Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.     

Topological Links between Duplex DNA and a Circular DNA Single Strand

DNA nanostructures of building blocks topologically linked at a precise position can be assembled from DNA duplexes and circularized oligonucleotides with the aid of peptide nucleic acids (PNAs). Shown schematically is a linked catenane yielding an earring topological DNA label.     

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.     

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.     

Molecular-glue-triggered DNA assembly to form a robust and photoresponsive nano-network

A robust and photoresponsive DNA network has been designed and constructed from branched DNA and molecular glue. The molecular glue is photoswitchable and can specifically bind to G-G mismatched double-stranded DNA. The assembly process can be reversibly controlled by manipulating the wavelength of light. The approach is flexible, allowing tuning of the size, morphology as well as the cavity of the network by variation of the molar ratio and the isotropic/anisotropic character of the branched building blocks. The assembled architectures are versatile and heat tolerant. These properties should allow the use of the network in further applications.     

Electrochemical Study of the Interaction of the Alkylating Agent Busulfan with Double Strand DNA

Damage of salmon sperm double strand ss dsDNA in solution or immobilized on screen‐printed carbon electrode (SPCE) induced by incubation of DNA with the antineoplastic alkylating agent busulfan (BUS) at various conditions was detected for the first time by simple electrochemical methods. Chemical changes in DNA bases can be detected through the altered electroactivity of the DNA. Electrochemical voltammetric sensing of damage caused by BUS to dsDNA in solution was monitored by the appearance of peaks diagnostic of the oxidation of guanine and adenine. Moreover, crystal violet, which interacts with the DNA immobilized on SPCEs, was used as an effective electroactive indicator, in combination with cyclic voltammetry and differential pulse voltammetry techniques to monitor the cross‐links or damage to DNA. The interaction between BUS and DNA were determined by the changes in the voltammetric peak of crystal violet. The effects of various conditions upon the crystal violet signal were investigated.     

Rapid Photoactuation of a DNA Nanostructure using an Internal Photocaged Trigger Strand

A reconfigurable DNA nano‐tweezer is reported that can be switched between a closed and open state with a brief pulse of UV light. In its initial state, the tweezer is held shut using a hairpin with a single‐stranded poly‐A loop. Also incorporated in the structure is a poly‐T trigger strand bearing seven photocaged residues. Upon illumination with 365 nm light, the cages are removed and the trigger strand hybridizes to the loop, opening the tweezer and increasing the distance between its arms from 4 to 18 nm. This intramolecular process is roughly 60 times faster than adding an external trigger strand, and provides a mechanism for the rapid interconversion of DNA nanostructures with light.     

A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay

Protein in, DNA out: A "binding-induced molecular translator" is able to convert an input target protein into an output DNA that can be readily detected and potentially be used to assemble DNA nanodevices. Successful molecular translation is mediated by binding-induced DNA assembly on a gold nanoparticle (AuNP) scaffold, thereby achieving efficient target-dependent strand displacement.     

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single‐molecule imaging of triple helix formation in DNA nanostructures. The binding of the single‐molecule third strand to double‐stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson–Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high‐speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.     

Triple Helices of Optimally Capped Duplex DNA (σ-DNA) with Homopyrimidine DNA and RNA at Neutral pH

An optimally capped duplex DNA (σ-DNA) was synthesized in which the cytosines in the homopyrimidine strand of σ-DNA 1 were replaced by 5-methylcytosine leading to σ-DNA 2 . Although only involving 13 base pairs, this modification resulted in very high melting temperatures above 90°. In addition, σ-DNA 2 was able to form triple helices with the corresponding homopyrimidine DNA or RNA even at neutral pH. This opens up the possibility to use σ-DNA in a triple-helix approach to modulate gene expressions on the level of the translation process.     

