by the electric field generated by the electrolyte gradient. We present a simple equation for the field to guide selection of appropriate trapping electrolytes. Experiments with carboxylated silica particles demonstrate that the diffusiophoretic force is long‐ranged, extending over hundreds of micrometers. As an application, we explore the reversible self‐assembly of branched DNA nanostructures in the trap into a macroscopic gel. The structures assemble in the presence of an electrolyte gradient, and disassemble upon its removal, representing a prototypical adaptive response to a macroscopic non‐equilibrium state. [ABSTRACT FROM AUTHOR]

Encoded nanostructures afford an ideal platform carrying multi‐channel signal components for multiplexed assay and information security. However, with the demand on exclusivity and reproducibility of coding signals, precise control on the structure and composition of nanomaterials featuring fully distinguishable signals remains challenging. By using the multiplexing capability of mass spectrometry (MS) and spatial addressability of DNA origami nanostructures, we herein propose a quality control methodology for constructing mass‐encoded nanodevices (namely MNTs‐TDOFs) in the scaffold of compartmented tetrahedral DNA origami frames (TDOFs), in which the arrangement and stoichiometry of four types of mass nanotags (MNTs) can be finely regulated and customized to generate characteristic MS patterns. The programmability of combinatorial MNTs and orthogonality of individual compartments allows further evolution of MNTs‐TDOFs to static tagging agents and dynamic nanoprobes for labeling and sensing of multiple targets. More importantly, structure control at single TDOF level ensures the constancy of prescribed MS outputs, by which a high‐capacity coding system was established for secure information encryption and decryption. In addition to the multiplexed outputs in parallel, the nanodevices could also map logic circuits with interconnected complexity and logic events of c‐Met recognition and dimerization on cell surface for signaling regulation by MS interrogation. [ABSTRACT FROM AUTHOR]

Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA‐based structures decorated with reporter tags and recognition elements. We have rationally re‐engineered tile‐based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof‐of‐principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti‐Dig, Anti‐DNP and Anti‐MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA‐based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: DNA‐based nanostructure allows the construction of molecular devices useful in biological computing and information processing. Herein, an addressable and editable DNA information processing system established on a fluorescence intensity signal detection platform to save and encrypt information is proposed. The system operates by encoding information into distinct and changeable units of the trigger strands decoding by fluorescence intensity signal detection. Through toehold‐mediated strand displacement reactions, the trigger strand can be precisely added to and removed from the memorizer and reporter to implement the function of editing, encrypting, and decrypting. Our strategy is simple to implement, requiring only two mixing steps at room temperature for each operation and fluorescence intensity signal detection to read the data. And the system can realize accurate retrieval of specific individual information, eliminating all unnecessary redundant readouts. Because of its point‐to‐point accurate readout and programmability, the system is expected to become a powerful tool for the future development of information storage and sensing of biological molecules. [ABSTRACT FROM AUTHOR]

Expansions of short tandem repeats (STRs) are associated with approximately 50 human neurodegenerative diseases. These pathogenic STRs are prone to form non-B DNA structure, which has been considered as one of the causative factors for repeat expansions. Minidumbbell (MDB) is a relatively new type of non-B DNA structure formed by pyrimidine-rich STRs. An MDB is composed of two tetraloops or pentaloops, exhibiting a highly compact conformation with extensive loop-loop interactions. The MDB structures have been found to form in CCTG tetranucleotide repeats associated with myotonic dystrophy type 2, ATTCT pentanucleotide repeats associated with spinocerebellar ataxia type 10, and the recently discovered ATTTT/ATTTC repeats associated with spinocerebellar ataxia type 37 and familial adult myoclonic epilepsy. In this review, we first introduce the structures and conformational dynamics of MDBs with a focus on the high-resolution structural information determined by nuclear magnetic resonance spectroscopy. Then we discuss the effects of sequence context, chemical environment, and nucleobase modification on the structure and thermostability of MDBs. Finally, we provide perspectives on further explorations of sequence criteria and biological functions of MDBs.

