Oligonucleotides, DNA, and RNA

Conventionally, oligonucleotides are presented by starting from the 5-hydroxyl terminus and writing along the phosphodiester chain towards the 3-hydroxyl terminus, i.e., from the 5 to the 3 end or from the phosphate to the ribose, respectively (Fig. 12.34). 

Oligonucleotides built from nucleotides based on the furanose ribose are termed ribonucleic acids (RNAs), those based on deoxyribose are termed deoxyribonucleic acids (DNAs). The bases attached to the pentose moieties are nitrogen-rich heterocyclic compounds. 

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Near-field scanning microwave microscopy Oligonucleotide DNA and RNA — (42)... 

The three-dimensional structures of oligonucleotides, DNA and RNA can be obtained from either NDB at http //ndbserver.rutgers.edu/ or PDB at http //... 

Figure 22. (Bio)mesogens approaching pre-life states (7 a, 17, 18, 43] a) von Kiedrowski s and Orgel s minimal models of replication on the basis of self-complementary oligonucleotide DNA and RNA systems [44a-d, f-h] b) distant nucleic acid strand-analogs as matrix reaction models [7a, 18, 19, 39f-i] c) Rebek s self-replicational and evolutionary nucleoside analog model [45] d) von Kiedrowski s self-replicational amidinium-carboxylate model, being suggestive of exponential growth kinetics [44 e] e) Lehn s...

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

DNA and RNA quantification, SNP typing, hybridization, and structural alteration have been widely carried out by modified oligonucleotides possessing pyrene derivatives [104-113]. As is known, pyrene-1-carboxaldehyde fluorescence is considerably dependent on solvent polarity [114], being strong in methanol but insignificant in nonpolar solvents [115]. Owing to this property, Tanaka and collaborators developed a pyrenecarboxamide-tethered modified DNA base, PyU 46, and applied it to SNP discrimination in DNA [116-120],... 

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. 

These are artificial/natural oligonucleotides (DNA or RNA), in which the principle of the biological lock-and-key recognition is preserved (Fig. 2.5a). 

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