Chemically induced hairpin formation in DNA monolayers

A naphthyridine dimer that binds specifically to G-G mismatches has been used to induce hairpin formation in oligonucleotides immobilized onto chemically modified gold surfaces. Surface plasmon resonance (SPR) imaging measurements of DNA microarrays were used to demonstrate that binding of the naphthyridine dimer to G-G mismatches within the stem portion of an immobilized 42-mer oligonucleotide could be used to induce hairpin formation that prevented hybridization of DNA complementary to the loop sequence. In addition, the selectivity of the naphthyridine dimer for G-G mismatches was verified through SPR imaging measurements of the hybridization adsorption of an 11-mer oligonucleotide to a four-component DNA array of zero- and single-base mismatch sequences.     

New solid support for the synthesis of 3'-oligonucleotide conjugates through glyoxylic oxime bond formation

A novel solid support 1 was synthesized to incorporate glyoxylic aldehyde functionality at the oligonucleotide 3'-terminus. 6-mer and 11-mer oligonucleotide sequences containing 3'-glyoxylic aldehyde functionality were prepared by using this support. These modified oligonucleotides were coupled to reporters containing an aminooxy group to prepare oligonucleotide 3'-conjugates through glyoxylic oxime bond formation. The hydrolytic stability of a glyoxylic oxime linkage was also investigated. [reaction: see text].     

Nanowire Transistor‐Based Ultrasensitive Virus Detection with Reversible Surface Functionalization

We have applied a reusable silicon nanowire field‐effect transistor (SiNW‐FET) as a biosensor to conduct ultrasensitive detection of H5N2 avian influenza virus (AIV) in very dilute solution. The reversible surface functionalization of SiNW‐FET was made possible using a disulfide linker. In the surface functionalization, 3‐mercaptopropyltrimethoxysilane (MPTMS) was first modified on the SiNW‐FET (referred to as MPTMS/SiNW‐FET), with subsequent dithiothreitol washing to reduce any possible disulfide bonding between the thiol groups of MPTMS. Subsequently, receptor molecules could be immobilized on the MPTMS/SiNW‐FET by the formation of a disulfide bond. The success of the reversible surface functionalization was verified with fluorescence examination and electrical measurements. A surface topograph of the SiNW‐FET biosensor modified with a monoclonal antibody against H5N2 virus (referred to as mAb_H5/SiNW‐FET) after detecting approximately 10^?17 M H5N2 AIVs was scanned by atomic force microscopy to demonstrate that the SiNW‐FET is capable of detecting very few H5N2 AIV particles.     

Fabrication of DNA-protein conjugate layer on gold-substrate and its application to immunosensor

The fabrication of antibody thin film using both protein G and oligonucleotide was carried out by self-assembly (SA) technique for immunosensor. A mixture of 11-mercaptoundecanoic acid (MUA) and oligonucleotide with thiol (SH) end group was self-assembled of gold (Au) surface for two-dimensional (2D) configuration. Protein G was chemically adsorbed on the 11-MUA surface, and then the antibody was immobilized on the protein G region. On the immobilized single-stranded DNA, the complementary DNA–antibody conjugate was hybridized for the oriented immobilization of antibody. The formation of self-assembled 11-MUA/oligonucleotide layer, protein G immobilization, antibody layer, and antigen binding was investigated using surface plasmon resonance (SPR). The topographies of the fabricated surfaces were observed by atomic force microscopy (AFM). When compared with the amount of antigen binding on the antibody thin film fabricated by protein G only, the proposed biosurface fabricated with both protein G and oligonucleotide showed better binding capacity, which implicates the improvement of the detection limit.     

Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers

Microarray-based technology is in need of flexible and cost-effective chemistry for fabrication of oligonucleotide microarrays. We have developed a novel method for the fabrication of oligonucleotide microarrays with unmodified oligonucleotide probes on nanoengineered three-dimensional thin films that are deposited on glass slides by consecutive layer-to-layer adsorption of polyelectrolytes. Unmodified oligonucleotide probes were spotted and immobilized on these multilayered polyelectrolyte thin films (PET) by electrostatic adsorption and entrapment on the porous structure of the PET film. The PET provides higher probe binding capacity and thus higher hybridization signal than that of the traditional two-dimensional aminosilane and poly-L-lysine coated slides. Immobilized probe densities of 3.4 x 10(12)/cm2 were observed for microarray spots on PET with unmodified 50-mer oligonucleotide probes, which is comparable to the immobilized probe densities of alkyamine-modified 50-mer probes end-tethered on an aldehyde-functionalized slide. The study of hybridization efficiency showed that 90% of immobilized probes on PET film are accessible to target DNA to form duplex format in hybridization. The DNA microarray fabricated on PET film has wider dynamic range (about 3 orders of magnitude) and lower detection limit (0.5 nM) than the conventional amino- and aldehyde-functionalized slides. Oligonucleotide microarrays fabricated on these PET-coated slides also had consistent spot morphology. In addition, discrimination of single nucleotide polymorphism of 16S rRNA genes was achieved with the PET-based oligonucleotide microarrays. The PET microarrays constructed by our self-assembly process is cost-effective, versatile, and well suited for immobilizing many types of biological active molecules so that a wide variety of microarray formats can be developed.     

Amperometric detection of DNA hybridization on a gold surface depends on the orientation of oligonucleotide chains

We tested the possibility of amperometric detection of DNA hybridization on a gold surface influenced by the immobilization of oligonucleotide giving different orientations of single stranded DNA relative to the gold surface. The DNA sensor was fabricated by chemisorption of 18-mer oligonucleotide modified by a phosphorothioate group either at its 3' or both 3' and 5' terminal. After immobilization of oligonucleotide to the gold support, the sensor was immersed in 11-mercaptoundecanoic acid (MUA) solution. Further chemisorption of MUA resulted in approximately 10-fold increase of resistance of the organic layer. Addition of complementary oligonucleotide resulted in an increase of conductivity for DNA sensor oriented perpendicular to the gold support (DNA with one thiol group), while the conductance decreased for DNA sensor with single stranded DNA oriented parallel to the gold support (with DNA modified by thiol groups at both 3' and 5' terminals). Addition of non-complementary chain resulted a slight decrease or no change of sensor conductivity. The hybridization process at both types of DNA orientations is not cooperative and can be described by Langmuir isotherms. The hybridization event on gold support has been confirmed by mass detection using the quartz crystal microbalance technique.     

Bridged nucleic acid conjugates at 6'-thiol: synthesis, hybridization properties and nuclease resistances

The bridged nucleic acid (BNA) containing a thiol at the 6'-position in the bridged structure was synthesized from the disulfide-type BNA and conjugated with various functional molecules via the thioether or the disulfide linkage post-synthetically and efficiently in solution phase. The disulfide-linked conjugate was cleaved under reductive conditions derived from glutathione and an oligonucleotide bearing a free thiol was released smoothly. Conjugated functional molecules had great effects on duplex stability with the DNA complement. In contrast, the molecules little influenced the stability with the RNA complement. Moreover, the oligonucleotides with functional groups at the 6'-position had as high or higher resistances against 3'-exonuclease than phosphorothioate oligonucleotide (S-oligo).     

Kinetics and Equilibria of the Thiol/Disulfide Exchange Reactions of Somatostatin with Glutathione

Rate and equilibrium constants are reported for the thiol/disulfide exchange reactions of the peptide hormone somatostatin with glutathione (GSH). GSH reacts with the disulfide bond of somatostatin to form somatostatin-glutathione mixed disulfides (Cys(3)-SH, Cys(14)-SSG and Cys(3)-SSG, Cys(14)-SH), each of which can react with another molecule of GSH to give the reduced dithiol form of somatostatin and GSSG. The mixed disulfides also can undergo intramolecular thiol/disulfide exchange reactions to re-form the disulfide bond of somatostatin or to interconvert to the other mixed disulfide. Analysis of the forward and reverse rate constants indicates that, at physiological concentrations of GSH, the intramolecular thiol/disulfide exchange reactions that re-form the disulfide bond of somatostatin are much faster than reaction of the mixed disulfides with another molecule of GSH, even though the intramolecular reaction involves closure of a 38-membered ring. Thus, even though the disulfide bond of somatostatin is readily cleaved by thiol/disulfide exchange, it is rapidly reformed by intramolecular thiol/disulfide exchange reactions of the somatostatin-glutathione mixed disulfides. By comparison with rate constants reported for analogous reactions of model peptides measured under random coil conditions, it is concluded that disulfide bond formation by intramolecular thiol/disulfide exchange in the somatostatin-glutathione mixed disulfides is not completely random, but rather it is directed to some extent by conformational properties of the mixed disulfides that place the thiol and mixed disulfide groups in close proximity. A reduction potential of -0.221 V was calculated for the disulfide bond of somatostatin from the thiol/disulfide exchange equilibrium constant.     