Simultaneously studying different biomarker types (DNA, RNA, proteins, etc.) could improve understanding and diagnosis of many complex diseases. However, biomarker detection involves several complex or expensive methodologies, requiring specialized laboratories and personnel. A multiplexed assay would greatly facilitate the use of biomarker data. Here, we present a multiplexed biomarker detection technique using variable‐length DNA payload chains, which are systematically disassembled in the presence of specific biomarkers. The resulting distinctly‐sized fragments yield characteristic gel electrophoresis band patterns. This has enabled us to detect with high sensitivity and specificity DNA sequences including BRCA1 (limit of detection, LOD, ∼3 nM), RNA (miR‐141, LOD ∼19 nM) and the steroids aldosterone and cortisol (LOD ∼200–250 nM). We show that our assay is multiplexable, and suffers limited sensitivity loss in fetal bovine serum and can be applied using capillary electrophoresis, which may be more amenable to automation and integration in healthcare settings. [ABSTRACT FROM AUTHOR]

G-quadruplexes (G4s) are short secondary DNA structures located throughout genomic DNA and transcribed RNA. Although G4 structures have been shown to form in vivo, no current search tools that examine these structures based on previously identified G-quadruplexes and filter them based on similar sequence, structure, and thermodynamic properties are known to exist. We present a framework for clustering G-quadruplex sequences into families using the CD-HIT, MeShClust, and DNACLUST methods along with a combination of Starcode and BLAST. Utilizing this framework to filter and annotate clusters, 95 families of G-quadruplex sequences were identified within the human genome. Profiles for each family were created using hidden Markov models to allow for the identification of additional family members and generate homology probability scores. The thermodynamic folding energy properties, functional annotation of genes associated with the sequences, scores from different prediction algorithms, and transcription factor binding motifs within a family were used to annotate and compare the diversity within and across clusters. The resulting set of G-quadruplex families can be used to further understand how different regions of the genome are regulated by factors targeting specific structures common to members of a specific cluster. [ABSTRACT FROM AUTHOR]

DNA nanotechnology has emerged as a groundbreaking field, using DNA as a scaffold to create nanostructures with customizable properties. These DNA nanostructures hold potential across various domains, from biomedicine to studying ionizing radiation-matter interactions at the nanoscale. This review explores how the various types of radiation, covering a spectrum from electrons and photons at sub-excitation energies to ion beams with high-linear energy transfer influence the structural integrity of DNA origami nanostructures. We discuss both direct effects and those mediated by secondary species like low-energy electrons (LEEs) and reactive oxygen species (ROS). Further we discuss the possibilities for applying radiation in modulating and controlling structural changes. Based on experimental insights, we identify current challenges in characterizing the responses of DNA nanostructures to radiation and outline further areas for investigation. This review not only clarifies the complex dynamics between ionizing radiation and DNA origami but also suggests new strategies for designing DNA nanostructures optimized for applications exposed to various qualities of ionizing radiation and their resulting byproducts., (© 2024 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

With the rapid advancement of DNA technology, intelligent DNA nanoreactors (iDNRs) have emerged as sophisticated tools that harness the structural versatility and programmability of DNA. Due to their structural and functional programmability, iDNRs play an important and unique role in in vivo tumor diagnosis and therapy. This review provides an overview of the structural design methods for iDNRs based on advanced DNA technology, including enzymatic reaction-mediated and enzyme-free strategies. This review also focuses on how iDNRs achieve intelligence through functional design, as well as the applications of iDNRs for in vivo tumor diagnosis and therapy. In summary, this review summarizes current advances in iDNRs technology, discusses existing challenges, and proposes future directions for expanding their applications, which are expected to provide insights into the development of the field of in vivo tumor diagnostics and targeted therapies., (© 2024 Wiley-VCH GmbH.)

The bending and twisting of DNA origami structures are important features for controlling the physical properties of DNA nanodevices. It has not been fully explored yet how to finely tune the bending and twisting of curved DNA structures. Traditional tuning of the curved DNA structures was limited to controlling the in-plane-bending angle through varying the numbers of base pairs of deletions and insertions. Here, we developed two tuning strategies of curved DNA origami structures from in silico and in vitro aspects. In silico, the out-of-plane bending and twisting angles of curved structures were introduced, and were tuned through varying the patterns of base pair deletions and insertions. In vitro, a chemical adduct (ethidium bromide) was applied to dynamically tune a curved spiral. The 3D structural conformations, like chirality, of the curved DNA structures were finely tuned through these two strategies. The simulation and TEM results demonstrated that the patterns of base pair insertions and deletions and chemical adducts could effectively tune the bending and twisting of curved DNA origami structures. These strategies expand the programmable accuracy of curved DNA origami structures and have potential in building efficient dynamic functional nanodevices. [ABSTRACT FROM AUTHOR]

