Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment

Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility

A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness. A comprehensive computer simulation study employing dendritic models with different levels of coarse-graining, and two theoretical approaches based on effective, pair-potential interactions, remarkably confirmed the origin of this unusual liquid-like behavior. The results demonstrate that the precise control of the internal structure of the dendritic scaffold conferred by the DNA can be potentially used to engineer a rich palette of novel ultrasoft interaction potentials that could offer a route for directed self-assembly of intriguing soft matter phases and experimental realizations of a host of unusual phenomena theoretically predicted for ultrasoft interacting systems.

Ultrasoft Classical Systems at Zero Temperature

At low temperatures, classical ultrasoft particle systems develop interesting phases via the self-assembly of particle clusters. In this study, we reach analytical expressions for the energy and the density interval of the coexistence regions for general ultrasoft pairwise potentials at zero temperatures. We use an expansion in the inverse of the number of particles per cluster for an accurate determination of the different quantities of interest. Differently from previous works, we study the ground state of such models, in two and three dimensions, considering an integer cluster occupancy number. The resulting expressions were successfully tested in the small and large density regimes for the Generalized Exponential Model α, varying the value of the exponent.

Steric Hindrance On-Off Mass-Tagged Probe Set Enables Detection of Protein Homodimer in Living Cells

The major challenge in the detection of protein homodimers is that the identical monomers in a homodimer are indistinguishable using most conventional methods and cannot be sequentially recognized. In this study, a steric hindrance on-off mass-tagged probe set strategy was developed for the quantification of HER2 homodimer in living cells. The probe set contained a hindrance probe and a detection probe. The hindrance probe had a DNA dendrimer as a hindrance group to achieve the steric hindrance on-off function and thus the assignment of monomer identity. The detection probe contained a mass tag released for mass spectrometric quantification. Using the steric hindrance on-off mass-tagged probe set, the level of HER2 homodimer in various breast cancer cell lines was quantified. This is the first report to determine the quantity of protein homodimers, and the steric hindrance on-off probe set developed herein can facilitate the illustration of protein function in cancer.

Self assembling cluster crystals from DNA based dendritic nanostructures

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals. We fabricate dendritic-linear-dendritic triblock composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons of the first and second generation. Conclusive small-angle X-ray scattering (SAXS) evidence reveals that solutions of these triblock at sufficiently high concentrations undergo a reversible phase transition from a cluster fluid to a body-centered cubic (BCC) cluster crystal with density-independent lattice spacing, through alteration of temperature. Moreover, a rich concentration-temperature phase diagram demonstrates the emergence of various ordered nanostructures, including BCC cluster crystals, birefringent cluster crystals, as well as hexagonal phases and cluster glass-like kinetically arrested states at high densities.

Experimental realization of cluster crystals- periodic structures with lattice sites occupied by several, overlapping building blocks, has been elusive. Here, the authors show the existence of well-controlled soft matter cluster crystals composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons.

Multifunctional DNA dendrimer nanostructures for biomedical applications

DNA nanomaterials have attracted ever-increasing attention over the past decades due to their incomparable programmability and multifunctionality. In particular, DNA dendrimer nanostructures, as a major research focus, have been applied in the fields of biosensing, therapeutics, and protein engineering, benefiting from their highly branched configuration. With the aid of specific recognition probes and inherent signal amplification, DNA dendrimers can achieve ultrasensitive detection of nucleic acids, proteins, cells, and other substances, such as lipopolysaccharides (LPS), adenosine triphosphate (ATP), and exosomes. By virtue of their void-containing structures and biocompatibility, DNA dendrimers can deliver drugs or functional nucleic acids into target cells in chemotherapy, immunotherapy, and gene therapy. Furthermore, DNA dendrimers are being applied in protein engineering for efficient directed evolution of proteins. This review summarizes the main research progress of DNA dendrimers, concerning their assembly methods and biomedical applications as well as the emerging challenges and perspectives for future research.