UV‐Induced Disulfide Formation and Reduction for Dynamic Photopatterning

UV‐induced disulfide formation (UV‐DF) and disulfide reduction (UV‐DR) reactions for surface functionalization and dynamic photopatterning are presented. Both photochemical reactions allow for the spatially and temporally controlled, reversible transition between thiol‐ and disulfide‐functionalized surfaces. The dynamic photopatterning strategy was demonstrated by the UV‐induced attachment, exchange, and detachment on thiol‐modified substrates.     

Reversible Inter- and Intra-Microgel Cross-Linking using Disulfides

Thermoresponsive hydrogel nanoparticles composed of poly(N-isopropylmethacrylamide) (pNIPMAm) and the disulfide-based cross-linker N,N'-bis(acryloyl)cystamine (BAC) have been prepared using a redox-initiated, aqueous precipitation polymerization approach, leading to improved stability of the disulfide bond compared to traditional thermally-initiated methods. The resultant particles demonstrate complete erosion in response to reducing conditions or thiol competition. This stands in contrast to the behavior of thermally-initiated particles, which retain a cross-linked network following disulfide cleavage due to uncontrolled chain-branching and self-cross-linking side reactions. The synthetic strategy has also been combined with the non-degradable cross-linker N,N-methylenebisacrylamide (BIS) to generate "co-cross-linked" pNIPMAm-BAC-BIS microgels. These particles are redox-responsive, swell upon BAC cross-link scission and present reactive thiols. This pendant thiol functionality was demonstrated to be useful for conjugation of thiol-reactive probes and in reversible network formation by assembling particles cross-linked by disulfide linkages.     

New approach to oligonucleotide microarrays using zirconium phosphonate-modified surfaces

A new approach to oligonucleotide arrays is demonstrated that utilizes zirconium phosphonate-derivatized glass slides. The active slides are prepared by binding Zr(4+) to surfaces terminated with organophosphonate groups previously deposited using either Langmuir-Blodgett or self-assembled monolayer methods. Oligonucleotide probes modified with a terminal phosphate bind strongly to the active zirconium phosphonate monolayer, and arrays for detecting fluorescent targets have been prepared using commercial spotting and scanning instruments. Preferred binding to the surface of the terminal phosphate of the modified probes instead of the internal phosphate diester groups is demonstrated and shown to yield increased fluorescence intensity after hybridization with labeled targets. A significant decrease in background signal is achieved by treating the slides with bovine serum albumin after spotting and before hybridization. A further increase in fluorescence after hybridization is observed when using a poly-guanine spacer between the probe oligomer and the terminal phosphate. Combining these modifications, an intensity ratio of nearly 1000 is achieved when comparing 5'-phosphate-modified 33-mer probes with unmodified probes upon hybridization with fluorescent targets.     

Dual Temperature and Thiol‐Responsive POEOMA‐Multisegmented Polydisulfides: Synthesis and Thermoresponsive Properties

New thermoresponsive polydisulfides of POEOMA multiblocks linked with disulfide bonds having redox‐responsive properties are reported. These POEOMA‐multisegmented polydisulfides were synthesized by a new method employing a combined RAFT/aminolysis and reversible thiol‐disulfide redox reaction that centers on the synthesis of new disulfide‐labeled difunctional RAFT agent. RAFT polymerization proceeded in living fashion, yielding well‐defined POEOMA copolymers with middle disulfides and terminal RAFT species. They were then used as precursors for thiol‐disulfide polyexchange induced by aminolysis and reductive reaction followed by oxidation: these polydisulfides with different molecular weights and end groups ex hibited tunable thermoresponsive properties and thiol‐responsive degradation.     