The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental D2O. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between D2O and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing D2O proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and D2O and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and D2O. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules. [ABSTRACT FROM AUTHOR]

Despite the expected direct effects of radiation on DNA through its direct interaction with the biomolecule, research indicates that radiation also interacts with the DNA's environment, resulting in indirect effects. Therefore, in this study, we explored the feasibility of using the quartz tuning fork (QTF) sensor system in biomedical applications, specifically in detecting DNA damage caused by low doses of gamma radiation, directly and indirectly. We differentiated between direct and indirect damage by analyzing the fork's resonance frequency changes. This experiment was divided into three stages: before, during, and after irradiation. Each stage involved samples of pure DNA and DNA in a 60-µL aqueous solution, evaluated under identical conditions. Before irradiation, we measured frequency shifts (Δ f) over a 20-min period, resulting in values of 19.34, 20.25, and 7.6 Hz for water, DNA, and DNA in water, respectively. Subsequently, the samples were irradiated with cesium-137 for the specified duration, resulting in frequency shifts of ∼ 39.21, 28.37, and 41.23 Hz for the same conditions. Our investigations showed an increase in Δ f from 20.25 to 28.3 Hz at doses ranging from 7.5 to 30 µGy for pure DNA. Interestingly, DNA in aqueous solution exhibited hypersensitivity to radiation, with frequency shifts ranging from 7.6 to 41.23 Hz. Furthermore, we observed a significant difference in frequency shift after irradiation between pure DNA and DNA in water, with shifts of ∼ 70.75–98.45 Hz and 56.32–79.28 Hz for DNA and DNA in water, respectively. This result indicates a significant increase in DNA damage in aqueous environments, driven by the generation of active hydroxyl radicals (OH−), resulting in base damage and an associated increase in strand breaks. Consequently, our research indicates a lack of substantial direct impact on DNA repair owing to the absence of a conducive postirradiation environment. Therefore, QTF is a valuable biomarker for radiation sensitivity and is promising for future applications as a mass-sensitive biosensor. [ABSTRACT FROM AUTHOR]

We demonstrate here the use of DNA repair enzymes to control the assembly of DNA‐based structures. To do so, we employed uracil‐DNA glycosylase (UDG) and formamidopyrimidine DNA glycosylase (Fpg), two enzymes involved in the base excision repair (BER) pathway. We designed two responsive nucleic acid modules containing mutated bases (deoxyuridine or 8‐oxo‐7,8‐dihydroguanine recognized by UDG and Fpg, respectively) that, upon the enzyme repair activity, release a nucleic acid strand that induces the self‐assembly of DNA tiles into tubular structures. The approach is programmable, specific and orthogonal and the two responsive modules can be used in the same solution without crosstalk. This allows to assemble structures formed by two different tiles in which the tile distribution can be accurately predicted as a function of the relative activity of each enzyme. Finally, we show that BER‐enzyme inhibitors can also be used to control DNA‐tile assembly in a specific and concentration‐dependent manner. [ABSTRACT FROM AUTHOR]

DNA B−Z transitions play an important role in biological systems and have attracted much attention in DNA nanotechnology. DNA and its analogues have also been used as templates to construct helical chromophore associates with π‐interactions. We prepared DNAs with consecutive non‐nucleoside pyrene residues in the middle of d(CG) repeat sequences. The pyrene‐labelled DNAs adopted a unimolecular hairpin structure, in which the pyrenes associated in the loop region. They exhibited inversion of exciton‐coupled circular dichroism signals that can be ascribed to pyrene association through a DNA B−Z transition. This indicates that the conformation of pyrene associates can be switched from right to left by the DNA B−Z transition. The fluorescence of the pyrene‐labelled DNA changed when switching the association. Thus, pyrene‐labelled DNA can be utilized as a chiroptical molecular switch. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: Inspired by nature, precise spatial organization of enzyme cascades of interest is crucial to the improvement of catalytic performance. Herein, DNA scaffolds were introduced to construct a toolkit for versatile immobilization of enzyme pairs on dextran‐coated magnetic nanoparticles (MNPs). After the glucose oxidase (GOx) and horseradish peroxidase (HRP) pair was immobilized through random covalent, DNA‐directed and DNA tile‐directed strategies, the immobilized GOx/HRP pair on the MNP‐based carrier assembled with DNA tile (TD@MNPs) exhibited the highest activity due to rational spatial organization and less conformational change of constituent enzymes. With a decrease in interenzyme distance on TD@MNPs, furthermore, the catalytic efficiency of the HRP/GOx pair increased further for both substrates, 2,2'‐azinobis(3‐ethyl‐benzthiazoline‐6‐sulfonate) (ABTS) and 3,3',5,5'‐tetramethyl benzidine (TMB). As the assembled HRP was closer to the carrier surface, the catalytic efficiency of the GOx/HRP pair increased by 6.2‐fold for positively charged TMB and only by 62% for negatively charged ABTS compared with the free GOx/HRP pair. Moreover, a reversal of catalytic efficiency was found after the GOx/HRP pair was assembled on a positively charged carrier (TD@pMNPs). This research demonstrated that MNP‐based carriers had the potential to become a versatile toolkit for shedding an insight into catalytic performance and the development of new biocatalysts. [ABSTRACT FROM AUTHOR]

