Polyaniline nanowires on Si surfaces fabricated with DNA templates

It is essential to put individual, free-standing nanowires onto insulating substrates and integrate them to useful devices. Here we report a strategy for fabrication of conducting polymer nanowires on thermally oxidized Si surfaces by use of DNA as templates. The direct use of stretched and immobilized DNA strands as templates avoids the agglomeration of DNA caused by shielding of charges on DNA when polyaniline/DNA complexes formed in solution. Most importantly, the oriented DNA strands immobilized on the Si surface predetermine the position and the orientation of the nanowires. The approach described here is the first step toward uniting the programmable-assembly ability of DNA with the unique electronic properties of conducting polymers for high-density functional nanodevices. The conductivity of the nanowires is very sensitive to the proton doping-undoping process, suggesting that the nanowires hold great promise for sensitive chemical sensor applications.     

Methods of stretching DNA molecules using flow fields

Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out and deposit the DNA onto a hydrophobic surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and that the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree than those that are air-blown; fewer are deposited at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial alignment. Our results are a first step toward understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.     

Positioning isolation and biochemical analysis of single DNA molecules based on nanomanipulation and single-molecule PCR

Recently, the isolation and biochemical analysis of DNA at the single-molecule level has been recognized as very important for genetic research and clinical analysis. A unique technique for the positioning, dissection, and isolation of single DNA molecules using atomic force microscopy (AFM) has been demonstrated. Full-length genome DNA molecules were first deposited and stretched by a modified "molecular combing" technique onto a 3-aminopropyl triethoxysilane-coated mica substrate. A single DNA fragment was dissected from one of those genome DNA strands with the AFM tip at the desired position, and then isolated (or picked up) after a special operation called "kneading". All the operations including imaging, dissection, and isolation could be carried out with one tip. The isolated DNA fragment on the AFM tip could be successfully amplified by single-molecule PCR.     

"分子梳"研究进展

“分子梳”是DNA被可移动的气-液界的均匀拉直,该技术涉及两个过程:DNA分子末端与基底表面的特异性结合和移动的气-液界面对DNA分子的均匀拉直。该技术在构建纳米材料/结构,研究DNA转录和复制,绘制基因物理图谱等方面得到了应用。预计“分子梳”技术将在以下方面取得进展:以拉直的DNA为模板构建纳米器件和纳米材料;用于基因突变的临床检测;结合原子力显微术(AFM),建立“原子力显微术原位杂交”技术以替代荧光原位杂交。     

Hydrophobic Actuation of a DNA Origami Bilayer Structure

Amphiphilic compounds have a strong tendency to form aggregates in aqueous solutions. It is shown that such aggregation can be utilized to fold cholesterol‐modified, single‐layered DNA origami structures into sandwich‐like bilayer structures, which hide the cholesterol modifications in their interior. The DNA bilayer structures unfold after addition of the surfactant Tween 80, and also in the presence of lipid bilayer membranes, with opening kinetics well described by stretched exponentials. It is also demonstrated that by combination with an appropriate lock and key mechanism, hydrophobic actuation of DNA sandwiches can be made conditional on the presence of an additional molecular input such as a specific DNA sequence.     

Single-walled carbon nanotube combing during layer-by-layer assembly: from random adsorption to aligned composites

Oriented SWNTs in polymer composites have shown dramatic improvements in the physical properties of a composite because of the anisotropic shape and properties of SWNTs. Controlled alignment of SWNTs during composite fabrication implies better material function performance. This letter reports a new fabrication technique whereby aligned SWNTs and robust SWNT-polymer composites can be made using a fusion method of SWNT combing and layer-by-layer (LBL) assembly. As we previously reported, LBL assembly demonstrated exceptional processing ability in constructing the uniform distribution of a SWNT-polymer composite. Combined with this uniformity, this SWNT combing technique endows controlled alignment of single-stranded SWNTs in a SWNT-polymer composite system. SWNT combing employs air-water interfacial forces to change the molecular topography from the random adsorption state to the stretched alignment of SWNTs. More specifically, air-water interfacial forces are associated with an excess viscous drag force and an intrinsic dewetting rate along SWNTs. Moreover, the alignment efficiency of SWNTs is high enough to construct a multilayered LBL film with horizontal-linear weaving structures. This simple method also can be applied for aligning other nanowire materials because it utilizes simple geometric features of SWNTs.     

