Uracil base triplet

After the discovery of three-letter codons, researchers were anxious to answer the next question Which triplets of bases (codons) code for which amino acids In 1961, Marshall Nirenberg and his coworkers at the National Institutes of Health (NIH) in Bethesda, Maryland, attempted to break the code in a very ingenious way. They made a synthetic molecule of mRNA consisting of uracil bases only. Thus, this mRNA contained only one codon, the triplet UUU. They incubated this synthetic mRNA with ribosomes, amino acids, tRNAs, and the appropriate enzymes for protein synthesis. The exciting result of this experiment was that a polypeptide that consisted only of phenylalanine was synthesized. Thus, the first word of the genetic code had been deciphered UUU phenylalanine. 

A set of coding rules are in action as in the translation process. First, a set of three adjacent nucleotides compose the code for each amino acid. A single amino acid can have several triplet codes or codons. Since there are four different nucleotides (or four different bases) in DNA and RNA, there exist 4 = 64 trinucleotide combinations. For instance, using U as a symbol for uracil, which is present in RNA, the triplet or code or codon UUU is specific for phenylalanine. 

Daniels352 has shown that the excitation spectra for triplet state formation and fluorescence emission from uracil and thymine in neutral aqueous solution at room temperature were anomalous when compared with the UV absorption spectra of these pyrimidines. These experimental facts have been critically examined with respect to three molecular models, of which the model based on tautomerism of uracil in aqueous solution is, in the opinion of Daniels, the best. The data suggested that the fluorescing tautomer contained an enol group, and the UV data favored the 4-hydroxy structure, i.e., form 28. The second tautomer, from which the triplet originated, was expected to be the predominant diketo form (32). 

An overview of protein synthesis is shown in Fig. S.A12. The linear sequence in mRNA that is translated to protein contains four bases, adenine, uracil, guanine and cytosine. The four letters A,U,G and C constitute the mRNA alphabet . This basic alphabet is used in triplets of bases called codons. The codons on mRNA pair up with anticodon or complementary triplets on the tRNA, thus matching the mRNA code to an amino-acid sequence. 

By means of the calculation of the MEP on the (inr HL) PEH of uracil as discussed in previous Section 16.2, two STC can be located. Figure 16-10 contains a scheme of the different mechanisms found in uracil for efficient population of the lowest triplet state based on computed MEPs and PEHs crossings. More details can be found elsewhere [91], At the 4.6 eV along the MEP the STC (3n0Tr /1Tnr )sxc... 

Figure 16-10. Scheme, based on CASPT2 results, of the photochemistry of uracil focused on the population of the lowest-energy triplet state. (Reproduced from Ref. [91] with permission from Elsevier.)... 

MO methods have calculated that the bond order of the C(5)-C(6) bond in the first triplet of a series of pyrimidines is lower than in the first excited singlets of the corresponding molecules, and have concluded that dimerization of the bases occurs via the triplet state. They divided the pyrimidines into three groups the pyrimidines which are known to be easily dimerizable (uracil, 6-methyluracil, thymine, orotic acid—for these molecules the Pse values in their T state are of the order of 0.09-0.12), those which dimerize not so easily (5-aminouracil, cytosine, 5-methylcytosine—Pge 0.13-0.17), and the bases which do not dimerize at all or only with considerable difficulty (2-thiothymine, Pgg = 0.31 isocytosine, Pgg = 0.39 and 5-nitrouracil). The relative distribution of the bases within groups leads sometimes to only limited agreement with available experimental data. For instance, as the Pgg = 0.085 in T of uracil is lower than Pgg = 0.106 in T of thymine, uracil should dimerize more easily than thymine, a conclusion in disagreement with experiment. ... 

The fundamental residues of the inverse temperature transition are hydrophobic, and there is a unique family of the genetic code that is entirely hydrophobic. As shown in Table 6.2, the hydrophobic family is the one with U as the second base of the triplet codon, namely, XUY. Any of the four bases of RNA—A (adenine), U (uracil), G (guanine), and C (cytidine)—can be in positions 1 and 3 of the triplet code, but U is always found as the second base of the codon for the hydrophobic family. A change in position 1 and position 3 simply allows selection of one member of the hydrophobic family from another. Position 3 in the cases of Leu (CUY) and Val (GUY) gives redundancy, that is, four different codons encode for Leu as do four different codons encode for Val. Therefore, it is said that both Val and Leu have a redundancy of four. For the Leu and Val residues, a change in the base in position 3 does not change the amino acid residue. 

The reactions between the triplet excited state of l,8-dihydro>yan-thraquinone and cytosine, thymine or uracil have been investigated by nanosecond laser flash photolysis. The transient absorption spectra and the decay dynamics are consistent with electron transfer and hydrogen abstraction from the pyrimidine bases. ... 

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