Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2.5 helical turns respectively, and their parallel lozenge tiling lattices were demonstrated by high resolution AFM images, where the former lozenge unit cell has a lattice constant of 13.6 nm, and the latter has a larger lattice constant of 17.0 nm. Modification of the triangle tile with infinitesimal disturbance on side lengths and insertion of one thymine single stranded loop at every vertex resulted in comparably similar nanotubes.

Polymer brushes of polymethacrylic acid (PMAA) and PMAA-associated polymer blends of PMAA/PNIPAM (poly-N-isopropylacrylamide) were prepared on porous silicon for further investigation of the EDC/NHS (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide) activation mechanisms by infrared spectroscopy. When the fragmentation degree of PMAA blocks in PMAA-associated polymer blends is increased, the production of anhydride wanes from dominant to recessive, whereas a complementary product of the NHS-ester waxes from recessive to dominant. The Thorpe–Ingold effect was applied to explain the formation of anhydride: the gem-dialkyl groups of PMAA next to the carboxylic acids compress the acid side chains close to each other; thus, once the intermediate of O-acylisourea forms, it will be attacked by the intramolecular neighboring acid much faster than any other nucleophiles such as NHS and water, and therefore the six-membered ring of the anhydride will be formed. All acid side chains in PMAA standing next to each other will form an anhydride, primarily due to the Thorpe–Ingold effect, unless they are sterically hindered, whereas only isolated acid side chains form the NHS-ester. The EDC/NHS activation results for four small molecules of dicarboxylic acids in aqueous media, namely, glutaric acid and 2,2-dimethyl glutaric acid, which generate disuccinimidyl ester with high yield, and succinic acid and 2,2-dimethyl succinic acid, which remain intact, can also be explained by the Thorpe–Ingold effect. A clear understanding of the EDC/NHS activation mechanisms of PMAA will take us a step closer for resolving the mechanistic ambiguity of the carbodiimide/additive coupling reactions for amide bond formation.

Tethered with bistable 2′,6′-dimethylazobenzene (DMazo) via a glycerol linker, an artificial 35 nt-long DNA has performed photoresponsive hybridization and reversible light-driven strand displacement.

Small circular DNA molecules with designed lengths, for example 64 and 96 nucleotides (nt), after hybridization with a few 32-nt staple strands respectively, can act as rigid motifs for the construction of DNA nanotubes with excellent uniformity in ring diameter. Unlike most native DNA nanotubes, which consist of longitudinal double helices, nanotubes assembled from circular DNAs are constructed from lateral double helices. Of the five types of DNA nanotubes designed here, four are built by alternating two different rings of the same ring size, while one is composed of all the same 96-nt rings. Nanotubes constructed from the same 96-nt rings are 10–100 times shorter than those constructed from two different 96-nt rings, because there are fewer hinge joints on the rings.

The long single-stranded RNAs produced from Rolling Circle Transcription (RCT) were used as scaffolds to be folded with a few short DNA staples into RNA–DNA hybrid nanowires.

Thousands of nucleotide(nt)-long single strand DNAs, generated from rolling-circle-amplification (RCA), were used as scaffolds to create DNA nanoscale wires and plates with a few short staple strands by following the origami design principle with a crossover at 1.5 turns. The core sequence of the circle template, for producing tens and hundreds of tandemly repeated copies of it by RCA, was designed according to Seeman’s sequence design principle for nucleic acid structural engineering (Seeman, N. C. J. Biomol. Struct. Dyn. 1990, 8, 573). The significance for folding the RCA products into nanoscale shapes lies in the design flexibility of both staple and scaffold strand codes, simplicity of a few short staple strands to fold the periodic sequence of RCA products, and lower cost.