We report the first in vitro selection of DNA nanostructures that switch their conformation when triggered by change in pH. Previously, most pH-active nanostructures were designed using known pH-active motifs, such as the i-motif or the triplex structure. In contrast, we performed de novo selections starting from a random library and generated nanostructures that can sequester and release Mipomersen, a clinically approved antisense DNA drug, in response to pH change. We demonstrate extraordinary pH-selectivity, releasing up to 714-fold more Mipomersen at pH 5.2 compared to pH 7.5. Interestingly, none of our nanostructures showed significant sequence similarity to known pH-sensitive motifs, suggesting that they may operate via novel structure-switching mechanisms. We believe our selection scheme is general and could be adopted for generating DNA nanostructures for many applications including drug delivery, sensors and pH-active surfaces.

Here, we describe the design and synthesis of a new reduction‐cleavable spacer (RCS) based on a nitrobenzene scaffold for constructing reduction‐responsive oligonucleotides according to standard phosphoramidite chemistry. In addition, we demonstrate that the introduction of the RCS in the middle of an oligonucleotide (30 nt) enables the construction of a self‐assembled microsphere capable of exhibiting a reduction‐responsive disassembly. [ABSTRACT FROM AUTHOR]

Cancer diagnosis and determining its tissue of origin are crucial for clinical implementation of personalized medicine. Conventional diagnostic techniques such as imaging and tissue biopsy are unable to capture the dynamic tumor landscape. Although circulating tumor DNA (ctDNA) shows promise for diagnosis, the clinical relevance of ctDNA remains largely undetermined due to several biological and technical complexities. Here, cancer stem cell‐ctDNA is used to overcome the biological complexities like the inability for molecular analysis of ctDNA and dependence on ctDNA concentration rather than the molecular profile. Ultrasensitive quantum superstructures overcome the technical complexities of trace‐level detection and rapid diagnosis to detect ctDNA within its short half‐life. Activation of multiple surface enhanced Raman scattering mechanisms of the quantum superstructures achieved a very high enhancement factor (1.35 × 1011) and detection at ultralow concentration (10−15 M) with very high reliability (RSD: 3–12%). Pilot validation with clinical plasma samples from an independent validation cohort achieved a diagnosis sensitivity of ≈95% and specificity of 83%. Quantum superstructures identified the tissue of origin with ≈75–86% sensitivity and ≈92–96% specificity. With large scale clinical validation, the technology can develop into a clinically useful liquid biopsy tool improving cancer diagnostics. [ABSTRACT FROM AUTHOR]

Abstract We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson–Crick base pairing, using dispersion‐corrected DFT at the BLYP‐D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better‐known effects of partial desolvation. Furthermore, we show that the sequence‐dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so‐called “diagonal interactions” or “cross terms”. Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson–Crick base pairing, using dispersion‐corrected DFT at the BLYP‐D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better‐known effects of partial desolvation. Furthermore, we show that the sequence‐dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so‐called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases. [ABSTRACT FROM AUTHOR]

Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA‐based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so‐called "material voxels", to realize designer nanomaterials with desired functions. [ABSTRACT FROM AUTHOR]

Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term "The anti-dsDNA antibody". "The anti-dsDNA antibody" holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher's Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. "one antibody - one disease". In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis. [ABSTRACT FROM AUTHOR]

