Poly 6- uracil

How the code has been worked out is illustrated by the following experiment. An enzyme solution obtained from bacterial cells and added to a solution of all twenty amino acids produces a polypeptide chain consisting only of residues of the amino acid phenylalanine when provided with a synthetic RNA consisting of poly-uracil (that is, U-U-U-U-. . . ). Hence UUU is the codon for phenylalanine, as shown in the table. Much of this work was done by the American scientists M. W. Nirenberg, H. G. Khorana, and R. H. Holley, and their collaborators, with use of enzymes that had been discovered by A. Kornberg and S. Ochoa. 

Nucleic acid-directed synthesis may have also been important in early peptide formation. Weber and Orgel showed that when the amino acid glycine is esterified to derivatives of adenosine (in the same manner that amino acids are bonded to tRNA in extant protein synthesis), the amino acids will form peptide bonds, resulting in cyclic Gly-Gly dipeptides [29]. Further, when poly-uracil (poly(U)) is added to the mixture, the amount of cyclic Gly-Gly formed increases about 3 times [30]. The temperature and concentration effects of the reactions suggested dependence on formation of a poly(U) hehx specifically, a triple helix of two strands of poly(U) complexed with the glycine-esterified adenosine derivatives. While the exact mechanism of peptide bond formation in this case has not been established, the increased yield of dipeptide could be due to increased local concentration/ optimal orientation of the glycine derivatives based on specific interactions between poly(U) and adenosine. 

FIGURE 14. Boronate ester formation produces poly(adenosme) RNA mimics that coordinate with poly(uracil) to produce organized duplex RNA motifs. 

In one of the early experiments designed to elucidate the genetic code, Marshall Nirenberg of the U.S. National Institutes of Health (Nobel Prize in physiology or medicine, 1968) prepared a synthetic mRNA in which all the bases were uracil. He added this poly(U) to a cell-free system containing all the necessary materials for protein biosynthesis. A polymer of a single amino acid was obtained. What amino acid was polymerized ... 

The derivatives of poly-L-lysine having pendant nucleic acid bases, that is, adenine, thymine and uracil were prepared as shown in the following scheme ... 

The contents of the nucleic acid bases in the poly-L-lysine derivatives were determined by UV spectra of the polymers after hydrolysis The polymers were hydrolyzed in 6 N-hydrochloric acid at 105°C for 24 hr, into lysine dihydrochloride and the carboxyethyl derivatives of the nucleic acid bases. The quantitative calculation was made relative to the standard sample of the carboxyethyl derivative of the nucleic acid bases. The analytical data are listed in Table 1. It was found that the thymine and uracil derivatives was completely substituted to polylysine. Low value in case of adenine base in the polymer may be attributed to the unstability of the activated ester, Ade-PNP (2), and may also be explained in terms of the steric interaction among bulky pendant groups of the polymer. When the poly-L-lysine containing about 50 mol % adenine units was again treated with Ade-PNP, the adenine unit content in the polymer increased up to 74 mol %(,] ). 

Figure 3. NMR spectrum of poly-iAysine having pendant uracil moieties...

FIGURE 9.4 Chromatograms of a reversed-phase test mixture. Plot A is the chromatogram at 30°C and ImL/min, and plot B is the chromatogram at 100°C and 5mL/min. Solutes 1, uracil 2, p-nitroaniline 3, methyl benzoate 4, phenetole 5, toluene. 2.1% (w/w) poly-butadiene coated zirconia column, mobile phase 20% ACN, flow rate was l.OmL/min at 30°C and 5mL/min at 100°C. detection 254 nm. (Reprinted from Li, J. et al., Anal. Chem., 69, 3884, 1997. Copyright 1997, American Chemical Society. With permission.)... 

An attempt has been made to apply the Cohen and Reiss theory to dimer and hydrate formation in RNA.158 The results were inconclusive, probably because of a poor choice of example. Application of the theory to RNA was complicated by the necessity of estimating the distribution of uracil residues on the chain. The results are made still more tentative by the fact that Tanaka ignored the probability of dimer formation between cytosine residues, mixed dimers between cytosine and uracil, and hydrate formation in cytosine as well as the resultant deamination phenomena. A better choice of example would have been poly-uridylic acid. 

The fraction of dimers in irradiated poly U (Fig. 28) reaches a maximum of 16%, because not only uracil but also uracil hydrate is formed... 

Fig. 28. The fraction of uracil dimers in irradiated poly U as a function of the dose of 265 nm light (Swenson and Setlow48).

