Nucleic acid oligonucleotide structure

Mishra, R.K., Le Tinevez, R. and Toulme, J.J. (1996) Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection. Proc. Natl. Acad. Sci. USA, 93, 10679-10684. 

Metabolomics, Metabonomics and Metabolite Profiling 10 Ribozymes and RNA Catalysis 11 Protein-Nucleic Acid Interactions Structural Biology 12 Therapeutic Oligonucleotides... 

Nucleic Acids Database Structures of oligonucleotides and nucleic acids. 1,904... 

Recently, Switzer and co-workers have further extended the multi-stranded motifs for nucleic acids with the formation of a quintet assembly with oligonucleotides containing 2,deoxy-iso-guanosine (74). To support the quintet, metal ions larger than those appropriate for quartet stabilization were required, and Cs+ ions were found to best meet this requirement. From modeling studies, a structure in which a central Cs+ interacts with ten 02 iG atoms at a distance of 3.5 A was proposed. 

Kostenko E, Dobrikov M, Phshnyi D, Petyuk V (2001) 5 -Bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure. Nucleic Acids Res 29 3611-3620... 

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. 

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. 

First, consider oligonucleotide structure. Unmodified nucleic acid probes may be viewed as negatively charged polymers (they are polyanions)... 

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