Construction of oligonucleotide arrays on a glass surface using a heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA)

Surface functionalization chemistries on highly sensitive silica-based sensor chips

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor. Based on these analyses, the sensor surfaces modified with glutaraldehyde (Glu) and carbonyldiimidazole were found to be good for molecules of different sizes. In addition, it can be inferred that the Glu-modified surface may be suitable for small molecules with diameters around 5 nm owing to its surface roughness. The modified surface with carbonyldiimidazole is suitable for the direct immobilization of larger molecules especially for biomolecular assemblies without intermediate chemical modifications.

Waveguide-mode sensors as aptasensors

Aptamers are artificial nucleic acid ligands that can be generated by in vitro selection through partition and amplification. Aptamers can be generated against a wide range of biomolecules through the formation of versatile stem-loop structures. Because aptamers are potential substitutes for antibodies and drugs, the development of an aptamer-based sensor (aptasensor) is mandatory for diagnosis. We previously reported that waveguide-mode sensors are useful in the analysis of a wide range of biomolecular interactions, including aptamers. The advantages of the waveguide-mode sensor that we developed include physical and chemical stability and that higher sensitivity can be achieved with ease by perforating the waveguide layer or using colored materials such as dyes or metal nanoparticles as labels. Herein, we provide an overview of the strategies and applications for aptamer-based analyses using waveguide-mode sensors.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon]

The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

Evaluation of nucleic acid duplex formation on gold over layers in biosensor fabricated using Czochralski-grown single-crystal silicon substrate

With a view to developing an economical and elegant biosensor chip, we compared the efficiencies of biosensors that use gold-coated single-crystal silicon and amorphous glass substrates. The reflectivity of light over a wide range of wavelengths was higher from gold layer coated single-crystal silicon substrates than from glass substrates. Furthermore, the efficiency of reflection from gold layers of two different thicknesses was examined. The thicker gold layer (100 nm) on the single-crystal silicon showed a higher reflectivity than the thinner gold film (10 nm). The formation of a nucleic acid duplex and aptamer-ligand interactions were evaluated on these gold layers, and a crystalline silicon substrate coated with the 100-nm-thick gold layer is proposed as an alternative substrate for studies of interactions of biomolecules.

Chemical strategies for immobilization of oligonucleotides

The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area.

Immobilization of self-quenched DNA hairpin probe with a heterobifunctional reagent on a glass surface for sensitive detection of oligonucleotides

A new sensitive method for the detection of nucleic acids on a glass surface has been described. The self-quenched DNA hairpin probe is immobilized on a glass surface utilizing heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(isothiocyanatomethyl)-cyclohexane-1-carboxamide (TPICC). In the closed state fluorescence intensity was quenched due to the presence of guanosine residues in close vicinity of fluorophore while on hybridization with perfectly matched complementary target strand fluorescence was restored. Efficiency and specificity of immobilization as well as thermal stability at variable temperature and pH conditions have been discussed in detail. The method employed has potential for the detection of single nucleotide variations and other diagnostic studies.

Polymer supported synthesis of aminooxyalkylated oligonucleotides, and some applications in the fabrication of microarrays

A new protocol has been described for solid phase preparation of 3'- and 5'-aminooxylalkylated oligonucleotides using commercially available reagents. This involves attachment of linker 4 either with an LCAA-CPG support via succinoylation followed by synthesis (3'-aminooxyalkylated oligomers) or formation of its phosphoramidite 6 followed by coupling with desired oligomer (for generating 5'-aminooxyalkylated oligomers). Both the routes produced modified oligonucleotides in sufficiently high yields and purity (on HPLC) via conventional oligonucleotide synthesis on an automated synthesizer and deprotection step using aqueous ammonia (16 h, 60 degrees C). Aminooxyalkylated oligonucleotides were used to construct microarrays on glass surface (biochips). The performance of the biochips was evaluated by immobilizing modified oligonucleotides on epoxylated glass microslides under different sets of conditions with respect to pH, temperature and time. Further, the constructed microarrays were successfully used for detection of nucleotide mismatches and bacterial typhoid.

