Nucleic base triplet

Figure 8.4.4 Enzymatic aminoacylation of a specific tRNA is the key step in the translation of nucleic base triplet sequences of DNA into amino acid sequences of proteins.

In 1994, a conference with the title Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code was held in Berkeley, California its patron was the Institute of Advanced Studies in Biology. The conference dealt with the development of the synthetases and that of the genetic code (see Sect. 8.2), i.e., the assignment of the various amino acids to the corresponding base triplets of the nucleic acids. 

As there are 20 proteinogenic amino acids (see p. 60), the nucleic acid language has to contain at least as many words (codons). However, there are only four letters in the nucleic acid alphabet (A, G, C, and U or T). To obtain 20 different words from these, each word has to be at least three letters long (with two letters, there would only be 4 = 16 possibilities). And in fact the codons do consist of three sequential bases (triplets). 

In 1985, Lyamichev et al. [15] called H-DNA to the intramolecular triplex of sequence PyPuPy in order to indicate the high H+ concentration of the media where this triplex exists. This requires protonation of one cytosine in each base-triplet and the two pyrimidine strands must run antiparallel. These form has undergone much research recently [16, 17], as it is very important to understand what is the role of triplex DNA in the nucleic acid characteristics and biotechnological applications may be of great relevance. 

Although the base triplets are of only minor importance in double-stranded nucleic acids, they have a structural role in determining and stabilizing the tertiary structure of transfer RNA, as discussed in Chapter 20. Base quadruplets where two Watson-Crick base pairs are associated as shown in Fig. 16.17 have been invoked to play a role in DNA-DNA aggregation and DNA recombination, but there is no direct evidence for their occurrence. 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

Table 9. The relative energies of the lowest excited states (triplet) in the nucleic base pairs (A-T and G-C) and in the isolated bases. The results of embedding calculations with not-polarized environment axe given in parentheses. Data taken from [Wesolowski, J. Am. Chem. Soc., 126, (2004) 11444],...

In another approach, all the possible 64 combinations of three out of four nucleic bases, called triplets, were considered. A cubic matrix 4x4x4 was constructed whose entries denote the frequencies of occurrence of all the 64 triplets in a DNA sequence [Randic, Guo et al, 2001]. However, in practice, the cubic matrix is not used directly, but three groups of four bidimen-... 

The way in which the coding strand of DNA specifies the sequence of amino acids in a protein is known as the genetic code. The code is made up of triplets of nucleic acid bases, known as codons. A given series of three bases in the coding strand DNA of a gene will unambiguously specify a particular amino acid and no other. 

This type of mutation arises from the addition or deletion of a base to the nucleic acid molecule. This puts the triplet code of the genome out of sequence. Consequently, transcription of the information is erroneous when it is carried out distal to the mutant addition or deletion. In illustration of this, the following code makes sense when read in groups of three ... 

Phosphorescence and photochemistry of aromatic amino acids have been reported.481-483 Triplet states of nucleic acids have also been detected. For example, the phosphorescence of DNA equals the sum of the slow emissions from deoxyadenosine and deoxyguanosine monophosphates present, indicating that only the purine bases phosphoresce.484... 

Ma J, Lin W, Wang W, Flan Z, Yao S, Lin N (2000) Triplet state mechanism for electron transfer oxidation of DNA. J Photochem Photobiol B Biol 57 76-81 Maeda M, Nushi K, Kawazoe Y (1974) Studies on chemical alterations of nucleic acids and their components VII. C-alkylation of purine bases through free radical process catalyzed by ferrous ion. Tetrahedron 30 2677-2682... 

Wood PD, Redmond RW (1996) Triplet state interactions between nucleic acid bases in solution at room temperature Intermolecular energy and electron transfer. Journal of the American Chemical Society 118 4256-4263. 

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