Nucleic Acid Complexes Research Articles

Multifunctional DNA-Collagen Biomaterials: Developmental Advances and Biomedical Applications.

The complexation of nucleic acids and collagen forms a platform biomaterial greater than the sum of its parts. This union of biomacromolecules merges the extracellular matrix functionality of collagen with the designable bioactivity of nucleic acids, enabling advances in regenerative medicine, tissue engineering, gene delivery, and targeted therapy. This review traces the historical foundations and critical applications of DNA-collagen complexes and highlights their capabilities, demonstrating them as biocompatible, bioactive, and tunable platform materials. These complexes form structures across length scales, including nanoparticles, microfibers, and hydrogels, a process controlled by the relative amount of each component and the type of nucleic acid and collagen. The broad distribution of different types of collagen within the body contributes to the extensive biological relevance of DNA-collagen complexes. Functional nucleic acids can form these complexes, such as siRNA, antisense oligonucleotides, DNA origami nanostructures, and, in particular, single-stranded DNA aptamers, often distinguished by their rapid self-assembly at room temperature and formation without external stimuli and modifications. The simple and seamless integration of nucleic acids within collagenous matrices enhances biomimicry and targeted bioactivity, and provides stability against enzymatic degradation, positioning DNA-collagen complexes as an advanced biomaterial system for many applications including angiogenesis, bone tissue regeneration, wound healing, and more.

Abstract B022: Systematic analysis of tumor and immune EV subset changes with radiation therapy

Abstract Background: Although radiation is known to modulate immune responses, it remains challenging to identify effective combinations of radiation and immune-based therapies. Because tumor, immune, and other cells release extracellular vesicles (EVs) continuously and because those vesicles are composed of lipid membrane-bound complexes of proteins and nucleic acids, we have developed a suite of tools to enable systematic subset characterization of tumor and immune EV subsets. Broadly speaking, these tools provide a new, informative approach for interrogating tumor and immune biomarkers that may be used not only for predictive and prognostic purposes, but also for adaptive treatment strategies. In this study, we hypothesized that EV subsets could be used to monitor tumor and immune responses to radiation. The objective of this study was to evaluate radiation-induced changes in tumor-cell derived EVs from cell culture and from patient serum EV subsets. Methods: For these studies, we have developed and refined a set of rigorous tools and protocols for the enumeration, labeling, and sorting of EVs individually or as subsets. We applied these methods to EVs isolated at a series of timepoints from a panel of tumor cell lines irradiated at different doses. In a parallel fashion, we also applied these methods to clinical serum samples obtained from patients before, at the completion of, and one month following radiation therapy. For all samples, EV repertoires were evaluated by multiplex EV repertoire assays, and selected EV subsets were further enriched by immunoaffinity for cargo analysis. Results: EV surface marker repertoires demonstrated both donor-specific and treatment response-specific signatures, for both tumor-associated and immune-associated EVs. For patients with bladder and colon cancer, characteristic EV tumor and immune marker signatures were noted between patients, including CD326 and CD69, and various donor-specific changes in tetraspanins (CD63, -81, and -9), CD42a, and CD62P were observed at the completion of radiation treatment. Certain EV subsets could be consistently isolated with affinity chromatography from donor serum samples but were not strongly represented in multiplex assay based on co-expression of tetraspanins. Conclusions: Our results establish feasibility for future EV subset studies, particularly in clinical trials investigating tumor and immune biomarkers for patients receiving combined radiation and immunotherapy treatments. Specifically, we demonstrate a robust method for evaluation of individual donor responses, including kinetic changes in tumor-associated markers (CD326) and immune-associated markers (CD69). Furthermore, each patient’s serum EVs demonstrated distinctive treatment-response patterns, with inter-donor differences appearing to relate to tumor-specific attributes and/or radiation parameters, such as marrow volume irradiated. Ongoing studies are further exploring EV-borne RNA signatures using a total RNAseq pipeline that is customized for EV RNA. Citation Format: Jubin George, Stephanie Chidester, Michelle L. Pleet, Kevin Camphausen, Freddy Escorcia, Jennifer C. Jones. Systematic analysis of tumor and immune EV subset changes with radiation therapy. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr B022.