Porous silicon (PSi) prepared from Pt metal-assisted chemical etching (MaCE) was demonstrated to possess higher hydrosilylation efficiency (∼57%) than anodized PSi (∼11%) by surface reaction with ω-undecenyl alcohol (UO). Deconvolution of the SiHx (x = 1-3) stretching bands revealed the abundance of SiH2 species on MaCE PSi was 53%, ∼10% higher than on anodized samples, while both of SiH1 and SiH3 were ∼5% lower correspondently on MaCE PSi than on anodized samples. The surface SiHx abundances were suggested to account for the higher hydrosilylation efficiency on MaCE PSi. Optimization of Pt-assisted chemical etching parameters suggested a 7–15 nm thick Pt-coating and an etching time of 3–10 min for biochip applications. Scanning electron microscopy images revealed that an isotropic top meso-porous layer was beneficial for hydrosilylation and long-term durability under ambient conditions. To end, an example of histidine-tagged protein immobilization and microarray was illustrated. Combining the materials’ property, surface chemistry, and micro-fabrication technology together, we envision that silicon based biochip applications have a prosperous future.

Microarrays hold considerable promise in large-scale biology on account of their analytical, massive and parallel nature. In a step toward further enabling such a capability, we describe the application of rolling circle amplification (RCA) for a sensitive and multiplex detection of nucleic acid targets on oligonucleotide-conjugated polymer brushes covalently grown from porous silicon. Both RCA and polymer brushes have been taken to increase the loading quantity of target molecules and thus improve the detection sensitivity without loss of multiplexing. Besides, polymer brushes were employed to protect porous silicon and to provide biologically simulated environments, making the attached biomolecules maintain bioactivity. This approach can reach a detection limit of 0.1 nM target analytes and three orders of magnitude dynamic range of 0.1–100 nM, with a fluorescence scanner. A two-colour DNA microarray was achieved via RCA of two kinds of circular DNA targets on one chip simultaneously. The porous silicon chip-based RCA technique is promising for the multiplex detection of deoxynucleic acids on microarrays.

Two surface chemistry approaches were realized to complete click reactions at covalently grafted polymer brushes of poly(poly(ethylene glycol) monomethacrylate) on a planar silicon surface (Si-g-P(PEGMAOH)). On one hand, the hydroxyls from Si-g-P(PEGMAOH) brushes can be replaced by chlorines of thionyl chloride and then chlorines can be substituted with azides of sodium azide to achieve azide-terminated (Si-g-P(PEGMAN3)) brushes. On the other hand, the terminal acetylene (Si-g-P(PEGMACH2CCH)) brushes can be prepared easily by reaction between Si-g-P(PEGMAOH) and propargyl bromide. Model compounds of acetylene-terminated propargylamine, propiolic acid, and 10-undecynoic acid as well as azide-terminal benzyl azide were chosen to investigate the surface click reactions catalyzed with Cu(II)/sodium L-ascorbate by microwave irradiation under very mild conditions at 30 °C for 1 h. The stepwise modifications were characterized by two surface-sensitive techniques, Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) and X-ray Photoelectron Spectroscopy (XPS), and their spectra were analyzed in detail. The triazole ring v(HC) stretching at 3139 cm−1 and the XPS high-resolution scan of N 1s directly confirm the click reactions. By quantifying their infrared spectra before and after click reactions, we conclude that the click reactions on silicon surfaces by microwave irradiation possess high yield and efficiency. Hence, the microwave irradiated click reaction approaches might open convenient avenues to fabricate functional and hybrid organic/silicon devices.Graphical abstractPoly(poly(ethylene glycol) monomethacrylate) brushes grafted from a planar silicon hydride surface were converted to azide-/acetylene-terminated brushes. Then surface click reactions were executed by microwave irradiation under extremely mild conditions.Highlights► Click reactions were executed on polymer brushes via silicon surface induced ATRP. ► Microwave irradiation assisted surface click reactions at 30 °C for 1 h. ► MTR-IR Spectroscopy reveals tiny details of click reactions. ► Microwave-assisted surface reactions could have broad application.