DNA three‐way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)‐modified DNA 3WJ by using a newly designed bpy‐modified nucleoside, Ubpy‐3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy‐modified 3WJ was greatly enhanced by the formation of an interstrand NiII(bpy)3 complex at the junction core (ΔTm=+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy‐modified nucleoside Ubpy‐2, the degree of the NiII‐mediated stabilization observed with Ubpy‐3 was comparable to that of Ubpy‐2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of NiII ions. Furthermore, NiII‐mediated self‐sorting of 3WJs was performed by using the bpy‐modified strands and their unmodified counterparts. Both transformations were driven by the formation of NiII(bpy)3 complexes. The structural induction and self‐sorting of bpy‐modified 3WJs are expected to have many potential applications in the development of metal‐responsive DNA materials. [ABSTRACT FROM AUTHOR]

Four models of DNA including A‐DNA, B‐DNA, Triple helix‐DNA (T‐DNA), and Z‐DNA along with a COF molecule were prepared. Molecular dynamics simulations were performed on all DNAs and their complex with COF (embedded DNAs in the central hole of COF). Comprehensive analyses such as Base pair distance, hydrogen bonding, Van der Waals, and electrostatic interaction numbers were carried out to investigate the effect of COF molecule on DNA intermolecular interactions. Furthermore, quantum‐mechanics studies were performed to explore the accuracy of intermolecular and intramolecular interactions. The results obtained based on promolecular density in two selected base pairs. Noncovalent interaction (NCI) analysis to investigate the strength of hydrogen bonds, Van der Waals interactions, and steric effect was done. Density Overlap Regions Indicator (DORI) analysis was accomplished to study the accuracy of π‐π stacking interactions between adjacent bases. δg functions were evaluated to analyze the strength of chemical bonds, hydrogen bonds and also the steric effect. The average distance between O...H, N...H, and H...O that are contributing in H‐bonding are ∼1.88, 1.97, and 1.95 Å in A‐DNA, respectively. Also, the average number of H‐bonding numbers in A‐DNA calculated to be 14.43 and 13.04 in pure and complex form. All the achieved results showed that designed COF did not make any changes in DNA structures, but in some cases, had some effects on the interactions of DNAs. [ABSTRACT FROM AUTHOR]

Ab initio DNA synthesis refers to the unusual synthesis of dsDNA (with a length ranging from tens of bp to kbp) by thermophilic DNA polymerases from free dNTPs in the complete absence of added DNAs. As commonly believed, the reaction product is a linear double-stranded DNA in the B form. However, an extremely low efficiency of cloning and the failure to hydrolyze high-molecular-weight DNA, as well as the presence short repeats, palindromes, and AT-rich repeats in the sequence, mean that a more complex spatial structure of this DNA can be assumed. The AFM coupled with nuclease analysis revealed that high-molecular-weight dsDNA products branched and formed net-like structures. The DNA contained single-stranded and triple-stranded segments. These net-like structures may be assumed to be three-dimensional (3D). The present work was the first detailed investigation of ab initio synthesis products. The results may be useful to develop techniques requiring the synthesis of large amounts of DNA with complex spatial structures.

In this work, FT‐IR absorbance spectra of genomic DNAs isolated from four strains of Escherichia coli (A, B, C and D) and two strains of Salmonella (E and F), respectively, have been analyzed in both untreated and UV femtosecond laser pulses irradiated samples, to investigate their screening characteristics and their structural radiotolerance at 256 nm. Spectroscopic band assignments and structural aspects are discussed in the 600–1800 cm−1 and 3000–4000 cm−1 spectral ranges. DNA structural changes at the level of nucleic acids backbone, sugar, PO2− group, nitrogenous base ring and deoxycytidine (C2=O2) have been observed. Consequently, modifications in DNA conformations have been found. Bacterial strain dependent femtosecond laser pulses irradiation effects on DNA structure were observed. Based on FT‐IR biomarkers novel early diagnosis and screening tools for routine use in health care and life sciences can be developed. Furthermore, cancer research could benefit from ultra‐fast lasers technology. Besides, analyzing the interaction mechanisms of DNA with femtosecond laser pulses is highly appreciated for understanding the pathways of irradiation damaged DNA response in living cells. [ABSTRACT FROM AUTHOR]

In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

We report the structural effect of 2'‐deoxy‐2',2'‐difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self‐complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars. [ABSTRACT FROM AUTHOR]