Sequence-Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies

DNA-modified lanthanide-doped upconversion nanoparticles (DNA-UCNPs) that combine the functions of DNA and the optical features of UCNPs have shown great promise in a wide range of fields. However, challenges remain in precisely tethering and orienting the DNA strands on the UCNP surface. Herein, we systematically investigate the sequence dependence of DNAs in their interactions with UCNPs, and reveal that poly-cytosine (poly-C) has high affinity for the UCNP surface. A general approach to synthesize monodispersed DNA-UCNP conjugates is developed using poly-C-containing diblock DNA strands. The poly-C segment of the DNA strand binds to the surfaces of UCNPs and the second segment is oriented perpendicularly on the UCNP surface, making the DNA-UCNPs highly stable and monodispersed in aqueous solution. The dense layer of DNA on the UCNP surface enables the programmable assembly of UCNPs with other DNA-functionalized nanoparticles or DNA origamis through hybridization, resulting in the formation of well-organized complex structures.     

Fabricating and aligning pi-conjugated polymer-functionalized DNA nanowires: atomic force microscopic and scanning near-field optical microscopic studies

We report a simple method to functionalize DNA with pi-conjugated polymer, forming highly aligned and integrated arrays of pi-conjugated polymer nanowires of a few nanometers diameter. pi-conjugated polymer, polyphenazasiline, having alkylammonium salts on the N atom (PPhenaz-TMA), synthesized in this study can be directly attached to DNA, which can be organized along stretched and aligned DNA molecules on surfaces as a template. Furthermore, PPhenaz-TMA/DNA nanowires were stretched and aligned on surfaces, even when PPhenaz-TMA/DNA complexes formed in solutions. The resulting PPhenaz-TMA/DNA nanowires could be easily converted to oxidized states or metallic nanowires by using adequate oxidant or metal salts. The direct visualization of PPhenaz-TMA/DNA nanowires and its structural changes have been studied by atomic force microscopy and scanning near-field optical microscopy.     

Creation of mammalian single- and double-stranded DNA surfaces: a real-time QCM-D study

The quartz crystal microbalance with dissipation monitoring (QCM-D) is an excellent method for studying the creation of DNA-based surfaces and films. Previous studies have used QCM-D to focus on the construction of DNA surfaces composed of short synthetic DNA oligomers or plasmid DNA. Here, we have used QCM-D to monitor the creation of genomic single- and double-stranded calf thymus DNA surfaces on a polycation adsorbed to a SiO2 support. We have successfully monitored the hybridization between the ssDNA surfaces and their complementary strands in solution and have also shown that DNA multilayer formation can be observed using denatured calf thymus DNA. We have furthermore established that the ssDNA and dsDNA surfaces show different binding characteristics to ethidium bromide, a common dsDNA intercalator, demonstrating the potential use of such surfaces to identify possible DNA ligands.     

Complex Reconfiguration of DNA Nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold‐mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural‐reconfiguration method that utilizes the modularly interconnected architecture of single‐stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two‐dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three‐dimensional DNA cuboid.     

