Simultaneous AFM manipulation and fluorescence imaging of single DNA strands.

We report combined atomic force and far-field fluorescence microscopic experiments which allow the simultaneous atomic force manipulation and optical observation of individual dye-labeled DNA molecules. A detailed understanding of the binding properties of DNA to different transparent surfaces is prerequisite for these investigations. Atomic force spectroscopy and fluorescence microscopy of single DNA strands yielded detailed insight into two different types of DNA binding onto transparent polylysine-coated and silanized glass surfaces. We subsequently demonstrate how the different binding can be exploited to perform two types of nanomanipulation experiments: On polylysine, strong electrostatic interactions over the whole length of the DNA strand enable the writing of micrometer-sized patterns. By contrast, the strong pointwise attachment of DNA to silanized surfaces allows horizontal stretching of single DNA strands to lengths exceeding 1.6 times the contour length of the DNA strand. With this new approach it is possible to directly observe the rupture of the strongly bonded DNA strand.     

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

We demonstrate the single‐molecule imaging of the catalytic reaction of a Zn²⁺‐dependent DNAzyme in a DNA origami nanostructure. The single‐molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high‐speed atomic force microscopy (AFM). This nanostructure‐based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single‐molecule level.     

Cooperative,Reversible Self‐Assembly of Covalently Pre‐Linked Proteins into Giant Fibrous Structures

We demonstrate a simple bioconjugate polymer system that undergoes reversible self‐assembling into extended fibrous structures, reminiscent of those observed in living systems. It is comprised of green fluorescent protein (GFP) molecules linked into linear oligomeric strands through click step growth polymerization with dialkyne poly(ethylene oxide) (PEO). Confocal microscopy, atomic force microscopy, and dynamic light scattering revealed that such strands form high persistence length fibers, with lengths reaching tens of micrometers, and uniform, sub‐100 nm widths. We ascribe this remarkable and robust form of self‐assembly to the cooperativity arising from the known tendency of GFP molecules to dimerize through localized hydrophobic patches and from their covalent pre‐linking with flexible PEO. Dissipative particle dynamics simulations of a coarse‐grained model of the system revealed its tendency to form elongated fibrous aggregates, suggesting the general nature of this mode of self‐assembly.     

Cooperative,Reversible Self‐Assembly of Covalently Pre‐Linked Proteins into Giant Fibrous Structures

We demonstrate a simple bioconjugate polymer system that undergoes reversible self‐assembling into extended fibrous structures, reminiscent of those observed in living systems. It is comprised of green fluorescent protein (GFP) molecules linked into linear oligomeric strands through click step growth polymerization with dialkyne poly(ethylene oxide) (PEO). Confocal microscopy, atomic force microscopy, and dynamic light scattering revealed that such strands form high persistence length fibers, with lengths reaching tens of micrometers, and uniform, sub‐100 nm widths. We ascribe this remarkable and robust form of self‐assembly to the cooperativity arising from the known tendency of GFP molecules to dimerize through localized hydrophobic patches and from their covalent pre‐linking with flexible PEO. Dissipative particle dynamics simulations of a coarse‐grained model of the system revealed its tendency to form elongated fibrous aggregates, suggesting the general nature of this mode of self‐assembly.     

An assembling strategy for DNA cages with minimum strands

DNA polyhedra are artificial cage-like architectures based on interlocked and interlinked DNA double-strands. Using fewer strands to construct DNA cages shows an important role in the design of single-stranded DNA molecules. However, construction methods for DNA polyhedra from topological perspective remains not well understood. In this study, we theoretically propose an assembling strategy for DNA polyhedra with minimum strands based on computer algorithm. The results show that this efficient method could search DNA polyhedra with fewer strands faster. Our research provides new insights into design and synthesis for DNA polyhedra with required topological structures.     