A facile approach was established to construct polyamidoamine (PAMAM) dendrons from polymer brushes of poly(poly(ethylene glycol) monomethacrylate) (Si-g-P(PEGMA-OH)) grafted from a planar silicon hydride surface. First the Si-g-P(PEGMA-OH) brushes were grown via surface-initiated atom transfer radical polymerization with robust Si–C links on silicon surfaces. The side-chain hydroxyl groups of Si-g-P(PEGMA-OH) were chlorinated with thionyl chloride and further chlorines were substituted with amino groups of ethylenediamine, giving terminal primary amines. Borrowing the solution synthesis approach, we constructed second and third generations of PAMAM dendrons on-chip by surface-initiated alternative growth of two monomers, methyl acrylate and ethylenediamine. Two applications of silicon-based PAMAM dendrons were shown: the dense amino groups were activated via a cross-linker, N-succinimidyl-6-maleimidylhexanoate, to capture a free-thiol-carrying peptide of oxytocin and the third generation of PAMAM dendrons was used as a platform to on-chip synthesize a three amino acid peptide of Arg-Gly-Asp (RGD). The above conclusions were mainly derived from a home-built multiple transmission-reflection infrared spectroscopy, and complemented by X-ray photoelectron spectroscopy, UV–Vis spectroscopy and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry.Three generations of polyamidoamine dendrons were constructed from poly(poly(ethylene glycol) monomethacrylate) brushes grafted from a planar silicon hydride surface. Silicon-based PAMAM dendrons were applied to immobilize a free-thiol-carrying peptide of oxytocin and to on-chip synthesize a three amino acid peptide of Arg-Gly-Asp (RGD).Research Highlights► Polyamidoamine (PAMAM) dendrons were grafted on hydrosilylated silicon. ► Dense amines of PAMAM dendrons are required in fabricating biochip and biosensor. ► On-chip synthesis of a three amino acid peptide of Arg-Gly-Asp was exemplified.

Porous silicon (PSi) was applied as a supporting substrate for stepwise covalent derivatization of undecylenic acid, N-hydroxysuccinimidyl ester (NHS-ester) and nitrilotriacetic acid (NTA). By taking the advantages of porous silicon as a supporting matrix such as high surface area to volume ratio, infrared transparency, porous semiconductors for laser desorption/ionization mass spectroscopy, and low fluorescence background, a multi-mode detection biochip prototype can be realized. We prepared such a protein microarray by spotting NTA microarray dots on NHS-ester derivatized PSi, converting the rest of chip area into poly(ethylene glycol) background, loading NiII, and finally affinity-binding histidine-tagged (His-tagged) proteins. With the multi-mode analyses of infrared spectroscopy, X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS), and fluorescence scanning, two example proteins, His-tagged thioredoxin-urodilatin and His-tagged aprotinin, were well qualified and quantified.

The durability of porous silicon (PS) in solutions was improved by grafting a molecule, 2,4,6,8-tetramethyl-2,4,6,8-tetravinyl-1,3,5,7,2,4,6,8-tetraoxatetrasilocane (TE), with four terminal vinyl groups. With a native PS sample as control, we compared the long-term durability of three modified PS samples: TE-, undec-10-enoic acid (UA)-, and TE/UA(TE first and UA followed)-grafted PS, in a weak organic base of dimethyl sulfoxide, an aqueous mineral solution of CuBr2, and phosphate buffered saline respectively. Results indicate that TE-grafting is a straightforward and impactful approach to protect PS from oxidation and degradation. Further we used the TE-grafted PS to fabricate a prototype protein microarray by post-grafting UA and subsequently converting UA to nitrilotriacetic acid/Ni2+ for binding histidine-tagged proteins.

Infrared spectroscopy was applied to investigate the well-known EDC/NHS (N-ethyl-N′-(3-(dimethylamino)propyl)carbodiimide/N-hydroxysuccinimide) activation details of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) brushes grafted on porous silicon. Succinimidyl ester (NHS-ester) is generally believed to be the dominant intermediate product, conveniently used to immobilize biomolecules containing free primary amino groups via amide linkage. To our surprise, the infrared spectral details revealed that the EDC/NHS activation of PMAA generated anhydride (estimated at around 76% yield and 70% composition), but not NHS-ester (around 5% yield and 11% composition) under the well-documented reaction conditions, as the predominant intermediate product. In contrast, EDC/NHS activation of PAA still follows the general rule, i.e., the expected NHS-ester is the dominant intermediate product (around 45% yield and 57% composition), anhydride the side product (40% yield and 28% composition), under the optimum reaction conditions. The following amidation on PAA-based NHS-esters with a model amine-containing compound, l-leucine methyl ester, generated approximately 70% amides and 30% carboxylates. In contrast, amidation of PAA- or PMAA-based anhydrides with l-leucine methyl ester only produced less than 30% amides but more than 70% carboxylates. The above reaction yields and percentage compositions were estimated by fitting the carbonyl stretching region with 5 possible species, NHS-ester, anhydride, N-acylurea, unreacted acid, unhydrolyzed tert-butyl ester, and using the Beer–Lambert law. The different surface chemistry mechanisms will bring significant effects on the performance of surface chemistry-derived devices such as biochips, biosensors, and biomaterials.

