Nucleic acids alternative base pairs

Ion-exchange HPLC can also be useful in the separation of larger nucleic acid molecules. One such application is as an alternative to CsCl density gradient centrifugation in the preparation of plasmids. Plasmid molecules typically consist of between 1000 and 10 000 base pairs. The plasmid is first isolated from the bacterial cell by alkaline lysis and pure plasmid obtained from this crude extract by a one-step chromatographic separation. 

Where nucleic acids are concerned, the enhanced hydrophobicity of abiotic polyfluorinated aromatic bases (e.g., tetrafluorobenzene or tetrafluoroindole deoxyribose derivatives) was exploited as an alternative to natural hydrogen bonding to achieve selective and stable nucleic acid base pairing in duplex DNA [85], The DNA replication was examined using polyfluorinated-nucleotide analogs as substrates. A DNA polymerase active site was able to process the polyfluorinated base pairs more effectively than the analogous hydrocarbon pairs, demonstrating hydrophobic selectivity of polyfluorinated bases for other polyfluorinated bases [86]. 

Many DNA-based biosensors (genosensors) are based on the ability of complementary nucleic acid strands to selectively form hybrid complexes. The complementary strands anneal to one another in a Watson-Crick manner of base pairing. Hybridization methods used today, such as microhtre plates or gel-based methods, are usually quite slow, requiring hours to days to produce reliable results, as described by Keller and Manak [10]. Biosensors offer a promising alternative for much faster hybridization assays. 

More recently, the systematic exploration of alternative nucleic-acid systems from RNA s structural neighborhood has presented us with a further challenging observation. TNA, the threose-analog of RNA (a system containing only four instead of five carbon atoms in its sugar building block), turns out to be a marvelous Watson-Crick base-pairing system. Indeed, not only is TNA very similar to... 

The rich coordination chemistry of transition metal ions has been used not only to create metal-ligand complexes that play the role of alternative nucleo-base pairs within nucleic acid duplexes, but also to influence the secondary structure adopted by the nucleic acid, for example, hairpin, duplex, or triplex, and to create connectors for such nucleic acid structures. In this context, oligonucleotides that contain terminal ligands can lead to structures distinct from those accessible by using centrally-modified oligonucleotides, such as cyclic structures or hairpins (Fig. 3). 

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