AlphaFold 3 sheds insights into chemical enhancer-induced structural changes in Cas12a RNPs

BackgroundThe CRISPR/Cas12a system has revolutionized nucleic acid detection through trigger-activated nonspecific trans-cleavage activity. Enhancing this activity is vital for improving the sensitivity of CRISPR/Cas biosensing systems. Although various chemical enhancers have been shown to affect Cas12a ribonucleoprotein (RNP), the underlying mechanisms remain poorly understood. Investigating how these enhancers alter the structure of Cas12a RNPs is essential for elucidating the enhancement mechanisms involved.ResultsThis study focuses on elucidating the structural changes in Cas12a RNPs induced by various chemical enhancers via AlphaFold 3, an emerging and powerful tool for analyzing structural changes in protein‒nucleic acid complexes. We validated the ability of AlphaFold 3 to simulate structural changes in Cas12a RNPs activated by triggers and subsequently analyzed the effects of specific enhancers, such as reducing agents (e.g., Dithiothreitol, namely DTT), divalent cations (e.g., Mg2+, Mn2+), and bovine serum albumin (BSA). Our findings revealed that DTT, simulated with a cysteine-to-serine Cas12a mutant, caused significant structural changes in Cas12a RNP, as evidenced by notable shifts in the distance between key residues (Val377 to Gln1136) and a high root mean square deviation (RMSD)(RMSD > 2). Conversely, divalent cations and BSA did not cause substantial structural changes, resulting in only minor shifts in residue distance and a low RMSD (RMSD < 2).ConclusionsThese results demonstrate that DTT enhances Cas12a activity by inducing significant structural rearrangements, whereas divalent cations and BSA-induced enhancements do not involve substantial structural modifications.Graphical Summary of structural changes from inactivated Cas12a RNP to activated Cas12a RNP and from activated Cas12a RNP to activated Cas12a RNP with an enhancer. The units of both the RMSD and distance are Å.

Applications of Surface Plasmon Resonance for Advanced Studies Involving Nucleic Acids

Surface plasmon resonance (SPR) is increasingly recognized as one of the most widely used techniques for studying nucleic acid interactions. The main advantage of SPR is its ability to measure the binding affinities and association/dissociation kinetics of complexes in real-time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. In the field of Nucleic Acid, SPR has been intensively used in the study of various artificial and naturally occurring RNA/DNA molecules interaction with large molecular weight mass proteins and small organic molecules because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This mini review aims to provide a short guideline for setting up SPR experiments to identify nucleic acid complexes and assess their binding affinity or kinetics. It covers protocols for (i) nucleic acid immobilization methods, including biotin-streptavidin, metal ion-based affinity, and amine coupling, (ii) analyte-binding analysis, (iii) affinity and kinetic measurements, and (iv) data interpretation. Determining the affinity and kinetics of nucleic acid interactions through SPR is essential for gaining insights into molecular-level binding mechanisms, thus supporting advancements in nucleic acid nanotechnology. The review also highlights the various sections of SPR applications in nucleic acid research, including nucleic acid-probe immobilization, interactions with biomolecules, aptamer studies, and small molecule binding, concluding with perspectives on future developments in the field.

Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications.

The development of new convenient tools for the design of multicomponent nucleic acid (NA) complexes is one of the challenges in biomedicine and NA nanotechnology. In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limited complexes by a pair of oligonucleotides using UV melting, circular dichroism spectroscopy, and a gel shift assay. Effects of the size of the linker between duplex-forming segments of the oligonucleotides on complexes' shape and number of subunits were compared and systematized for RNA/DNA, DNA/DNA, and RNA/RNA assemblies. The data on complex types summarized here as heat maps offer a convenient tool for the design of NA constructs. General rules found for RNA/DNA, DNA/DNA, and RNA/RNA complexes allow not only designing complexes with desired structures but also purposefully transforming their geometry. The A-form of the double helix of the studied RNA/DNA complexes was confirmed by circular dichroism analysis. Moreover, we show for the first time efficient degradation of RNA in hybrid self-limited complexes by RNase H and imidazole. The results open up new prospects for the design of supramolecular complexes as tools for nanotechnology, nanomachinery, and biomedical applications.

Introducing Degradable Cationic Nanogels Carrying TLR9 Stimulating Oligonucleotides.