A general approach to endow gold nanoshells a new function of controlled release was established by coating stimulus-responsive polymers on their surfaces via surface-initiated atom transfer radical polymerization. Incorporating boronic acid groups in polymer brushes, the controlled release of Alizarin Red S (ARS) was dynamically shown, through reversible covalent binding between boronic acid and diol.Graphical abstract. Gold nanoshells coated with polymer brushes, PMAA and PNIPAAM-co-PMAA, show saccharide- and temperature-responsive diol releases by incorporating boronic groups. This multifunctional nanomaterial provides a core for bioimaging and a shell for drug release.Highlights► PNIPAAM-co-PMAA polymer brushes were fabricated on gold nanoshells (AuNS) via SI-ATRP. ► Modify the hybrids of AuNS@PNIPAAM-co-PMAA with boronic acid to be drug carriers. ► Controlled releases were performed in vitro under saccharide substitution and temperature enhancement.

Here, a very unusual metal–organic nanotubular structure, [In(1,3-BDC)2]− (1,3-BDC = 1,3-benzenedicarboxylate) based on the 4-connected topology is reported. While 4-connected structures are widely sought after, such one-dimensional 4-connected tubular structures are extremely rare even though two- and three-dimensional 4-connected materials are common.

A Si(111)–H surface was modified via a direct reaction between Si–H and 1-undecylenic acid (UA) under microwave irradiation to form molecular monolayers with terminal carboxyl groups. After esterifying carboxylic acid being esterified with N-hydroxysuccinimide (NHS), aminobutyl nitrilotriacetic acid (ANTA) was bound to the silicon surface through amidation (pH = 8.0) between its primary amino group and NHS-ester, producing nitrilotriacetic acid (NTA) anions. Then hexa-histidine tagged thioredoxin–urodilatin (his-tagged protein) and FITC-labeled hexa-histidine tagged thioredoxin–urodilatin (FITC-his-tagged protein) can be anchored after NTA was coordinated with Ni2+. Furthermore, the NTA-terminated chip was acidified with 0.1 M HCl and subsequently esterified with NHS and then amidated with ANTA again to produce a second generation NTA. Thus the surface density of nitrilotriacetic acid anions was improved and resultantly that of anchored proteins was also enhanced through the iterative reactions. Both multiple transmission-reflection infrared spectroscopy (MTR-IR) and fluorescence scanning measurements demonstrated a proximate 1.63 times of anchored proteins on the second generation NTA/Ni2+ as that on the first generation NTA/Ni2+ monolayer.

A maximum fluorescence enhancement of 11 times was achieved by surface plasmon polaritons (SPPs) on a silver nanohole array region in reflection mode, compared to that on the nonarray area. A 30 nm dielectric SiO2 film was sputtered on the silver film as a spacer to separate the fluorophore from silver for attenuation of the fluorescence quenching. An array period of 550 nm and a nanohole radius of 100 nm were optimized to match the most efficient fluorescence excitation and emission of a boron-dipyrromethene fluorophore (BODIPY 630/650) on the array region.Keywords (keywords): fluorescence enhancement; fluorescence quenching; metal film; nanohole array; surface plasmon polaritons; Keywords: ;