Electrokinetic techniques applied to electrochemical DNA biosensors

Electrokinetic techniques are contact-free methods currently used in many applications, where precise handling of biological entities, such as cells, bacteria or nucleic acids, is needed. These techniques are based on the effect of electric fields on molecules suspended in a fluid, and the corresponding induced motion, which can be tuned according to some known physical laws and observed behaviours. Increasing interest on the application of such strategies in order to improve the detection of DNA strands has appeared during the recent decades. Classical electrode-based DNA electrochemical biosensors with combined electrokinetic techniques present the advantage of being able to improve the working electrode's bioactive part during their fabrication and also the hybridization yield during the sensor detection phase. This can be achieved by selectively manipulating, driving and directing the molecules towards the electrodes increasing the speed and yield of the floating DNA strands attached to them. On the other hand, this technique can be also used in order to make biosensors reusable, or reconfigurable, by simply inverting its working principle and pulling DNA strands away from the electrodes. Finally, the combination of these techniques with nanostructures, such as nanopores or nanochannels, has recently boosted the appearance of new types of electrochemical sensors that exploit the time-varying position of DNA strands in order to continuously scan these molecules and to detect their properties. This review gives an insight into the main forces involved in DNA electrokinetics and discusses the state of the art and uses of these techniques in recent years.     

Polarizability of DNA Block Copolymer Nanoparticles Observed by Electrostatic Force Microscopy

In this study, DNA block copolymer (DBC) micelles with a polystyrene (PS) core and a single‐stranded (ss) DNA shell were doped with ferrocene (Fc) molecules. Tapping mode atomic force microscopy (AFM) was used to study the morphology of the doped and undoped block copolymer aggregates. We show that introducing Fc molecules into the hydrophobic core does not affect the structural properties such as shape or size. In contrast, doping with Fc significantly changes the micelles' electrical properties, namely their polarizability. Electrostatic force microscopy (EFM) measurements reveal that the undoped micelles show no significant polarization signal, while the Fc‐doped aggregates exhibit strongly enhanced polarizability. Furthermore, the nucleic acid moieties were utilized in combination with complementary ssDNA strands to assemble single particles into linear arrays of DBC nanoobjects. The ability to tune the electrostatic properties of the polymer core and the presence of nucleic acids might open the way for using these bioorganic nanoparticles as building blocks for nanoelectronic or biosensing devices.

     

Preparation of a poly-nanocage dynamer: correlating the growth of polymer strands using constitutional dynamic chemistry and heteroleptic aggregation

A metallosupramolecular prismatic nanocage with altogether six reactive aldehyde terminals was utilized as a sophisticated "monomer" in a template-directed constitutional dynamic imine polymerization to prepare an unprecedented triple-stranded dynamer. To analyze the correlated growth in its three congener strands, a fully covalent triple-armed star polymer was fabricated from the metallodynamer through capping, imine reduction, and removal of the template. Atomic force microscopy analysis of 68 triple-armed star polymer molecules suggests that the growth of their arms is correlated to ~72%.     

Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors

Right out of the (logic) gate: Logic gates made from 3D DNA nanotetrahedra were constructed that are responsive to various ions, small molecules, and short strands of DNA. By including dynamic sequences in one or more edges of the tetrahedra, a FRET signal can be generated in the manner of AND, OR, XOR, and INH logic gates, as well as a half-adder circuit. These DNA logic gates were also applied to intracellular detection of ATP.     

Characterization of 3D DNA Assemblies Using Cryogenic Electron Microscopy

DNA nanotechnology utilizes DNA double strands as building units for self-assembly of DNA nanostructures.The specific base-pairing interaction between DNA molecules is the basis of these assemblies.After decades of development,this technology has been able to construct complex and programmable structures.With the increase in delicate nature and complexity of the synthesized nanostructures,a characterization technology that can observe these structures in three dimensions has become necessary,and developing such a technology is considerably challenging.DNA assemblies have been studied using different characterization methods including atomic force microscopy(AFM),scanning electron microscopy(SEM),and transmission electron microscopy(TEM).However,the three-dimensional(3D)DNA assemblies always collapse locally due to the dehydration during the drying process.Cryogenic electron microscopy(cryo-EM)can overcome the challenge by maintaining three-dimensional morphologies of the cryogenic samples and reconstruct the 3D models from cryogenic samples accordingly by collecting thousands of two-dimensional(2D)projection images,which can restore their original morphologies in solution.Here,we have reviewed several typical cases of 3D DNA-assemblies and highlighted the applications of cryo-EM in characterization of these assemblies.By comparing with some other characterization methods,we have shown how cryo-EM promoted the development of structural characterization in the field of DNA nanotechnology.     