Sequence‐Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies

DNA‐modified lanthanide‐doped upconversion nanoparticles (DNA‐UCNPs) that combine the functions of DNA and the optical features of UCNPs have shown great promise in a wide range of fields. However, challenges remain in precisely tethering and orienting the DNA strands on the UCNP surface. Herein, we systematically investigate the sequence dependence of DNAs in their interactions with UCNPs, and reveal that poly‐cytosine (poly‐C) has high affinity for the UCNP surface. A general approach to synthesize monodispersed DNA‐UCNP conjugates is developed using poly‐C‐containing diblock DNA strands. The poly‐C segment of the DNA strand binds to the surfaces of UCNPs and the second segment is oriented perpendicularly on the UCNP surface, making the DNA‐UCNPs highly stable and monodispersed in aqueous solution. The dense layer of DNA on the UCNP surface enables the programmable assembly of UCNPs with other DNA‐functionalized nanoparticles or DNA origamis through hybridization, resulting in the formation of well‐organized complex structures.     

Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times their contour length (unextended length, 16.2 microm) by the combing method on hydrophobic polymethylmetacrylate coated surfaces. The effects of sodium and magnesium ions and pH of the DNA solution were investigated. Interestingly, we observed force-induced melting of single DNA molecules.     

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.     

Selective pairing of polyfluorinated DNA bases

Novel selective non-hydrogen-bonding DNA base pairs utilizing fluorinated nucleoside analogues have been investigated. Melting studies of DNA duplexes containing 2,3,4,5-tetrafluorobenzene and 4,5,6,7-tetrafluoroindole bases on opposite strands show greater stabilization of the duplex compared with nonfluorinated hydrocarbon controls. Overall, these hydrophobic analogues are destabilizing compared with natural base pairs but are stabilizing compared with natural base mismatches. Such selective pairing may be due to solvent avoidance of these hydrophobic structures, burying their surfaces within the duplex. Our findings suggest that polyfluoroaromatic bases might be employed as a new, selective base-pairing system orthogonal to the natural genetic system.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

Role of host layer flexibility in DNA guest intercalation revealed by computer simulation of layered nanomaterials

Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.     

Patterning nanocluster polystyrene brushes grafted from initiator cores on silicon surfaces by lithography processing

In this study, we formed grafted polystyrene (PS) brushes possessing nanocluster structures through atom transfer radical polymerization from initiator cores presented on Si surfaces that had been generated using reactive ion etching (RIE). We established the surface grafting polymerization kinetics of the nanoclustered PS chains on the Si surfaces to fit their experimentally determined thickness (ellipsometry) and number-average molecular weight (M _n) of “free” PS (gel permeation chromatography). The propagation rate (k _p) and active grafting species deactivation rate (k _d) were obtained from reactions involving styrene concentrations from 0.2 to 2 M. We also used scanning electron microscopy to observe the morphologies of the PS grafted to the surfaces after various reaction times at various styrene concentrations. The PS brushes grafted onto the Si surfaces under styrene concentrations of 0.2, 0.5, 1, and 2 M exhibited clustered structures having cluster diameters of 12, 28, 42, and 45 nm, respectively; from these observations, we calculated the critical grafting density. In addition, we generated highly dense, well-defined patterns of PS on patterned Si(100) surfaces through the use of a very-large-scale integration process involving electron beam lithography and RIE. We employed the RIE system to generate a high density of reactive species at the bottom of the trenches for graft polymerization. After 21 h of grafting, AFM imaging revealed dense line patterns of nanoclustered PS.     

Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: an experimental-computational study

Detailed experimental and computational studies revealed the important role that hydrophobic interactions play in the aqueous assembly of rigid small molecule-DNA hybrid (rSMDH) building blocks into nanoscale cage and face-to-face (ff) dimeric structures. In aqueous environments, the hydrophobic surfaces of the organic cores in these nanostructures are minimized by interactions with the core in another rSMDHs, with the bases in the attached DNA strands, and/or with the base pairs in the final assembled structures. In the case that the hydrophobic surfaces of the cores could not be properly isolated in the assembly process, an ill-defined network results instead of dimers, even at low concentration of DNA. In contrast, if ff dimers can be formed with good minimization of the exposed hydrophobic surfaces of the cores, they are highly stable structures with enhanced melting temperatures and cooperative melting behavior.