Our recently developed multiple transmission−reflection infrared (MTR-IR) spectroscopy method was applied to measure arachidic acid Langmuir−Blodgett films on hydrophilic and hydrophobic silicon substrates. High-quality MTR-IR spectra at both s and p polarizations were obtained. The MTR-IR absorption intensity at different incident angles was found to be linearly correlated with the transmission times (N) for arachidic acid monolayers on a hydrophilic silicon substrate. Significant differences in polarization-dependent intensities were observed for some specific vibration modes, for example, CH3 and CH2 stretching, carboxylic acid stretching, and CH2 bending, on different types of monolayer and multilayer films. By means of polarization-dependent spectra, the molecular orientation was numerically calculated, and the molecular structures such as the crystalline packing of hydrocarbon chains and the trans and cis configurations of carboxylic acid species were deduced. Obvious and repeatable intensity differences for the same vibration mode from s to p polarization strongly confirmed the stability and credibility of our MTR-IR method.

An improved DIOS (desorption ionization on porous silicon) method for laser desorption/ionization mass spectrometry (LDI MS) by electroless plating of silver nanoparticles (AgNPs) on porous silicon (PSi) was developed. By addition of 4-aminothiophenol (4-ATP) into the AgNO3 plating solution, the plating speed can be slowed down and simultaneously 4-ATP self-assembled monolayers (SAMs) on AgNPs (4-ATP/AgNPs) were formed. Both AgNPs and 4-ATP/AgNPs coated PSi substrates present much higher stability, sensitivity and reproducibility for LDI MS than the un-treated porous silicon ones. Their shelf life in air was tested for several weeks to a month and their mass spectra still displayed the same high quality and sensitivity as the freshly prepared ones. And more 4-ATP SAMs partly play a role of matrix to increase the ionization efficiency. A small organic molecule of tetrapyridinporphyrin (TPyP), oligomers of polyethylene glycol (PEG 400 and 2300), and a peptide of oxytocin were used as examples to demonstrate the feasibility of the silver-plated PSi as a matrix-free-like method for LDI MS. This approach can obtain limits of detection to femtomoles for TPyP, subpicomoles for oxytocin, and picomoles for PEG 400 and 2300, comparable to the traditional matrix method and much better than the DIOS method. It simplifies the sample preparation as a matrix-free-like method without addition of matrix molecules and homogenizes the sample spread over the spot for better and more even mass signals.

The recently arising antithrombin drug, angiomax, was successfully conjugated with a 5′-amino oligonucleotide through click chemistry. This oligo-angiomax conjugate was assembled into a two-dimensional DNA lattice with other oligonucleotides together. Besides the plane sheet of DNA lattices, an interesting angiomax-involved DNA tubing structure, constructed by 40 to 50 angiomax stripes which are parallel to the longitudinal axis of the tube, was also imaged. After incubation of thrombins with the angiomax-involved DNA lattice, the binding of thrombins to arrayed angiomax peptides was observed. Finally a chromogenic substrate bioassay was employed to estimate the antithrombin activities as assembled oligo-angiomax DNA lattice ≈ 1.1, oligo-angiomax ≈ 2.7 angiomax. The functionalized DNA lattices have the potential to be used as a powerful platform for investigation of biomolecular interactions such as drug−protein, protein−protein, DNA−RNA, and DNA−protein interactions in the nano- and subnanoscales.

A visible rectification effect on the current–voltage curves of metal/porous silicon/p-silicon has been observed by current-sensing atomic force microscopy. The current–voltage curves of porous silicon membranes with different porosities, prepared through variation of etching current density for a constant time, indicate that a higher porosity results in a higher resistance and thus a lower rectification, until the current reaches a threshold at a porosity >55%. We propose that the conductance mode in the porous silicon membrane with porosities >55% is mainly a hopping mechanism between nano-crystallites and an inverse static electric field between the porous silicon and p-Si interface blocks the electron injection from porous silicon to p-Si, but with porosities ≤55%, electron flows through a direct continuous channel between nano-crystallites.