Switching the Switch: Ligand Induced Disulfide Formation in HDAC8

Human histone deacetylase 8 is a well-recognized target for T-cell lymphoma and particularly childhood neuroblastoma. PD-404,182 was shown to be a selective covalent inhibitor of HDAC8 that forms mixed disulfides with several cysteine residues and is also able to transform thiol groups to thiocyanates. Moreover, HDAC8 was shown to be regulated by a redox switch based on the reversible formation of a disulfide bond between cysteines Cys₁₀₂ and Cys₁₅₃. This study on the distinct effects of PD-404,182 on HDAC8 reveals that this compound induces the dose-dependent formation of intramolecular disulfide bridges. Therefore, the inhibition mechanism of HDAC8 by PD-404,182 involves both, covalent modification of thiols as well as ligand mediated disulfide formation. Moreover, this study provides a deep molecular insight into the regulation mechanism of HDAC8 involving several cysteines with graduated capability to form reversible disulfide bridges.     

A needle-and-thread approach to bilayer transport: permeation of a molecular umbrella-oligonucleotide conjugate across a phospholipid membrane

A di-walled molecular umbrella, composed of two choloyl groups, one spermidine moiety, and a 5-thiol(2-nitrobenzoyl) "handle", was covalently attached to a 16-mer oligonucleotide (S-dT16) through a disulfide bond. Incubation of this conjugate (1) with vesicles made from 1-palmitoyl-2-oleyol-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (95/5, mol/mol) (200 nm diameter, extrusion) that contained entrapped glutathione (GSH) at 37 degrees C resulted in the liberation of the oligonucleotide and the umbrella-bound 5-mercapto(2-nitrobenzoyl) moiety (USH) via thiolate-disulfide interchange. The appearance of USH, together with the absence of leakage of entrapped GSH and a vesicular capture of the oligonucleotide that matches the extent of USH formation, provides compelling evidence for delivery of S-dT16 into the aqueous compartment of these vesicles. In a sense, the molecular umbrella functions like a "needle" in providing a pathway for the oligonucleotide (the "thread") to cross the membrane.     

Tethered thiazole orange intercalating dye for development of fibre-optic nucleic acid biosensors

Single-stranded DNA (ssDNA) oligonucleotide in solution, or that is immobilized onto a surface to create a biosensor, can be used as a selective probe to bind to a complementary single-stranded sequence. Fluorescence enhancement of thiazole orange (TO) occurs when the dye intercalates into double-stranded DNA (dsDNA). TO dye has been covalently attached to probe oligonucleotides (homopolymer and mixed base 10mer and 20mer) through the 5′ terminal phosphate group using polyethylene glycol linker. The tethered TO dye was able to intercalate when dsDNA formed in solution, and also at fused silica surfaces using immobilized ssDNA. The results indicated the potential for development of a self-contained biosensor where the fluorescent label was available as part of the immobilized oligonucleotide probe chemistry. The approach was shown to be able to operate in a reversible manner for multiple cycles of detection of targeted DNA sequences.     

Cleaving Direct‐Laser‐Written Microstructures on Demand

Using an advanced functional photoresist we introduce direct‐laser‐written (DLW) 3D microstructures capable of complete degradation on demand. The networks consist exclusively of reversible bonds, formed by irradiation of a phenacyl sulfide linker, giving disulfide bonds in a radical‐free step‐growth polymerization via a reactive thioaldehyde. The bond formation was verified in solution by ESI‐MS. To induce cleavage, dithiothreitol causes a thiol–disulfide exchange, erasing the written structure. The mild cleavage of the disulfide network is highly orthogonal to other, for example, acrylate‐based DLW structures. To emphasize this aspect, DLW structures were prepared incorporating reversible structural elements into a non‐reversible acrylate‐based standard scaffold, confirming subsequent selective cleavage. The high lateral resolution achievable was verified by the preparation of well‐defined line gratings with line separations of down to 300 nm.     

Trace analysis of an oligonucleotide with a specific sequence using PNA-based ion-channel sensors

The gold electrodes modified with self-assembled monolayers of a 13-mer peptide nucleic acid (PNA) probe and 8-amino-1-octanethiol were used for the detection of a complementary oligonucleotide at a femtomolar level using the ion-channel sensor technique. No response to a one-base mismatched oligonucleotide was observed. The electrode surface was positively charged in a pH 7.0 buffer solution due to the protonation of an amine group of the thiol, where the electron transfer between the positively charged marker [Ru(NH3)6]3+ and the surface was hindered because of the charge-charge repulsion between them. Binding of the negatively-charged complementary oligonucleotide to the probe cancels the positive charge at the surface, and provides an excess negative charge at the surface, thereby facilitating the access of the marker to the electrode surface and its redox reaction. Using a 13-mer PNA probe for this sensing mode, we achieved the detection of the oligonucleotide at a femtomolar (approximately 10-15 M) level, improved by five orders of magnitude than the previously used 10-mer PNA probe.     