Hyperbranched DNA clusters

Taking advantage of the base-pairing specificity and tunability of DNA interactions, we investigate the spontaneous formation of hyperbranched clusters starting from purposely designed DNA tetravalent nanostar monomers, encoding in their four sticky ends the desired binding rules. Specifically, we combine molecular dynamics simulations and Dynamic Light Scattering experiments to follow the aggregation process of DNA nanostars at different concentrations and temperatures. At odds with the Flory-Stockmayer predictions, we find that, even when all possible bonds are formed, the system does not reach percolation due to the presence of intracluster bonds. We present an extension of the Flory-Stockmayer theory that properly describes the numerical and experimental results.

Ingenious Electrochemiluminescence Bioaptasensor Based on Synergistic Effects and Enzyme-Driven Programmable 3D DNA Nanoflowers for Ultrasensitive Detection of Aflatoxin B1

Aflatoxin B1 (AFB1), one of the most toxic mycotoxins, has undergone a wide range of studies over the years. The development of rapid, simple, and sensitive analytical methods remains a major challenge for the accurate detection of AFB1 in foodstuffs. In this study, we designed an enhanced and stable ingenious electrochemiluminescence bioaptasensor (IEC-BA) for ultrasensitive detection of AFB1 based on the synergistic effects and enzyme-driven programmable assembled 3D DNA nanoflowers (EPDNs). This synergistic effect was comprised by the competitive impact on auxiliary probes (AP) and the cutting effect of the Hae III. Compared to the traditional aptamer direct-competition method, the synergistic effects ensured that the aptamer was more efficiently and adequately competed away by the target. Also, the redundant double-stranded probes were removed, which greatly facilitates simple, quick, and sensitive detection of AFB1. Besides, a large chunk of positively charged Ru(II) complexes (Ru(bpy)₃²⁺) was accumulated by the utilization of EPDNs, which resulted in tremendous improvement of the sensitivity of the designed method. Thus, even in the presence of trace amounts of AFB1, a sharply visual electrochemiluminescent signal was generated. The proposed method can realize the quantification of AFB1 with a good linear range from 1 ppt (pg mL^-1) to 5 ppb (ng mL^-1) with a detection limit of 0.27 ppt. In addition, it can also be successfully applied for the analysis of AFB1 in a peanut and wheat, with total recoveries ranging from 93.7 to 106.6%. Furthermore, the IEC-BA also exhibited good selectivity, reproducibility, and stability, revealing prospective applications of food safety monitoring and environmental analysis.

Encoding quantized fluorescence states with fractal DNA frameworks

Signal amplification in biological systems is achieved by cooperatively recruiting multiple copies of regulatory biomolecules. Nevertheless, the multiplexing capability of artificial fluorescent amplifiers is limited due to the size limit and lack of modularity. Here, we develop Cayley tree-like fractal DNA frameworks to topologically encode the fluorescence states for multiplexed detection of low-abundance targets. Taking advantage of the self-similar topology of Cayley tree, we use only 16 DNA strands to construct n-node (n = 53) structures of up to 5 megadalton. The high level of degeneracy allows encoding 36 colours with 7 nodes by site-specifically anchoring of distinct fluorophores onto a structure. The fractal topology minimises fluorescence crosstalk and allows quantitative decoding of quantized fluorescence states. We demonstrate a spectrum of rigid-yet-flexible super-multiplex structures for encoded fluorescence detection of single-molecule recognition events and multiplexed discrimination of living cells. Thus, the topological engineering approach enriches the toolbox for high-throughput cell imaging.

Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.

Cold-swappable DNA gels

We report an experimental investigation of an all-DNA gel composed by tetra-functional DNA nanoparticles acting as network nodes and bi-functional ones acting as links. The DNA binding sequence is designed to generate at room and lower temperatures a persistent long-lived network. Exploiting ideas from DNA-nanotechnology, we implement in the binding base sequences an appropriate exchange reaction which allows links to swap, constantly retaining the total number of network links. The DNA gel is thus able to rearrange its topology at low temperature while preserving its fully-bonded configuration.

All-DNA System Close to the Percolation Threshold

We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.