Fabrication of DNA arrays

Arrays come in many different sizes and forms. For standard applications they can be purchased ready to use with the appropriate oligomers already immobilised. For 

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Different types of NA probes can be used in the fabrication of DNA arrays complementary DNA (cDNA), oligonucleotides (OND) and peptide nucleic acids (PNA). 

Silicon wafers can act as substrates in the fabrication of DNA arrays. Chemical functionalization of silicon surfaces is compUcated by the fact that silicon spontaneously oxidizes in air to produce an amorphous sihca layer. 

The attractive characteristics of electrodes based on conductive diamond films have led a number of research groups around the world to use these electrodes for electroanalytical applications. As a way to extend the analytical capabilities of diamond electrodes, researchers have also become interested in chemically modifying the diamond surface. One of the principal motivations is to impart selectivity for analytical purposes. Closely associated with this is the desire to impart electrocatalytic activity for specific electrochemical reactions, making use of diamond as a highly robust support. One of the more interesting recent applications of the modified diamond surface is the fabrication of DNA arrays. 

Constructing arrays with longer oligomers enables the analysis of longer stands of sample DNA. However, fabrication of the array becomes more complex as the required number of spots increases exponentially. For example, octanucleotides... 

Chow DC, Lee WK, Zauscher S, Chilkoti A (2005) Enzymatic fabrication of DNA nanostructures extension of a self-assembled oligonucleotide monolayer on gold arrays. J Am Chem Soc 127 14122-14123... 

Wegner GJ, Lee NJ, Marriott G, Com RM (2003) Fabrication of histidine-tagged fusion protein arrays for surface plasmon resonance imaging studies of protein-protein and protein-DNA interactions. Anal Chem 75 4740-4746... 

DNA arrays are fabricated by immobilizing the complementary DNA (cDNA) onto a solid substrate such as silicon, nylon or glass. This can be achieved by robotic printing of polymerase chain reaction (PCR) products (also known as direct-deposition approach), photolithographical synthesis of complementary oligonucleotides or piezoelectric inkjet printing of PCR products (also known as indirect-deposition approach). 

A typical DNA array fabrication and application process involves three major steps. First, nucleic acids (the capture sequences or probes) are immobilized at discrete positions on surface activated substrates. Secondly, the resulting array is hybridized with a complex mixture of fluorescently labelled nucleic acids (the target), and thirdly subsequent to hybridization, the fluorescent markers are detected using a high-resolution scanning laser that quantifies the interaction. This chapter focuses on the first of these processes and provides the reader with an overview of substrates, surface activation methods and dehvery systems available for nucleic acid immobilization. 

Classic solid phase substrates used in biotesting, such as microtiter plates, membrane filters or microscope slides, have been the first supports used for NA immobilization in array fabrication [27]. Desired attributes of any DNA array substrate include (i) chemical homogeneity (ii) thermal and chemical stability (iii) ability to control surface chemical properties such as polarity or hydrophobicity (iv) ability to be activated with a wide range of chemical functionalities (v) reproducibihty of the surface modification processes involved (vi) inert with respect to enzymatic activity especially ones involved in DNA manipulation and (vii) ultra-low intrinsic fluorescence. 

The term membrane encompasses a wide range of potential substrates that can be used for the immobihzation of NAs. It includes traditional polymeric cast membranes , such as nitrocellulose, nylon or polypropylene, and also innovations such as ceramic or track-etched materials (alumina membranes). Membranes as substrates in DNA array fabrication can possess advantages over other surfaces their surface area can be much greater (200% more in cast membranes and 500% more in aliuniniiun membranes) than certain other alternatives. This is primarily a consequence of their possession of pores. 

All of the supports discussed previously can be used in the fabrication of flat ( positional ) DNA arrays. New approaches to fabricating and applying arrays are continuously being developed, some of which do not rely on... 

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