B-type natriuretic peptide (BNP) is an important biomarker in early diagnosis of congestive heart failure. Many efforts have been made previously to evaluate the BNP level in human plasma. We developed a porous silicon (PSi) affinity chip to detect BNP present at low concentrations in human plasma by matrix assisted laser desorption/ionization–time of flight–mass spectrometry (MALDI-TOF–MS) directly. The PSi surface immobilized with antibodies captured and concentrated BNP through antibody–antigen interaction specifically and sensitively. A detection limit as low as 10 pg/mL BNP in human plasma was demonstrated by mass analysis. This effective on-chip recognition, enrichment, and detection strategy could be employed in identification of biomarkers in complex body fluids in diagnoses.

A new infrared spectroscopic measurement involving multiple transmissions and reflections for molecular monolayers adsorbed on silicon surfaces has been established. Compared to the well-known multiple internal reflection (MIR) method, the distinctive advantage of multiple transmission-reflection infrared spectroscopy (MTR-IR) is the convenient measurement using standard silicon wafers as samples, while in the MIR setup special fabrication of geometric shapes such as 45° bevel cuts on an attenuated total reflection silicon crystal is needed. Both p- and s-polarized spectra can be obtained reproducibly with the same order of sensitivity as by the MIR spectroscopy. Optimal conditions for spectral acquisition have been obtained from theoretical calculations. The ability of this methodology to gather high quality infrared spectra of adsorbed monolayers is demonstrated and the analysis of the surface packing and molecular orientation is discussed.

Porous silicon surfaces can be bio-functionalised by a simple three-step method. First the hydrogen-terminated porous silicon was oxidised and amino-silanised in a one-pot reaction by 3-aminopropyl(triethoxyl)silane with the aid of an organic base, diisopropylethylamine. Secondly, the primary amine reacted with either of two homobifunctional cross-linkers, bis(N-succinimidyl)carbonate and (N,N′-bis(p-maleimidophenyl)methylene. By modulating the reaction conditions, a high surface coverage of linking groups, succinimidyl ester or maleimide, can be obtained separately. Since homobifunctional cross-linkers can form bridged structures with both ends fixed to the surface, the reaction conditions were optimised for one end attached to the surface and the other end pendent. Succinimidyl ester is an amino-reactive group, therefore mouse monoclonal antibody bearing amino groups was grafted. An enzyme linked immunosorbent assay was used to evaluate the surface density of antibody at 0.008 ng cm−2. The other linker, (N,N′-bis(p-maleimidophenyl)methylene, was refluxed in acetonitrile with surface amines to result in maleimde-terminated surfaces. Then a reduced urokinase bearing accessible thiol groups was grafted and its enzymatic activity was assayed at 0.004 nmol cm−2 for urokinase. Transmission infrared, X-ray photoelectron, interferometric reflectance, UV-Vis, photoluminescence spectroscopies and a chromogenic assay were used to characterise the surfaces.

Surface reactions of 4-aminothiophenol (4-ATP) with a series of heterogeneous crosslinkers containing both maleimide and succinimidyl ester groups were investigated with infrared reflection absorption spectroscopy (IRRAS) and X-ray photoelectron spectroscopy (XPS). Two types of surface reactions exist: (1) for most crosslinkers, a dominant reaction of amine and succinimidyl ester gave homogeneous maleimide-pendant surfaces; (2) for other crosslinkers, a side reaction between amine and maleimide, accompanying the main reaction, yielded heterogeneous surfaces with two linking groups, maleimide and succinimidyl ester. A typical example for the second case is the reaction of surface amines with N-succinimidyl-6-maleimidylhexanoate (SMH). Finally, a peptide, H-Gly-Arg-Gly-Asp-Ser-Pro-Cys-OH (GRGDSPC), was immobilized on the SMH-derived surface as a bridging structure through two linkages, cysteine thioether and glycine amide.

Organic silicone, polydimethylsiloxane (PDMS), was covalently grafted onto the porous silicon (PS) surface to improve its stability to oxidation. Transmission Fourier-transform infrared (FTIR), photoluminescence (PL) and interferometric reflectance spectra have been recorded to evaluate the surface modification and the passivation effect. After modification, the porous nanostructure retained, the stability against oxidation was significantly improved and the PL still kept.

The long single-stranded RNAs produced from Rolling Circle Transcription (RCT) were used as scaffolds to be folded with a few short DNA staples into RNA–DNA hybrid nanowires.