Parallel Detection of Different DNA Sequences on One Gold Electrode

Motivated by the potential of electrochemical techniques to analyze hybridization events fast and in a simple and cost‐effective way we present here a detection system allowing a parallel electrochemical DNA analysis. For this purpose different probe DNA strands have been immobilized on one electrode. By the use of two different target DNA sequences, both marked with the redox active methylene blue, we can show that hybridization with the complementary probe sh“NA strands can occur without steric hindrance. Each target has been recognized down to 3nM with a very high specificity of the sensor. In addition, we can detect two different ssDNA targets labeled with different redox active molecules, methylene blue and ferrocene, on one sensor surface simultaneously.     

pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas.However,pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies;therefore,sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way.Here,we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion,glycine betaine(GB),as charge-regulation molecules.The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB,respectively.In an acidic environment,carboxylate group in GB was protonated and GB was positively charged,which facilitated to shield the inherent electrostatic repulsion of DNA strands.Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands.In a basic solution,carboxylate group in GB was deprotonated and GB was neutral,thus inducing the dissociation of DNA assembly.     

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study

DNA.RNA hybrid duplexes are biologically important molecules and are shown to have potential therapeutic properties. To investigate the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes, a molecular dynamics study using the CHARMM27 force field was undertaken. The structural properties of all four nucleic acids considered are in very good agreement with the experimental data. The backbone dihedral angles and the puckering of the (deoxy)ribose indicate that the purine rich strands retain their A-/B-like properties but the pyrimidine rich DNA strand undergoes A-B conformational transitions. The minor groove widths of the hybrid structures are narrower than those in the RNA duplex, a requirement for RNase H binding. In addition, sampling of noncanonical phosphodiester backbone dihedrals by the DNA strands, differential solvation properties and helical properties, most notably rise, are suggested to contribute to hybrids being RNase H substrates. Differential RNase H activity toward hybrids containing purine versus pyrimidine rich RNA strands is suggested to be due to sampling of values of the phosphodiester backbone dihedrals in the DNA strands. Notably, the present results indicate that hybrids have decreased flexibility as compared to RNA, in contrast to previous reports.     

One‐Step Formation of “Chain‐Armor”‐Stabilized DNA Nanostructures

DNA‐based self‐assembled nanostructures are widely used to position organic and inorganic objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA‐based templates that are robust against degradation at elevated temperatures, low ion concentrations, adverse pH conditions, and DNases, we built 6‐helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3′‐ends and azides on their 5′‐ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so‐called DNA catenanes. Strikingly, the structures stayed topologically intact in pure water and even after precipitation from EtOH. The structures even withstood a temperature of 95 °C when all of the 24 strands were chemically interlocked.     

Decomposing bridging adhesion between polyelectrolyte layers into single molecule contributions

A novel approach to analyze the force response of multiple polymer strands, which are bridged between two surfaces, is proposed. The response of single polymer strands is experimentally accessible by measuring the force upon separation of two polymer-coated surfaces with the atomic force microscope. Our approach is based on the decomposition of the stretching and desorption sequence into contributions of independently bridged chains and of the elimination of loops formed on the opposite surface during contact. This approach was applied to investigate the bridging adhesion of surfaces coated with poly(vinylamine) (PVA). The force response of single PVA molecules was described on the basis of a recently proposed model, which accounts for the discrete chain character of the polymer at higher extension forces. As exemplary results, we determined the length distributions of the individual chains and the loop number distribution of these bridging chains on the polyelectrolyte-coated surfaces. The former were compared with scaling theories of polymer adsorption.     

