DNA oligonucleotides probes

Metal NPs have received tremendous attention in the field of bio-analytical science, in particular the sequence-specific DNA detection [23,24]. This is attributed to their unique properties in the conjugation with biological recognition elements (e.g., DNA oligonucleotide probe) as well as in the signal transduction with optical [22,25], electrical [26], microgravimetric [27] and electrochemical [23,28-30] methods. 

Radio-labeled single stranded DNA oligonucleotide probes are allowed to anneal with the target strand in an oligonucleotide hybridization analyses. 

Saiki RK, Walsh PS, Levbnson CH., Erlich HA (1989) Genetic analysis of amplified DNA with immobilized sequence specific oligonucleotide probes. Proc. Natl Acad Sd USA 86 6230-6234. 

Nicolau DV, Sawant PD (2005) Scanning Probe Microscopy Studies of Surface-Immobilised DNA/Oligonucleotide Molecules. 260 113-160 Niessen HG, Woelk K (2007) Investigations in Supercritical Fluids. 276 69-110 Nilsson P, Olofsson K, Larhed M (2006) Microwave-Assisted and Metal-Catalyzed Coupling Reactions. 266 103-144... 

Figure 1.57 Base-pairing can occur between complementary bases in opposing oligonucleotide strands. These predictable interactions form the basis for using synthetic oligonucleotide probes to target particular DNA sequences.

Cyanine dyes also are used as labels for oligonucleotide probes. Unlike the hydrophilic cyanine dyes valuable for protein labeling, the use of dye-phosphoramidite compounds to synthesize DNA or RNA probes typically requires the use of more hydrophobic dye structures to make them compatible with the solvents and reactions of oligonucleotide synthesis. Thus, indol cyanines containing few or no sulfonates are used in these applications to label oligos for applications such as array detection, hybridization assays, and RT-PCR. 

To modify the unique chemical groups on nucleic acids, novel methods have been developed that allow derivatization through discrete sites on the available bases, sugars, or phosphate groups (see Chapter 1, Section 3 for a discussion of RNA and DNA structure). These chemical methods can be used to add a functional group or a label to an individual nucleotide or to one or more sites in oligonucleotide probes or full-sized DNA or RNA polymers. 

When photobiotin is irradiated in the presence of DNA the reaction process nonselectively couples a biotin label to every 100-200 base residues. The result is an oligonucleotide probe detectable by the use of (strept)avidin conjugates. The uses of photobiotin for DNA or RNA modification are summarized in Chapter 11, Section 4. 

Bugawan, T.L., Begovich, A.B., and Erlich, H.A. (1990) Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence-specific oligonucleotide probes. Immunogenetics 32, 231-241. 

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