Peptide Cyclization Mediated by Metal-Free S-Arylation: S-Protected Cysteine Sulfoxide as an Umpolung of the Cysteine Nucleophile

Covalent linking of side chains provides a method to produce cyclic or stapled peptides that are important in developing peptide-based drugs. A variety of crosslinking formats contribute to fixing the active conformer and prolonging its biological activity under physiological conditions. One format uses the cysteine thiol to participate in crosslinking through nucleophilic thiolate anions or thiyl radicals to form thioether and disulfide bonds. Removal of the S-protection from an S-protected Cys derivative generates the thiol, which functions as a nucleophile. S-Oxidation of a protected Cys allows the formation of a sulfoxide that operates as an umpolung electrophile. Herein, the applicability of S-p-methoxybenzyl Cys sulfoxide (Cys(MBzl)(O)) to the formation of a thioether linkage between tryptophan and Cys has been investigated. The reaction of peptides containing Cys(MBzl)(O) and Trp with trifluoromethanesulfonic acid (TFMSA) or methanesulfonic acid (MSA) in TFA in the presence of guanidine hydrochloride (Gn ⋅ HCl) proceeded to give cyclic or stapled peptides possessing the Cys-Trp thioether linkage. In this reaction, strong acids such as TFMSA or MSA are necessary to activate the sulfoxide. Additionally, Gn ⋅ HCl plays a critical role in producing an electrophilic Cys derivative that combines with the indole by aromatic electrophilic substitution. The findings led us to conclude that the less-electrophilic Cys(MBzl)(O) serves as an acid-activated umpolung of a Cys nucleophile and is useful for S-arylation-mediated peptide cyclization.     

Thermostable DNA immobilization and temperature effects on surface hybridization

Monolayer films of nucleic acids on solid supports are encountered in a range of diagnostic and bioanalytical applications. These applications often rely on elevated temperatures to improve performance; moreover, studies at elevated temperatures can provide fundamental information on layer organization and functionality. To support such applications, this study compares thermostability of oligonucleotide monolayers immobilized to gold by first coating the gold with a nanometer-thick film (an "anchor layer") of a polymercaptosiloxane, to which DNA oligonucleotides are subsequently tethered through maleimide-thiol conjugation, with thermostability of monolayers formed via widely used attachment through a terminal thiol moiety on the DNA. The temperature range covered is from 25 to 90 °C. After confirming stability of immobilization and, more importantly, retention of hybridization activity even under the harshest conditions investigated, these thermostable films are used to demonstrate measurements of (1) reversible surface melting transitions and (2) temperature dependence of competitive hybridization, when fully matched and mismatched sequences compete for binding to immobilized DNA oligonucleotides. The competitive hybridization experiments reveal a pronounced impact of temperature on rates of approach to equilibrium, with kinetic freezing into nonequilibrium states close to room temperature and rapid approach to equilibrium at elevated temperatures. Modeling of competitive surface hybridization equilibria using thermodynamic parameters derived from surface melting transitions of the individual sequences is also discussed.     

功能化纳米金增强的谷胱苷肽电化学检测和巯基识别

以冠有大量二茂铁的纳米金微粒/抗生蛋白链菌素结合物为标记物,将其标记于生物素修饰的巯基识别试剂上,制成了具有电化学活性和纳米金放大作用的传感器.首先将双官能团的羟基琥珀酰亚胺酯自组装于电极表面上,借助两步交联反应固定含巯基的蛋白质,并且引入巯基识别试剂标记生物素的马来酰亚胺,随后利用生物素与链霉抗生物素之间的特异性吸附作用,引入功能化的纳米金.采用伏安法测定修饰在纳米金上的二茂铁,可识别和测定表面固定的蛋白质,还原型谷胱苷肽在5μmol/L～0.1mmol/L浓度范围内存在线性关系,检测限可达到1nmol/L.