Cationic, core-crosslinked nanogel particles are prepared from synthetic biodegradable materials. These fully hydrophilic nanogels offer superior customizability compared to common lipid nanoparticles, thereby circumventing intrinsic immune stimulatory properties. Electrostatic loading allows for complexation of nucleic acids including the immune stimulatory Toll-like receptor 9 (TLR9) agonistCpG-ODN (cytidine-phosphate-guanosine oligodeoxynucleotide). Only when complexed inside nanogels, one can control CpG-ODN's biodistribution, prevent systemic toxicity, and increase bioavailability at target locations. Nanogels are prepared from cyclic aliphatic carbonate monomers with reactive pentafluorophenyl (PFP) esters. First, block copolymers are acquired via cationic ring opening polymerization (CROP) onto polyethylene glycol (PEG). Upon self-assembly in ethanol, the micelles' core is cationically core-crosslinked, and the resulting fully hydrophilic particles exhibit sizes of ≈20nm, also upon loading with CpG-ODN. In vitro, they promote intracellular delivery devoid of carrier-related toxicities, while retaining the immune stimulatory properties of the TLR agonist cargo. In vivo, the nanogels reduce systemic liver immune responses and remain near the injection site. Additionally, delivery into cDC1 (conventional dentritic cells type 1) antigen-presenting cells, which are highly relevant for antitumoral T-cell immune responses, is confirmed. Altogether, cationic, core-crosslinked polycarbonate nanogels show promise for nucleic acid delivery, showcasing controlled immunostimulatory cargo delivery and an enhanced hydrolytic biodegradability profile, highly valuable for cancer immunotherapy.

Hydrogel loop-mediated isothermal amplification for ultra-fast diagnosis of Helicobacter pylori in stool samples without nucleic acid extraction

BackgroundThe gastrointestinal diseases caused by Helicobacter pylori (H. pylori) infection made the accurate detection of H. pylori infection more important. Non-invasive methods, such as molecular diagnostic methods, had become a promising method for detection of H. pylori. Stool samples combined with loop-mediated isothermal amplification (LAMP), showed potential practicability for real-time detection. However, complex nucleic acid extraction steps were required to remove the large numbers of amplification inhibitors in stool samples before LAMP reaction. And the limited number of H. pylori made the detection with long reaction time and low sensitivity. The problems mentioned above were urgently to be solved. ResultsIn this study, we proposed a strategy for ultra-rapid sensitive detection of H. pylori in stool samples by hydrogel LAMP (hLAMP) without extraction. The hydrogel was combined with stool samples after simple thermal cracking, and amplification spaces were formed in its nanopore structures by nano-localization. The LAMP reaction was accelerated by nano space-localization. Besides, this method based on hLAMP could specifically and sensitively detect as low as 100 CFU/mL H. pylori within 40 min from sampling to result due to good anti-inhibition effect on complex samples of hydrogel. The whole process involved sample simple disposal for 10 min and LAMP reaction for 30 min. Furthermore, the excellent anti-inhibition mechanism of hydrogel was discussed, and the mechanism of hydrogel accelerating LAMP was explored. SignificanceThis is the first application of that hydrogel and LAMP systematically combined to detect H. pylori in stool samples. The developed method had been verified in actual clinical applications that the accuracy rate reached 88.9 % compared with routine histopathology. And it also provided a potential idea for the diagnosis and prevention of H. pylori.

Allosteric stem-loop multicomponent DNAzyme: A versatile stimuli-responsive switch for nanotweezer operations and multifunctional biosensing

DNAzyme, possessing the capabilities of both encoding information and catalyzing chemical reactions, holds significant value in advancing the widespread application of dynamic nanotechnology. Particularly, multicomponent DNAzyme (MNAzyme) has attracted considerable attention due to its remarkable versatility and practicality. However, the inevitable signal leakage of MNAzyme constrains the applications in complex nucleic acid reaction networks. Herein, we present an allosteric stem-loop multicomponent DNAzyme (ASLM) that incorporates a blocking domain to mitigate leakage resulting from secondary structures of MNAzyme while simultaneously stabilizing binding affinity during complex formation. As the sequence of blocking domain serves as an extension independent of the functional region in MNAzyme, this modulation structure can be flexibly assembled with conformation-switchable nanotweezer to form a time-responsive molecular device, enabling dynamic and dissipative operations through nucleic acid and RNase H. More importantly, the ASLM structure can be directly incorporated into DNA catalytic circuits for detecting multiple biomolecules (nucleic acid, protease, and small molecule). With its scalability and versatility, this effector-activated allosteric regulator will serve as a universal stimuli-responsive switch in complex and hierarchical DNA networks, expanding the scope of DNA nanotechnology in molecular device construction and diagnostic biosensing.