Surface Assembly of DNA Origami on a Lipid Bilayer Observed Using High-Speed Atomic Force Microscopy

The micrometer-scale assembly of various DNA nanostructures is one of the major challenges for further progress in DNA nanotechnology. Programmed patterns of 1D and 2D DNA origami assembly using specific DNA strands and micrometer-sized lattice assembly using cross-shaped DNA origami were performed on a lipid bilayer surface. During the diffusion of DNA origami on the membrane surface, the formation of lattices and their rearrangement in real-time were observed using high-speed atomic force microscopy (HS-AFM). The formed lattices were used to further assemble DNA origami tiles into their cavities. Various patterns of lattice–tile complexes were created by changing the interactions between the lattice and tiles. For the control of the nanostructure formation, the photo-controlled assembly and disassembly of DNA origami were performed reversibly, and dynamic assembly and disassembly were observed on a lipid bilayer surface using HS-AFM. Using a lipid bilayer for DNA origami assembly, it is possible to perform a hierarchical assembly of multiple DNA origami nanostructures, such as the integration of functional components into a frame architecture.     

Self-assembly of polymer brushes in the presence of a surfactant: A system of strands

This theoretical study is focused on the formation of a cylindrical microstructure in a planar polymer brush in the presence of a surfactant. It is assumed that the brush may be nonuniform in the direction along the grafting plane and that there are regions with constant concentrations of monomer units and regions occupied only by the surfactant. The surfactant molecule is simulated by a dimer whose parts interact in a different manner with the monomer units of the polymer. At the interface between these regions, dimer molecules are oriented mainly perpendicularly to this interface and the surface tension is reduced. If the surface energy becomes negative, the formation of a structured brush is more favorable in terms of energy than that of a uniform brush. As a result, there may appear a cylindrical microstructure in which grafted macromolecules are united into strands perpendicular to the grafting plane. The stretching of macromolecules and their interaction with the solvent within the strands are described by the Alexander-de Gennes model, whereas the surface energy is calculated with allowance for the surface curvature of strands at a high degree of amphiphilicity of the surfactant molecules. It is shown that the arising strands have radii of the order of the surfactant-molecule length, while the number of macromolecules per strand is proportional to the surface density of their grafting. With an increase in the grafting density, the strand length increases initially, while the volume fraction of the polymer in a strand remains constant. Furthermore, strands start to shorten and their density grows. Structural characteristics are calculated as a function of the parameter characterizing the degree of amphiphilicity of the solvent molecules, their sizes, and their average energy of interaction with monomer units.     

Combining electrochemistry and direct force measurements: from the control of surface properties towards applications

Direct force measurements contributed in the last years much to our understanding of the diffuse double layer of charged interfaces in electrolyte solutions. Such measurements have been performed with the atomic force microscope or the surface force apparatus. This review gives an overview over the recent studies based on force measurements with electrode surfaces. Not only bare metal electrodes but also electrodes modified by different organic layers, including electroactive films, have been studied by these techniques. Direct force measurements indicate that further effects besides classical Gouy–Chapman–Stern theory have to be taken into consideration in order to describe the force profiles. In addition to the long-range forces also the adhesion between surfaces can be tuned by potentiostatic control. New single-molecule techniques based on the atomic force microscope allow to probe the extension of polymer strands or their desorption from solid interfaces. In combination with electrochemistry, it became now possible to tune the desorption behavior of polymer strands or to measure the electromechanical coupling of motors from single strands of electroactive polymers.     

DNA共价结合在化学修饰云母片上的AFM研究

原子力显微镜(AFM)自1986年发明以来,已经成为生物学研究领域中的一个有效工具,尤其在核酸及其它生物大分子结构方面的应用已成为普遍关注的热点.原子力显微镜要求基底达到原子级平整,硅片和玻璃表面的起伏很大,因而原子级平整的云母具有重要的价值.