DNA building blocks

The use of click chemistry is a promising strategy as a postsynthetic ligation for nucleic acids in order to circumvent the time-consuming synthesis of phosphoramidites as DNA building blocks [31, 32]. This is particularly relevant for several fluorophores that are unstable under the acidic, oxidative, or basic conditions of automated DNA phosphoramidite chemistry and DNA workup. 

The synthesis of pyrimidines under specific prebiotic conditions, at low temperature, has apparently been carried out successfully (Fig. 4.8). The formation of the DNA building blocks was carried out by freezing out a dilute solution of cyanoacetaldehyde (CAA) and urea or guanidine. The concentration of CAA was only 1(T3 M, that of guanidine 1M. The reaction took 2 months at 273 K and a pH of 8.1. Yields were as follows ... 

Geneticists use maps to describe the location of a particular gene on a chromosome. One type of map uses the cytogenetic location to describe a gene s position. The cytogenetic location is based on a distinctive pattern of bands created when chromosomes are stained with certain chemicals. Another type of map uses the molecular location, a precise description of a gene s position on a chromosome. The molecular location is based on the sequence of DNA building blocks (base pairs) that make up the chromosome. 

Virustatic antimetabolites are false DNA building blocks (B) or nucleosides. A nucleoside (e.g., thymidine) consists of a nucleobase (e.g., thymine) and the sugar deoxyribose. In antimetabolites, one of the components is defective. In the body, the abnormal nucleosides undergo bioactivation by attachment of three phosphate residues (p.287). 

Experience teaches us that combinations of active compounds offer the most promising perspective - for example, the combination of AZT with 3TC of BioChemPharma (Laval, Quebec, Canada). Currently (2003), there are seven approved entities of nucleoside analogs (NRTIs) and three approved non-nucleosides (NNRTIs) that inhibit reverse transcriptase (RT) by mimicking the structure of DNA building blocks and thus the copy process of RNA into DNA by reverse transcriptase. In addition, five HIV protease inhibitors and one viral fusion inhibitor have been approved. 

O. Huertas, J. R. Bias, I. Soteras, M. Orozco and F. J. Luque, Benzoderivatives of nucleic acid bases as modified DNA building blocks, J. Phys. Chem. A, 110 (2006) 510-518. 

In cases A, B and C, the DNA base or sugar modifications can be introduced via automated solid-phase synthetic methods using suitable DNA building blocks. As an alternative route, DNA modifications can be introduced by solid-phase methods which are applied during or after the complete automated solid-phase synthesis, as is the case for the preparation of the DNA assays B and D. 

Chromophore Functionalization of DNA Bases via Synthesis of DNA Building Blocks... 

Fig. 12.6 Synthetic DNA building block strategy for the modification of DNA bases by chromophores. Bx = base Ch = chromophore.

Alternatively to the DNA modifications in the previous two sections where the chromophore was attached to one of the four DNA bases, chromophores can be incorporated as artificial DNA bases substituting a natural base or even a whole base-pair. There is a large number of recently reported syntheses of chromophores as DNA base surrogates, e.g. flavine derivatives [26] and thiazole orange derivatives [42]. Additionally, a variety of phosphoramidites as DNA building blocks for the introduction of fluorophores into DNA are commercially available, e.g. acridine derivatives. Clearly, the synthetic protocols for this kind of DNA modification do not follow a principle strategy which can be applied in a versatile fashion, as is the case for the DNA base modifications mentioned in the previous sections. It is important to point out that in many cases it turned out to be useful to replace the 2 -deoxyribose moiety with acyclic linker systems. This was also the case during our attempts to synthesize ethidium-modified DNA, which will be described here briefly. 

Goodman RP et al (2005) Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310 1661-1665... 

Inhibition of nudeobase synthesis (2). Tet-rahydrofolic acid (THF) is required for the synthesis of both purine bases and thymidine. Formation of THF from folic acid involves dihydrofolate reductase (p. 274). The folate analogues aminopterin and methotrexate (amethopterin) inhibit enzyme activity. Cellular stores of THF are depleted. The effect of these antimetabolites can be reversed by administration of folinic acid (5-formyl-THF, leucovorin, citrovorum factor). Hydroxyurea (hydroxycarbamide) inhibits ribonucleotide reductase that normally converts ribonucleotides into deoxyribonucleotides subsequently used as DNA building blocks. 

The primary structure of DNA is the way in which the DNA building blocks are linked together. Whereas proteins have over twenty building blocks to choose from, DNA has only four—the nucleosides deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine (Fig. 6.1). 

Osakada, Y., Kawai, K., Fujitsuka, M., and Majima, T. (2006) Charge ttansfer through DNA nanoscaled assembly programmable with DNA building blocks. Proc. Natl. Acad. Sci. USA, 103, 18072-18076. 

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