Nucleic acids oligonucleotide arrays

Ylstra B, Van den IJssel P, Carvalho B, et al. BAC to the future or oligonucleotides a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 2006 34 445 150. 

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

DNA arrays have been categorized into different formats based upon what is immobilized to the surface (also known as the solid phase, substrate, or chip) and what is captured from the sample solution. Definitions change depending upon the format. For the classic Southern dot blot, the sample was first spotted down on the surface, cross-linked, and then bathed with a radio-labeled oligonucleotide under hybridization (complementary nucleic acid strand base-pairing) conditions to detect the presence of a parhcular sequence within the sample. This was called probing. The oligonucleohde... 

Fung, E.T., Thulasiraman, V., Weinberger, S.R., and Dalmasso, E.A., Protein biochips for differential profiling, Curr. Opinion Biotechnol., 12, 65-69, 2001. Garland, P.B. and Serafinowski, P.J., Effects of stray light on the fidelity of photo-directed oligonucleotide array synthesism Nucleic Acid Res., 30(19), 1-9, 2002. 

Guo, Z., Guilfoyle, R.A., Thiel, A.J., Wang, R., and Smith, L.M., Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acid Res., 22(24), 5456-5465, 1994. 

Shchepinov, M.S., Case-Green, S.C., and Southern, E.M., Steric factors influencing hybridization of nucleic acids to oligonucleotide arrays. Nucleic Acid Res., 25(6), 1155-1161, 1997. 

Southern, E.M., Maskos, U., and Elder, J.K., Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides evaluation using experimental models, Gmomics, 13, 1008-1017, 1992. 

Robert (Bob) Matson, Ph.D., is a senior staff scientist in the Advanced Technology Center at Beckman Coulter, Inc., Fullerton, California. He has been involved in the development of both nucleic acid and protein array-based technology for the past 13 years. His initial introduction to array technology began in collaboration with Sir Edwin Southern in developing an in situ oligonucleotide array synthesis platform for the corporation. Later work by Dr. Matson and his research team produced some of the first plastic microplate-based microarrays. Beckman Coulter recently launched the pi te based upon the microplate "array of arrays" concept. 

An array of oligonucleotide which is composed of 20 80-mer oligos, or peptide nucleic acid probes, is synthesized either in situ (i.e., on-chip) or using conventional synthesis followed by on-chip immobilization. The resultant DNA array is then exposed to the labeled sample of DNA, hybridized, and the identity/abundance of complementary sequences determined. This method was developed at Affymetrix, Inc. and called DNA chips. Today, oligonucleotide-based chips are manufactured by many companies using alternative in situ synthesis or depositioning technologies. 

Niemeyer CM, Sano T, Smith CL, Cantor CR. Oligonucleotide-directed self-assembly of proteins Semisynthetic DNA-streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates. Nucleic Acids Res 1994 22(25) 5530-5539. 

Raddatz S, Mueller-Ibeler J, Kluge J, Wafi L, Burdinski G, Havens JR, Onofrey TJ, Wang D, Schweitzer M (2002) Hydrazide oligonucleotides new chemical modification for chip array attachment and conjugation. Nucleic Acid Res 30 4793-4802... 

The quality and reliability of microarray results largely depend on the quality and consistency of both the substrate and the reagents used to manufacture and process the arrays, but also on the considerable variation in the experimentalist s skills. A number of different substances have been tested as the solid support for nucleic acid immobilization [7,8], but glass slides are generally favored for DNA and oligonucleotide microarrays [9-11]. Optimal... 

While the capture on DNA chips of fluorophore-labelled targets, and the extension of arrayed primers with fluorophore-labelled nucleotides has been widely used for some time, it is only more recently that assay formats have developed that utilize immobilized nucleic acids already modified with fluorophores. Fundamental analyses of surface monolayer structures and chemistries can be readily performed by immobilizing such modified oligonucleotides into SAM structures [105,106], but it is those interactions that can be monitored using fluorescence quenching or fluorescence resonance energy transfer (FRET) that have gained the most attention. 

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