单根DNA短链构筑pH响应超分子水凝胶

设计合成了一条包含两段自互补序列和一段富含胞嘧啶(C)序列的DNA单链.在碱性条件下,两段自互补序列可通过分子间自组装形成一维DNA纳米线,调节p H至酸性条件后,胞嘧啶序列通过形成双分子i-motif结构将纳米线交联,从而形成DNA水凝胶.当加入酸或碱调节体系的p H时,水凝胶的力学强度会发生变化.在p H为5.3时,水凝胶力学强度达到最大,增大或减小p H都会使水凝胶强度降低.同时,改变DNA单链浓度也能够调节水凝胶的力学强度.此凝胶制备过程原料合成简便,无需涉及不同DNA链定量配比的问题,大大简化了实验操作;另外i-motif结构在形成与解离两态之间的转换非常迅速,在几秒钟之内便可完成,也赋予该凝胶快速p H响应的特性.     

Investigation of Metal Ion Effect on Specific DNA Sequences and DNA Hybridization

In this article, we investigated the sequence specific interaction of single (ssDNA) and double stranded (dsDNA) with silver ions (Ag⁺) with electrochemical methods. We, for the first time, examined the effect of base sequences, base content and physiochemical properties of different DNA sequences on interaction with Ag⁺ in detail. We used different base contents to show how the composition of nucleic acid influences the electrochemical signals. We first immobilized ssDNA probes on bare graphite electrodes. Then, we showed the sequence effect on oxidation signals of AgDNA complex by sensing Ag⁺ to the probe coated surfaces to interact with different ssDNA sequences. Furthermore, we investigated the effect of Ag⁺ on dsDNA. We measured the oxidation signals obtained from Ag⁺‐ssDNA and Ag⁺‐dsDNA complex at approximately 0.2 V and 1.0 V (vs Ag/AgCl), respectively with Differential Pulse Voltammetry (DPV). We showed that the oxidation signals of the AgDNA complex obtained from dsDNA‐modified electrodes is higher than the electrodes modified with ssDNA. More importantly, we showed that Ag⁺‐ssDNA and Ag⁺ ion‐dsDNA exhibit different electrochemical behaviors.     

“Printing” DNA Strand Patterns on Small Molecules with Control of Valency,Directionality, and Sequence

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule‐DNA hybrids with controllable valency, different sequences, and directionalities (5′–3′) using a “printing” process from a simple 3‐way junction structure. We also show that the DNA‐imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double Strand

Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.     

Interaction of Antitumor Drug Aclacinomycin‐A with DNA and Its Specific Sequence Site

Through UV and fluorescence spectrophotometries, the interaction of aclacinomycin‐A (ACM‐A) with DNA and its specific sequence have been investigated with the aid of circular dichroism spectrophotometry and differential pulse voltammetry method. The results demonstrated that ACM‐A was capable of intercalating DNA double helix, the π‐π electronic overlapping between π‐electrons of ACM‐A and base pair of DNA stabilized the ACM‐A‐DNA adduct, and through electrostatic interaction, the trisaccharide interacted with the minor groove of DNA owing to an amino group at C(3′). Electrochemical and spectroelectrochemical studies revealed that the original form of ACM‐A had higher affinity for DNA than the reduction form in which the trisaccharide group at C(7) was lost. According to the results obtained in this paper, ACM‐A showed preference for AT base pairs of the deoxyribonucleic acid duplex, and it was apt to interact with cytosine and thymine rather than the adenine of oligonucleotide.     

Electrochemically Modified Carbon and Chromium Surfaces for AFM Imaging of Double‐Strand DNA Interaction with Transposase Protein

Carbon and chromium surfaces were modified by electrochemical reduction of a diazonium salt formed in situ from the sulfanilic acid. The organic layer formed was activated by phosphorus pentachloride (PCl₅) to form a benzene sulfonil chloride (Ar? SO₂Cl). An electrochemical study of the blocking effect and the activity of this surface was carried out on a carbon electrode. The chromium surface study was completed by X‐ray photoelectron spectroscopy and atomic force microscopy to characterize the formation of a compact monolayer (0.8 nm height and roughness 0.2–0.3 nm). The compactness and the activity of this organic monolayer allowed us to affix a length dsDNA with the aim of analyzing the formation of a complex between dsDNA and a protein. The interaction of a transposase protein with its target dsDNA was investigated. The direct imaging of the nucleoproteic complex considered herein gives new insights in the comprehension of transposase–DNA interaction in agreement with biochemical data.