Success in the bottom‐up assembly of synthetic cells will depend on strategies for the division of protocellular compartments. Here, we describe the controlled division of phase‐separated giant unilamellar lipid vesicles (GUVs). We derive an analytical model based on the vesicle geometry, which makes four quantitative predictions that we verify experimentally. We find that the osmolarity ratio required for division is 2 , independent of the GUV size, while asymmetric division happens at lower osmolarity ratios. Remarkably, we show that a suitable osmolarity change can be triggered by water evaporation, enzymatic decomposition of sucrose or light‐triggered uncaging of CMNB‐fluorescein. The latter provides full spatiotemporal control, such that a target GUV undergoes division whereas the surrounding GUVs remain unaffected. Finally, we grow phase‐separated vesicles from single‐phased vesicles by targeted fusion of the opposite lipid type with programmable DNA tags to enable subsequent division cycles. [ABSTRACT FROM AUTHOR]

Minidumbbell (MDB) is a recently identified non‐B DNA structure that has been proposed to associate with genetic instabilities. It also serves as a functional structural motif in DNA nanotechnology. DNA molecular switches constructed using MDBs show instant and complete structural conversions with easy manipulations. The availability of stable MDBs can broaden their applications. In this work, we found that substitutions of cytosine with 5‐methylcytosine could lead to a significant enhancement in the thermal stabilities of MDBs. Consecutive methylations of cytosine in MDBs brought about cumulative stabilization with a drastic increase in the melting temperature by 23 °C. NMR solution structures of two MDBs containing 5‐methylcytosine residues have been successfully determined and revealed that the enhanced stabilities resulted primarily from favorable hydrophobic contacts, more stable base pairs and enhanced base‐base stackings involving the methyl group of 5‐methylcytosine. [ABSTRACT FROM AUTHOR]

Due to its advantages of high precision and low cost, automated Sanger sequencing technology remains useful for many applications despite the emergence of next-generation sequencing (NGS) platforms. Few studies revealed the sequence errors in sanger sequencing because the instrumentation and chemistry currently used for Sanger sequencing is highly reliable and reproducible. Unexpectedly, in our study, the sequencing artifacts were identified in sequencing the PCR product of rAAV-ITR (recombination Adeno-Associated Virusinverted terminal repeat) which formed highly stable T-shaped hairpin and played critical role in virus production. The artifactual sequences were characterized by the 3’ end palindromic sequence and nucleotide substitutions. We confirmed that the presence of stable hairpin in template results in sequencing artifacts by employing disruptor to eliminate the structure, sequencing the PCR product and the synthezized strands containing stable or weak hairpin respectively for comparation. Furthermore, we proposed that endonuclease activity of Taq polymerase cleaves the templates containing stable structure to generate annealed 3’end which acts as primer to synthesize the artifactual palindrome. [ABSTRACT FROM AUTHOR]

Metal‐mediated base pairs have widespread applications, such as in DNA‐metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non‐canonical DNA/DNA duplex containing 2′‐O,4′‐C‐methylene bridged nucleic acid in the presence of AgI ions. The X‐ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI‐mediated base pair between the N1 positions of anti‐conformation of adenines in the duplex was observed. In the central non‐canonical region, a hexad nucleobase structure containing AgI‐mediated base pairs between the N7 positions of guanines was formed. A highly bent non‐canonical structure was formed at the origin of AgI‐mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications. [ABSTRACT FROM AUTHOR]

Chemistry is ideally placed to replicate biomolecular structures with tuneable building materials. Of particular interest are molecular nanopores, which transport cargo across membranes, as in DNA sequencing. Advanced nanopores control transport in response to triggers, but this cannot be easily replicated with biogenic proteins. Here we use DNA nanotechnology to build a synthetic molecular gate that opens in response to a specific protein. The gate self‐assembles from six DNA strands to form a bilayer‐spanning pore, and a lid strand comprising a protein‐binding DNA aptamer to block the channel entrance. Addition of the trigger protein, thrombin, selectively opens the gate and enables a 330‐fold increase inw the transport rate of small‐molecule cargo. The molecular gate incorporates in delivery vesicles to controllably release enclosed cytotoxic drugs and kill eukaryotic cells. The generically designed gate may be applied in biomedicine, biosensing or for building synthetic cells. [ABSTRACT FROM AUTHOR]

