Attachment chemistry

In this chapter, we will survey the kinds of solid supports (substrates) and surface chemistries currently used in the creation of nucleic acid and protein microarrays. Which are the best supports and methods of attachment for nucleic acids or proteins Does it make sense to use the same attachment chemistry or substrate format for these biomolecules In order to begin to understand these kinds of questions, it is important to briefly review how such biomolecules were attached in the past to other solid supports such as affinity chromatography media, membranes, and enzyme-linked immxm-osorbent assay (ELISA) microtiter plates. However, the microarray substrate does not share certain unique properties and metrics with its predecessors. Principal among these are printing, spot morphology, and image analysis they are the subjects of subsequent chapters. 

Adsorptive attachment. PLL surfaces work reasonably well for creating cDNA microarrays, but the suitability of this surface chemistry for immobilization of short oligonucleotides has been questioned. However, as we have learned, covalent attachment chemistries can be problematic as well. In either case, if the oligonucleotide is constrained too close to the surface with multiple points of contact, it may not be able to fully participate in hybridization. 

The passivation of silicon, motivated by the centrality of this semiconductor to the microelectronics industry, has been well studied. In addition to excellent passivation allowed by the silicon oxide, silicon can also be passivated with silicon nitride (Si3N4), other dielectrics, metal layers, and hydrogen. Here we focus only on hydride termination, since in addition to acting as a passivating layer for the underlying silicon, the hydride groups provide a versatile starting point for subsequent attachment chemistry. 

IV. STRONGLY INTERACTING SYSTEMS A. Surface Attachment Chemistry... 

As discussed in the introduction, a major motivation for the development of methods to controllably functionalize silicon surfaces is the opportunity to create novel hybrid organic/silicon devices. By integrating organic molecules with silicon substrates it should be possible to expand the functionality of conventional microelectronic devices. Possibilities include high-density molecular memory and logic as well as chemical and biochemical sensors. Realization of these opportunities requires not only the development of the attachment chemistries, as discussed in the previous sections, but also detailed studies of the electronic properties of the resulting surfaces. 

The progress in developing controlled attachment chemistries has opened up a range of opportunities for designing and fabricating molecular scale electronic devices based on these monolayers. Electrical transport through alkyl monolayers on silicon has been relatively well studied, particularly using electrochemical methods and Hg drops. The work of... 

While the discussion in this chapter has focused on molecular layers on single crystal silicon surfaces, the attachment chemistries discussed here could easily be applied to functionalize silicon nanowires or nanoparticles. Silicon nanowires have been shown to exhibit interesting electrical transport characteristics and have been used to fabricate nanoscale pn junctions [95], field effect transistors [96] and biochemical sensors [97-100]. However, all these interesting phenomena have been reported on oxidized silicon nanowires. It is likely that better control over the surface properties, as could be achieved by employing some of the chemistry discussed here, could significantly improve the performance of these nanowire-based devices. From another perspective, silicon nanowires could prove extremely... 

Manning, M., Harvey, S., Galvin, P. and Redmond, G. (2003). A versatile multi-platform biochip surface attachment chemistry. Mater. Sci. Eng. C... 

Covalent Attachments Based on Organosilanes. Organosilane reagents are known to form stable chemical bonds to the surfaces of metal oxide electrodes (20, In). Included in this category are silane attachments to thin platinum oxide layers on platinum which are formed when clean Pt surfaces are held at positive potentials (+1.0 V vs. SCE) in aqueous solution. The subsequent attachment chemistry is based on the known propensity of chloro- and alkoxy-silanes to undergo reactions in which Si-O-M bonds are formed by metathesis, e.g.,... 

The shorthand nomenclature used here and later to describe the attachment chemistry is imposed by the absence of structural information concerning either the surface or the mode of binding of the silane to the surface. 

Based on measuring the change of charges on DNA monolayer on the surface of electrode, electrochemical method can be used in monitoring DNA hybridization processes [5], [6]. This is or detection of bio-molecules in terms of electrochmetrical methods. Hence, enhancement of the sensitivity of the electrodes of the sensors is a key for the improvement of the sensitivity of the sensors. Here, the sensitivity of the electrodes of the sensors is not only associated with the surface attachment chemistry but also related to the electric characteristics of the contact between the probe molecule and the surface of the electrodes. 

Many of the early first generation PEG reagents primarily utilized amine attachment chemistry... 

An important PEG attachment chemistry for reaction with amino groups involves PEG aldehydes. In this chemistry, PEG aldehyde reacts with amino group on the target protein to form a reversible Schiff base linkage. The imine intermediate is then reduced with a suitable reductant such as sodium cyanoborohydride (Eigure 24.3). The most notable feature of this reaction is that, when conducted at low pH, the reaction is specific for the amino terminus of the protein [42,43]. The reason for this selectivity is that, relative to other nucleophilic residues in the molecule, the amino terminus has a lower pKa. Therefore, this reaction scheme can be used to reduce the side reactions that form multipegylated products in other amine selective chemistries. 

The basic elements required for the DNA microarray are the solid substrate, the attachment chemistry of the probe to the solid support, the approach adopted to spot the probes at particular locations of the two-dimensional array, the method employed to bring the solution target to the appropriate location of the array (passive or active), and the readout modality. A brief discussion of some of these important elements is given in Sects. 3.2.1-3.2.3. 

McCarely et al. [219, 220] described a simplified photomodification protocol of PMMA and PC substrates through direct and controlled UV exposure of the substrates in an oxygen-rich environment to yield surface carboxylic acid moieties. Patterns of carboxylic acid sites could be formed by exposure of the polymers in auto UV irradiation at 254 nm with a power density of 15 mW/cm for 60 min without significant physical damage to the polymer surface. The so-formed chemical patterns allowed for further functionalization to yield arrays or other structured architectures through covalent attachment chemistry. 

Vaidya A A, Norton M L (2004). DNA attachment chemistry at the flexible silicone elastomer surface toward disposable microarrays. Langmuir. 20 11100-11107. 

Includes thermochemical safety and environmental. Attaches chemistry and microbiology documents as needed. 

Attachment chemistry Electrostatic for DNA and proteins, Covalent via Schiff base. 

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