Oligonucleotides and Nucleic Acids

The power and advantages of assessing cellular processes at their most fundamental level is propelling the science of oligonucleotide probe detection into one of the most prominent positions in bioconjugate chemistry. Oligonucleotide arrays containing hundreds or thousands of 

In this section, the chemistry and structure of nucleic acids and oligonucleotides is discussed with a view to creating functional conjugates with detectable molecules. The corresponding strategies and protocols associated with DNA or RNA modification and conjugation can be found in Chapter 27. 

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Hemiacetal hydroxyl groups of carbohydrate molecules also may be coupled to amine-containing molecules to form N-glycosidic linkages, such as those in nucleic acids and oligonucleotides. 

Modification of Nucleic Acids and Oligonucleotides with Cystamine... 

Other non-protein molecules, such as nucleic acids and oligonucleotides, may not normally possess primary amines of sufficient nucleophilicity to react with common modification reagents. The ability to add amine functionalities to these molecules is sometimes the only route to successful conjugation. Creating amines at specific sites within these molecules allows for site-directed modification at known positions, thus better assuring active conjugates once formed. 

The formation of an aldehyde group on a macromolecule can produce an extremely useful derivative for subsequent modification or conjugation reactions. In their native state, proteins, peptides, nucleic acids, and oligonucleotides contain no naturally occurring aldehyde residues. There are no aldehydes on amino acid side chains, none introduced by post-translational modifications, and no formyl groups on any of the bases or sugars of DNA and RNA. To create reactive aldehydes at specific locations within these molecules opens the possibility of directing modification reactions toward discrete sites within the macromolecule. 

The following sections describe the major enzymatic and chemical modification procedures used to label nucleic acids and oligonucleotides. 

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