DNA mismatch repair (MMR) is a highly conserved genome stabilizing pathway that corrects DNA replication errors, limits chromosomal rearrangements, and mediates the cellular response to many types of DNA damage. Counterintuitively, MMR is also involved in the generation of mutations, as evidenced by its role in causing somatic triplet repeat expansion in Huntington's disease (HD) and other neurodegenerative disorders. In this review, we discuss the current state of mechanistic knowledge of MMR and review the roles of key enzymes in this pathway. We also present the evidence for mutagenic function of MMR in CAG repeat expansion and consider mechanistic hypotheses that have been proposed. Understanding the role of MMR in CAG expansion may shed light on potential avenues for therapeutic intervention in HD. [ABSTRACT FROM AUTHOR]

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem‐loop duplex at either its 5′‐ or 3′‐terminus to mimic a quadruplex–duplex (Q–D) junction as a potential genomic target. High‐resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q–D hybrids with a very high affinity in the order Ka≈107 m−1 irrespective of the duplex location at the quadruplex 3′‐ or 5′‐end. NMR chemical shift perturbations identified the tetrad face of the Q–D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3′‐ or 5′‐terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3′‐Q–D junction, whereas non‐hydrophobic entropic contributions favor binding with formation of a 2:1 ligand‐quadruplex complex in case of the 5′‐Q–D hybrid. [ABSTRACT FROM AUTHOR]

DNA origami enables the manipulation of objects at nanoscale, and demonstrates unprecedented versatility for fabricating both static and dynamic nanostructures. In this work, we introduce a new strategy for transferring modular reconfigurable DNA nanostructures from two‐dimensional to three‐dimensional. A 2D DNA sheet could be modularized into connected parts (e.g. two, three, and four parts in this work), which can be independently transformed between two conformations with a few DNA "trigger" strands. More interestingly, the transformation of the connected 2D modules can lead to the controlled, resettable structural conversion of a 2D sheet to a 3D architecture, due to the constraints induced by the connections between the 2D modules. This new approach can provide an efficient mean for constructing programmable, higher‐order, and complex DNA objects, as well as sophisticated dynamic substrates for various applications. [ABSTRACT FROM AUTHOR]

The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high‐speed atomic‐force microscopy (HS‐AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real‐time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure. [ABSTRACT FROM AUTHOR]

G‐Quadruplexes (G4s) assembled from tandem G‐rich repeat sequences exhibit significant biological functions and applications, which may well depend on their structural features, such as the planar arrangement of G‐tetrads and flexibility of loop regions. It has been found that cytosine‐intercalated G‐repeat sequences also assemble to be quadruplex structures, involving the formation of nonplanar GCGC‐tetrads. Herein, to investigate the effect of GCGC‐tetrads on structural properties of G4s, some previously studied quadruplexes with or without GCGC‐tetrads were selected, and were used to interact with various developed G4 ligands. Our data show that stacked G‐tetrads in quadruplexes are important for the π–π stacking interactions, thus promoting the combination with end‐stacking ligands, such as porphyrins or planar small molecules. This is confirmed by the observation that the quadruplex formed by d(GGGCT4GGGC) with two internal G‐tetrads and two external GCGC‐tetrads can bind to planar ligands in the presence of specific G4‐stabilizing cations, including K+ and Pb2+, and can realize the sensitive detection of Pb2+. However, the quadruplex composed of two external G‐tetrads and two internal GCGC‐tetrads formed by d(GCGGT3GCGG) facilitates the binding of nonplanar ligands, such as triphenylmethane (TPM) dyes, owing to the structural flexibility induced by internal GCGC‐tetrads. This work provides new insights into the interaction between DNA quadruplexes and specific ligands, which is beneficial to the development of quadruplex‐based biosensors and the design of anticancer drugs. [ABSTRACT FROM AUTHOR]

Heterochiral DNA with hydrogen‐bonded and silver‐mediated base pairs have been constructed using complementary strands with nucleosides with α‐d or β‐d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the Tm values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7‐deazapurines resulted in stable parallel duplexes, thereby confirming Watson–Crick‐type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver‐mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α‐d configuration display mirror‐like shapes to those with the β‐d configuration, the CD spectra of the hydrogen‐bonded duplexes and those with a limited number of silver pairs show a B‐type double helix almost indistinguishable from natural DNA. Nonmelting silver ion–DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs. [ABSTRACT FROM AUTHOR]

Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base‐excision strategy to engineer existing aptamers to bind guanosine. Both a Na+‐binding aptamer and the classical adenosine aptamer have been manipulated as base‐excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16‐deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non‐SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition. [ABSTRACT FROM AUTHOR]