A facile method for the construction of oligonucleotide microarrays

In recent years, the oligonucleotide-based microarray technique has emerged as a powerful and promising tool for various molecular biological studies. Here, a facile protocol for the construction of an oligonucleotide microarray is demonstrated that involves immobilization of oligonucleotide-trimethoxysilyl conjugates onto virgin glass microslides. The projected immobilization strategy reflects high immobilization efficiency ( approximately 36-40%) and signal-to-noise ratio ( approximately 98), and hybridization efficiency ( approximately 32-35%). Using the proposed protocol, aminoalkyl, mercaptoalkyl, and phosphorylated oligonucleotides were immobilized onto virgin glass microslides. Briefly, modified oligonucleotides were reacted first with 3-glycidyloxypropyltriethoxysilane (GOPTS), and subsequently, the resultant conjugates were directly immobilized onto the virgin glass surface by making use of silanization chemistry. The constructed microarrays were then used for discrimination of base mismatches. On subjecting to different pH and thermal conditions, the microarray showed sufficient stability. Application of this chemistry to manufacture oligonucleotide probe-based microarrays for detection of bacterial meningitis is demonstrated. Single-step reaction for the formation of conjugates with the commercially available reagent (GOPTS), omission of capping step and surface modification, and efficient immobilization of oligonucleotides onto the virgin glass surface are the key features of the proposed strategy.

A simple gold nanoparticle-mediated immobilization method to fabricate highly homogeneous DNA microarrays having higher capacities than those prepared by using conventional techniques

A simple, highly efficient immobilization method to fabricate DNA microarrays, that utilizes gold nanoparticles as the mediator, has been developed. The fabrication method begins with electrostatic attachment of amine-modified DNA to gold nanoparticles. The resulting gold-DNA complexes are immobilized on conventional amine or aldehyde functionalized glass slides. By employing gold nanoparticles as the immobilization mediator, implementation of this procedure yields highly homogeneous microarrays that have higher binding capacities than those produced by conventional methods. This outcome is due to the increased three-dimensional immobilization surface provided by the gold nanoparticles as well as the intrinsic effects of gold on emission properties. This novel immobilization strategy gives microarrays that produce more intense hybridization signals for the complementary DNA. Furthermore, the silver enhancement technique, made possible only in the case of immobilized gold nanoparticles on the microarrays, enables simple monitoring of the integrity of the immobilized DNA probe.

Immobilization chemistries

Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.

2-O-[2-(4,4'-dimethoxytrityloxyethyl)]-hydroxy acetaldehyde: a universal reagent for spectrophotometric estimation of polymer-supported functional groups

A new universal reagent, 2-O-[2-(4,4'-dimethoxytrityloxyethyl)]-hydroxy acetaldehyde (DEA), has been synthesized and used for the estimation of surface-bound aminoalkyl, aminooxyalkyl, hydrazinyl, and semicarbazide functions. The reaction completes in just 10 min in the case of aminoalkylated supports and 30 min in hydrazinyl supports, whereas it takes approximately 60 min in both aminooxyalkylated and semicarbazide-modified polymer supports. DEA-treated supports, including glass slides and PP films on exposure to acid, liberates 4,4'-dimethoxytrityl cation, which was measured spectrophotometrically to estimate these functionalities. The method estimates accessible functional groups, useful for calculating the quantity of the ligands to be immobilized.