Miktoarm Star-polypept(o)ide-Based Polyion Complex Micelles for the Delivery of Large Nucleic Acids.

Miktoarm star polymers exhibit a captivating range of physicochemical properties, setting them apart from their linear counterparts. This study devised a synthetic pathway to synthesize cationic miktoarm stars utilizing polypept(o)ides (PeptoMiktoStars), comprising 3 or 6 polysarcosine (pSar) arms (AB3×100, AB6×50, overall 300) for shielding and a cross-linkable poly(S-ethylsulfonyl-l-homocysteine) (pHcy(SO2Et)20) block and a poly(l-lysine) ((pLys)20) block for nucleic acid complexation. Precise control over the DPn and narrow molecular weight distributions (D̵ ≈ 1.2) were achieved for both structures. Both PeptoMiktoStars efficiently complexed mRNA and pDNA into polyion complex micelles (PICMs). AB6-PICMs provided modest (mRNA) to high (pDNA) stability against glutathione and heparin sulfate (HS), while even cross-linked AB3-PICMs were susceptible to HS. All PICMs delivered pDNA and mRNA into D1 cells (over 80%) and Jurkat T cells (over 50%) in vitro. Despite payload- and cell-dependency, AB3 showed overall higher transfection efficiency, while AB6 demonstrated better shielding and enhanced stability.

The stage- and kinetics-dependent regulation of highly ordered sequential reactions by liquid–liquid phase separation

Understanding the reaction kinetics, thermodynamics, and molecular mechanisms of liquid–liquid phase separation (LLPS) holds immense significance in unraveling the cell’s spatiotemporal coordination of metabolic pathways and has the potential to revolutionize diverse fields, including diagnostics and catalysis. However, the current scope of LLPS-based investigations is primarily limited to simplistic models with one or two-step reactions, failing to capture the complexity necessary for comprehending LLPS’s impact on intricate reactions and hindering its widespread practical applications. In this study, we address this limitation by constructing and screening a tailored LLPS system and utilizing complex nucleic acid amplification as a representative example. Our findings reveal a significant departure from the continuous acceleration observed in simple reactions, as the acceleration of complex reactions is highly dependent on the kinetics and reactant concentration of each specific reaction stage. Furthermore, by incorporating LLPS and its stage-specific factors, we demonstrate the development of an LLPS-based molecular diagnostic tool with a shortened detection time, higher efficiency and sensitivity compared to traditional methods. Therefore, this newfound understanding sheds light on the intricate characteristics of LLPS-mediated complex reactions and offers a breakthrough in diagnostic advancements by enabling faster and more accurate detection of target molecules, leveraging LLPS in diagnostic advancements, and driving the unlocking of further potential for LLPS utilization in various fields.

A second life for the crystallographic structure of Berenil-dodecanucleotide complex: a computational revisitation thirty years after its publication

This study revisits the pioneering work of Professor Neidle, and co-workers, on the crystal structure of complexes formed between groove binders and DNA sequences. The original research revealed a DNA-ligand complex consisting of a dodecanucleotide bound with Berenil [1,3-bis(4′-amidinophenyl)-triazene] an anti-trypanocidal drug. This article aims to delve deeper into the structural dynamics of this system, showcasing the role played by water molecules in stabilizing the interaction between the ligand and the DNA. With this work, we reevaluate the findings from the original crystallographic study by employing modern molecular dynamics techniques, including Supervised Molecular Dynamics (SuMD) for generating binding trajectories, Thermal Titration Molecular Dynamics for assessing unbinding events, and AquaMMapS to identify regions occupied by stationary water molecules. The study addresses a minor and a major groove binding mode and assesses their strength and specificity using TTMD simulations, generating unbinding trajectories. This comprehensive approach integrates the understanding of the interaction of this DNA-ligand complex, which originated with the valuable work of Professor Neidle, resulting in an in-depth insight into the pivotal role of water molecules with this DNA, a behavior detected and extendable even to other nucleic acid complexes.