Influence of nanometric holes on the sensitivity of a waveguide-mode sensor: label-free nanosensor for the analysis of RNA aptamer-ligand interactions

Evanescent-field-coupled (EFC) waveguide-mode sensors can be used to detect nucleic acids or proteins from the changes in the local index of refraction upon adsorption of the target molecule on a waveguide surface. We recently described an EFC waveguide-mode sensor in which nanometric holes on a waveguide film resulted in an improved sensitivity in the analysis of the interactions of biomolecules. In the present study, we have shown that sensitivity depends upon the diameter of the holes, where increase in diameter of holes increases spectral shift resulting in an improved sensitivity. Using this improved EFC waveguide-mode sensor, we could detect interactions between RNA and a small ligand, cyanocobalamin (vitamin B 12), and between RNA and a protein (human coagulation factor IXa). These two interactions were monitored on surfaces modified with biotin-streptavidin-biotin and N-(2-trifluoroethanesulfonatoethyl)- N-(methyl)triethoxysilylpropyl-3-amine, respectively.

Construction of oligonucleotide microarrays (biochip) using heterobifunctional reagents

A number of hetero- and homobifunctional reagents have been reported to immobilize biomolecules on a variety of supports. However, efforts are on to search for a method, which is relatively simple, involving minimum of steps, cost effective, easy to reproduce, and that produces stable oligonucleotide arrays. Two new reagents, viz., [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], and [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide] have been designed considering the above points. These reagents contain different functional groups at their two ends. In [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], one end (triethoxysilyl) is capable of binding to the virgin glass surface and the other one consists of trifluoroethanesulfonate (tresyl) function specific toward aminoalkyl and mercaptoalkyl functionalities, which are easy to introduce at the 3'- or 5'-end of oligonucleotides. Likewise, in [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide], one end consists of photoactivatable moiety (anthraquinone) capable of reacting to a C-H containing surface and the tresyl function at the other end reacts specifically with aminoalkyl and mercaptoalkyl functionalities in modified oligonucleotides. These reagents have successfully been utilized to construct a number of oligonucleotide arrays and subsequently used for the detection of mismatches.

Choice of polymer matrix, its functionalization and estimation of functional group density for preparation of biochips

Oligonucleotide microarray has become an important and powerful tool for various genomic analyses, where, unlike conventional methods, one can identify simultaneously a large number of targets in a given sample. Postsynthesis immobilization, the most widely used method, involves the noncovalent and covalent fixing of suitably modified oligonucleotides on the solid supports. Among the various functional groups aminoalkyl, hydroxyalkyl, mercaptoalkyl, aldehyde, epoxy, and carboxyl the most frequently used functional groups on the polymeric surfaces. Because glass and polypropylene, the most widely used materials, are nonporous in nature, the functional groups density on the surface remains very low. In order to know the exact concentration of a ligand to be immobilized, it is essential to estimate the accessible functional groups on these surfaces. For this purpose, sensitive methods are required to estimate exact density of available functional groups on the surfaces. Apart from physical methods, a number of sensitive chemical methods, by making use of high extinction coefficient of 4,4'-dimethoxytrityl cation (epsilon(498) = 70,000 L mol-1 cm-1), have been reported to estimate accessible functional groups on the glass based polymer supports. In this chapter, use of these reagents for spectrophotometric determination of functional group density on glass microslides and polypropylene film has been discussed.

Immobilization of oligonucleotides on glass surface using an efficient heterobifunctional reagent through maleimide-thiol combination chemistry

An efficient heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl) cyclohexanamide (TPMC), was developed for the immobilization of thiol-modified oligonucleotides on an unmodified glass surface. The heterobifunctionality of the reagent was used for the construction of a DNA microarray in which the triethoxysilyl functionality has specificity toward a glass surface, whereas the maleimide functionality has thiol-modified oligonucleotides via a stable thioether linkage. Immobilization of DNA was achieved by two alternative approaches. In the first approach, the reagent TPMC was treated with oligonucleotides to get triethoxysilyl-oligonucleotide conjugate, which was then covalently attached via specific triethoxysilyl functionality to an unmodified glass surface. In the second approach, the reagent was first covalently linked with an unmodified glass surface to get maleimide functionality on a glass surface, which was then used for the immobilization of oligonucleotides via a stable thioether linkage. The applicability of the reagent was explored by hybridization studies with the fluorescein-labeled complementary DNA strand and in mismatch discrimination.