Therapeutic framework nucleic acid complexes targeting oxidative stress and pyroptosis for the treatment of osteoarthritis

Osteoarthritis (OA) is one of the most prevalent joint diseases and severely affects the quality of life in the elderly population. However, there are currently no effective prevention or treatment options for OA. Oxidative stress and pyroptosis play significant roles in the development and progression of OA. To address this issue, we have developed a novel therapeutic approach for OA that targets oxidative stress and pyroptosis. We synthesized tetrahedral framework nucleic acid (tFNAs) to form framework nucleic acid complexes (TNCs), which facilitate the delivery of the naturally occurring polymethoxyflavonoid nobiletin (Nob) to chondrocytes. TNC has demonstrated favorable bioavailability, stability, and biosafety for delivering Nob. Both in vitro and in vivo experiments have shown that TNC can alleviate OA and protect articular cartilage from damage by eliminating oxidative stress, inhibiting pyroptosis, and restoring the extracellular matrix anabolic metabolism of chondrocytes. These findings suggest that TNC has significant potential in the treatment of OA and cartilage injury.

Synthetic polypeptides inhibit nucleic acid-induced inflammation in autoimmune diseases by disrupting multivalent TLR9 binding to LL37-DNA bundles.

Complexes of extracellular nucleic acids (NAs) with endogenous proteins or peptides, such as LL37, break immune balance and cause autoimmune diseases, whereas NAs with arginine-enriched peptides do not. Inspired by this, we synthesize a polyarginine nanoparticle PEG-TK-NPArg, which effectively inhibits Toll-like receptor-9 (TLR9) activation, in contrast to LL37. To explore the discrepancy effect of PEG-TK-NPArg and LL37, we evaluate the periodic structure of PEG-TK-NPArg-NA and LL37-NA complexes using small-angle X-ray scattering. LL37-NA complexes have a larger inter-NA spacing that accommodates TLR9, while the inter-NA spacing in PEG-TK-NPArg-NA complexes mismatches with the cavity of TLR9, thus inhibiting an interaction with multiple TLR9s, limiting their clustering and damping immune induction. Subsequently, the inhibitory inflammation effect of PEG-TK-NPArg is proved in an animal model of rheumatoid arthritis. This work on how the scavenger-NA complexes inhibit the immune response may facilitate proof-of-concept research translating to clinical application.

Mix-and-Read Digital MicroRNA Analysis Based on Flow Cytometric Counting of Target-Clicked Nanobead Dimer.

A one-step, enzyme-free, and highly sensitive digital microRNA (miRNA) assay is rationally devised based on flow cytometric counting of target miRNA-clicked nanobead dimers via a facile mix-and-read manner. In this strategy, highly efficient miRNA-sandwiched click chemical ligation of two DNA probes may remarkably stabilize and boost the dimer formation between two kinds of fluorescence-coded nanobeads, and the number of as-produced bead dimers will be target dose-responsive, particularly when the trace number of miRNA is much less than that of employed nanobeads. Finally, each fluorescence-coded bead dimer can be easily identified and digitally counted by a powerful flow cytometer (FCM) and accordingly, the amount of target miRNA can be accurately quantified in a digital way. This new digital miRNA assay can be accomplished with a facile mix-and-read operation just by simply mixing the target miRNA with two kinds of preprepared DNA probe-functionalized nanobeads, which do not require any nucleic acid amplification, purification, and complex operation procedures. In spite of the extremely simple one-step operation, benefiting from the low-background but high target-mediated click ligation efficiency, and the powerfully digital statistical capability of FCM, this strategy achieves high sensitivity with a quite low detection limit of 5.2 fM target miRNA as well as high specificity and good generality for miRNA analysis, pioneering a new direction for fabricating digital bioassays.

Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.

Bioinformatics is a scientific field that uses computer technology to gather, store, analyze, and share biological data and information. DNA sequences of genes or entire genomes, protein amino acid sequences, nucleic acid, and protein-nucleic acid complex structures are examples of traditional bioinformatics data. Moreover, proteomics, the distribution of proteins in cells, interactomics, the patterns of interactions between proteins and nucleic acids, and metabolomics, the types and patterns of small-molecule transformations by the biochemical pathways in cells, are further data streams. Currently, the objectives of bioinformatics are integrative, focusing on how various data combinations might be utilized to comprehend organisms and diseases. Bioinformatic techniques have become popular as novel instruments for examining the fundamental mechanisms behind neonatal diseases. In the first few weeks of newborn life, these methods can be utilized in conjunction with clinical data to identify the most vulnerable neonates and to gain a better understanding of certain mortalities, including respiratory distress, bronchopulmonary dysplasia, sepsis, or inborn errors of metabolism. In the current study, we performed a literature review to summarize the current application of bioinformatics in neonatal medicine. Our aim was to provide evidence that could supply novel insights into the underlying mechanism of neonatal pathophysiology and could be used as an early diagnostic tool in neonatal care.