Oligonucleotide microarrays: immobilization of phosphorylated oligonucleotides on epoxylated surface

A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization strategy has been analyzed for its performance in DNA microarray under both microwave and thermal conditions. It reflects high immobilization efficiency ( approximately 23%), and signal-to-noise ratio ( approximately 98) and resulted in high hybridization efficiency ( approximately 36%) in comparison to those obtained with standard methods, viz., NTMTA ( approximately 9.76%) and epoxide-amine ( approximately 9.82%). The probes immobilized through the new strategy were found to be heat-stable, since the performance of microarray decreased by only approximately 7% after subjecting it to 20 PCR-like heat cycles, suggesting that the chemistry could be used in integrated PCR/microarray devices. The immobilization of probes following the proposed chemistry resulted in spots of superior quality in terms of spot morphology, spot homogeneity, and signal reproducibility. The constructed microarrays have been successfully used for the discrimination of nucleotide mismatches. In conclusion, these features make the new immobilization strategy ideal for facile, efficient, and cost-effective manufacturing of DNA microarrays.

N-(3-Triethoxysilylpropyl)-4-(N'-maleimidylmethyl)cyclohexanamide (TPMC): a heterobifunctional reagent for immobilization of oligonucleotides on glass surface

A new heterobifunctional reagent, namely, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl)cyclohexanamide (TPMC) was developed and its potentiality for fixing of thiol (-SH) modified oligonucleotides were tested. The covalent attachment of oligonucleotides with the reagent was achieved through its maleimide functionality at one end via stable thioether linkage while the other end bearing triethoxysilyl functionality has been utilized for coupling with the virgin glass surface with simplified methodologies. Immobilization of oligonucleotides was achieved by two alternating ways. The PATH-1 involves formation of conjugate of reagent and SH-modified oligonucleotides through thioether linkage and was subsequently immobilized on unmodified glass surface through triethoxysilyl group and alternatively, PATH-2 involves reaction of reagent first with unmodified glass surface to get maleimide functionality on the surface and then the SH-modified oligonucleotides were immobilized via thioether linkage. The specificity of immobilization was tested by hybridization study with complementary fluorescein labeled oligonucleotide strand.

N-(Iodoacetyl)-N'-(anthraquinon-2-oyl)-ethylenediamine (IAED): a new heterobifunctional reagent for the preparation of biochips

Design and synthesis of a new heterobifunctional reagent, N-(iodoacetyl)-N'-(anthraquinon-2-oyl)-ethylenediamine (IAED), have been described for the preparation of oligonucleotide-based biochips. The performance of the featured reagent is probed by the immobilization of thiolated and thiophosphorylated oligonucleotides on modified glass microslides via two routes (routes A and B). The immobilization procedure was accelerated by performing a chemical reaction between thiolated oligomers and the iodoacetyl moiety of the reagent under microwaves (MW), where it is completed in just 10 min. The quality of the constructed oligonucleotide microarrays was tested by performing a hybridization assay with a complementary target and subsequently used for the detection of base mismatches. The immobilized probes were found to be thermally stable.

An improved gel-based DNA microarray method for detecting single nucleotide mismatch

3-D polyacrylamide gel-based DNA microarray platforms provide a high capacity for nucleic acids immobilization and a solution-mimicking environment for hybridization. However, several technological bottlenecks still remain in these platforms, such as difficult microarray preparation and high fluorescent background, which limit their application. In this study, two new approaches have been developed to improve the convenience in microarray preparation and to reduce the background after hybridization. To control the polymerization process, solutions containing acrylamide-modified oligonucleotide, acrylamide, glycerol and ammonium persulfate are spotted onto a functionalized glass slide, and then the slide is transferred to a vacuum chamber with TEMED, so that TEMED is vaporized and diffused into the spots to induce polymerization. By applying an electric field across a hybridized microarray to remove the nonspecifically bound labeled targets, this approach can solve the problem of high fluorescent background of the gel-based microarray after hybridization. Experimental results show that our immobilization method can be used to construct high quality microarrays and exhibits good reproducibility. Moreover, the polymerization is not affected by PCR medium, so that PCR products can be used for microarray construction without being treated by commercial purification cartridges. Electrophoresis can improve the signal-to-noise significantly and has the ability to differentiate single nucleotide variation between two homozygotes and a heterozygote. Our results demonstrated that this is a reliable novel method for high-throughput mutation analysis and disease diagnosis.

N-(3-Triethoxysilylpropyl)-6-(N-maleimido)-hexanamide: An efficient heterobifunctional reagent for the construction of oligonucleotide microarrays

Synthesis of a new heterobifunctional reagent, N-(3-triethoxysilylpropyl)-6-(N-maleimido)-hexanamide (TPMH), for the preparation of oligonucleotide microarrays is described. Its triethoxysilyl function is specific toward virgin glass surface and maleimide function undergoes conjugate addition to 3'- or 5'-thiol-modified oligonucleotides. The construction of microarrays using TPMH has been realized via two routes. In Route A, TPMH was reacted first with 3'- or 5'-thiol-modified oligonucleotide under microwaves, thereby producing oligonucleotide-triethoxysilyl conjugate in 15min, which was then brought in contact with virgin glass microslide, resulting in immobilization of an oligonucleotide sequence. In Route B, immobilization involves generation of maleimide functions on virgin glass surface by the reaction with TPMH, followed by coupling with thiol-modified oligonucleotides under microwaves in 15 min to produce surface-bound oligonucleotides. The microarrays constructed using both routes were analyzed by hybridizing with tetrachlorofluorescein-labeled complementary oligonucleotide. Subsequently, these microarrays were successfully used in the discrimination of single and double nucleotide mismatches based on fluorescence intensity.

An efficient and versatile approach for the construction of oligonucleotide microarrays

A new immobilization chemistry for covalent attachment of phosphorylated oligonucleotides on epoxy-activated glass surface via opening of oxirane ring is described. The proposed strategy results in excellent immobilization efficiency, spot homogeneity, and morphology. The constructed microarray was successfully demonstrated for discrimination of nucleotide mismatches.

Spectrophotometric estimation of functional groups on microslides for preparation of biochips

A universal reagent 1-O-(4,4'-dimethoxytrityl)-6-aminohexanol (DTAH) is described for the estimation of surface-bound functionalities (epoxy, aldehyde, and carboxyl) required for preparation of oligonucleotide arrays (biochips). The method involves the reaction of universal reagent DTAH with surface-bound functionality under microwaves for 10 min, followed by washings to remove the excess reagent. In the subsequent step, a weighed amount of DTAH-treated surface is exposed to acid to liberate 4,4'-dimethoxytrityl cation, which is measured at 505 nm to determine the functional group loading on the surface.

Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy

Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the incidence of molecular interactions through the simultaneous analysis, within a single experiment, of a number of samples containing small quantities of potential targets, in the presence of thousands of variables. A simple, accurate and robust methodology was established and is here presented, for the assembling of DNA sensors on the unoxidized, crystalline Si(100) surface, by loading controlled amounts of a monolayer DNA-probe through a two-step procedure. At first a monolayer of a spacer molecule, such as 10-undecynoic acid, was deposited, under optimized conditions, via controlled cathodic electrografting, then a synthetic DNA-probe was anchored to it, through amidation in aqueous solution. The surface coverage of several DNA-probes and the control of their efficiency in recognizing a complementary target-DNA upon hybridization were evaluated by fluorescence measurements. The whole process was also monitored in parallel by Atomic Force Microscopy (AFM).