Dynamic Covalent Boronate Chemistry Accelerates the Screening of Polymeric Gene Delivery Vectors via In Situ Complexation of Nucleic Acids.

Gene therapy provides exciting new therapeutic opportunities beyond the reach of traditional treatments. Despite the tremendous progress of viral vectors, their high cost, complex manufacturing, and side effects have encouraged the development of nonviral alternatives, including cationic polymers. However, these are less efficient in overcoming cellular barriers, resulting in lower transfection efficiencies. Although the exquisite structural tunability of polymers might be envisaged as a versatile tool for improving transfection, the need to fine-tune several structural parameters represents a bottleneck in current screening technologies. By taking advantage of the fast-forming and strong boronate ester bond, an archetypal example of dynamic covalent chemistry, a highly adaptable gene delivery platform is presented, in which the polycation synthesis and pDNA complexation occur in situ. The robustness of the strategy entitles the simultaneous evaluation of several structural parameters at will, enabling the accelerated screening and adaptive optimization of lead polymeric vectors using dynamic covalent libraries.

Data-driven regularization lowers the size barrier of cryo-EM structure determination

Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is improved by the application of deep learning to exploit prior knowledge about biological macromolecular structures that would otherwise be difficult to express mathematically. We train a denoising convolutional neural network on pairs of half-set reconstructions from the electron microscopy data bank (EMDB) and use this denoiser as an alternative to a commonly used smoothness prior. We demonstrate that this approach, which we call Blush regularization, yields better reconstructions than do existing algorithms, in particular for data with low signal-to-noise ratios. The reconstruction of a protein–nucleic acid complex with a molecular weight of 40 kDa, which was previously intractable, illustrates that denoising neural networks will expand the applicability of cryo-EM structure determination for a wide range of biological macromolecules.

Toward Bioactive Hydrogels: A Tunable Approach via Nucleic Acid-Collagen Complexation

PurposeNucleic acid-collagen complexes (NACCs) are unique biomaterials formed by binding short, monodisperse single-stranded DNA (ssDNA) with type I collagen. These complexes spontaneously generate microfibers and nanoparticles of varying sizes, offering a versatile platform with potential applications in tissue engineering and regenerative medicine. However, the detailed mechanisms behind the nucleic acid-driven assembly of collagen fibers still need to be established. We aim to understand the relationship between microscopic structure and bulk material properties and demonstrate that NACCs can be engineered as mechanically tunable systems.MethodsWe present a study to test NACCs with varying molar ratios of collagen to random ssDNA oligonucleotides. Our methods encompass the assessment of molecular interactions through infrared spectroscopy and the characterization of gelation and rheological behavior. We also include phase contrast, confocal reflectance, and transmission electron microscopy to provide complementary information on the 3D structural organization of the hydrogels.ResultsWe report that adding DNA oligonucleotides within collagen robustly reinforces and rearranges the hydrogel network and accelerates gelation by triggering rapid fiber formation and spontaneous self-assembly. The elasticity of NACC hydrogels can be tailored according to the collagen-to-DNA molar ratio, ssDNA length, and collagen species.ConclusionOur findings hold significant implications for the design of mechanically tunable DNA-based hydrogel systems. The ability to manipulate hydrogel stiffness by tailoring DNA content and collagen concentration offers new avenues for fine tuning material properties, enhancing the versatility of bioactive hydrogels in diverse biomedical applications.Lay SummaryThis work is an example of forming fibers and gels with tunable elasticity that stems from the complexation of short-length nucleic acids (on the order of size of aptamers) and collagen, which can be potentially extended to a variety of functionalized hydrogel designs and tailored biomedical applications. Incorporating DNA induces mechanical changes in NACCs.Graphical

Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms.

Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here, we use biophysical assays to interrogate the k on, k off, and K d for DNA and RNA binding of two model human TFs, ERα and Sox2. Unexpectedly, we found that both proteins exhibit multiphasic nucleic acid-binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics can be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, in which two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid-binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.

Abstract NG04: Targeting DHX9 to trigger viral mimicry and immunotherapy responsiveness in small cell lung cancer

Abstract NG04: Targeting DHX9 to trigger viral mimicry and immunotherapy responsiveness in small cell lung cancer