The existence of photoreversible, but not of heat-reversible, absorbance change in irradiated poly dI dC was taken to prove that the photoproducts are entirely dimers (in contrast to those in poly C irradiations where the product is almost entirely the hydrate82a). It was possible to detect dimers of uracil as well as those of cytosine, by means of the much slower photoreversal of uracil dimers. In the acid hydrolysates of irradiated dl-dC, both uracil dimers and uracil could be identified. Enzymatic hydrolysis (snake venom phosphodiesterase) does not split pyrimidine dimers, and the products of such hydrolysis of irradiated tritium-labeled poly dl dC contained trinucleotides shown by radioactivity to contain cytosine dimers. Thymine dimers were formed in the photolysis of the poly dA dT, and were detected and assayed by the same methods. The yield of thymine dimers in irradiated poly... 

Little is known about the chemistry of silver(I) complexes of unsubstituted pyrimidine however, an extensive range of substituted pyrimidine complexes have been investigated due to their use in the preparation of nucleic acid constituents.85 94 In these reactions, which lead to the formation of glycosides, silver salts of uracils or thymines are treated with poly-0-... 

Chatterjee A, Magee JL (1985) Theoretical investigation of the production of strand breaks in DNA by water radicals. Radiat Protect Dosimetry 13 137-140 Deeble DJ, von Sonntag C (1984) y-Radiolysis of poly(U) in aqueous solution. The role of primary sugar and base radicals in the release of undamaged uracil. Int J Radiat Biol 46 247-260 Deeble DJ, von Sonntag C (1986) Radiolysis of poly(U) in oxygenated solutions. Int J Radiat Biol 49 927-936... 

In poly(U), the slow component shows all the kinetic properties of strand break formation by the -OH-adducts (Schulte-Frohlinde et al. 1985). Thus, it is reasonable to assume that the fast component has been induced by the rapid transformation of the Ura radical cation into the C(2 ) radical (for a mechanistic discussion of the analogous Cyd system see Aravindakumar et al. 2003 and Chap. 10.2). The branching (60% fast to 40% slow) maybe due to a competition of C(2 )OH and water for the uracil radical cation. 

Grachev SA, Kropachev EV, Litvjakova Gl (1995) Formation of 5-hydroxy-5,6-dihydrouracil and release of undamaged uracil as a result of poly(U) irradiation in N20-saturated aqueous solution. Int J Radiat Biol 68 543-551... 

Pitha and co-wodcers (43) have been able to demonstrate in a series of studies the poly(vinyl uracil) [10] and polyfvinyladenin) [22] to show in fact antiviral activity, but probably no interferon induction. Rather, it has been shown, that these electrically neutral polymers with a molecular weight... 

Finally, two other polymers may be mentioned in this chapter which are formed by poly condensation of known active substances. A polymeric derivative of fluoro-uracil with the following formula 36, synthesized by Schmahl and his co-workers (104), showed an improved and extended activity in comparison with the low molecular substance, whereas no activity has been observed by Goodman and his coworkers (105) for a peptide-like polymer of sarcolysin. 

As in the case of electrochemical reduction, the photochemical transformation of 5-fluorouracil derivatives differs from that of the other 5-halogeno uracils. The primary photoproduct of 5-fluorouracil, its glycosides and poly(5-FU) is the photohydrate. However, at shorter wavelengths of irradiation, e.g. 254 nm where the photohydrate exhibits absorption, there is elimination of HF from the 5,6 bond and formation of barbituric acid 129 13I>. There is also some evidence for acetone photosensitized formation of cyclobutane dimers of 5-fluorouracil132), as well as dimer formation in irradiated poly(5-FU)133>. 

In the homopolymers formed by uridine or 2-thiouridine, base pairs with twofold symmetry are feasible, as described in Part II, Chapter 16 [529, 699]. The situation is more complex, however, because the homopolymer folds back on itself, giving rise to a hairpin-like structure where the polynucleotide strands are necessarily antiparallel and the base pairs are of the form shown in Fig. 20.10. Not surprisingly, a comparable double helix is also observed for polyxanthylic acid poly (X) [700]. The purine base of xanthosine displays the same hydrogen-bonding functional groups as uracil and therefore, the same base pair can be formed, but the purine-purine pair requires a larger separation between the glycosidic links and consequently a wider helix radius. 

Poly-9-(f -methacryloyloxyethyl)adenine (polyMAOA, 25 a), poly-l-(fi-methacryloyl-oxyethyl)uracil (polyMAOU, 27 a), -thymine (poly-MAOT, 29 a), poly-9-(f -acryloyl-oxyethyl)adenine (polyAOA, 25b), poly-1 -(fi-acryloyloxyethyl)uracil (polyAOU, 27b) and -thymine (polyAOT, 29 b) were prepared by free-radical polymerization of their corresponding monomers26,27). PolyMAOA and polyAOA are soluble in DMSO, ethylene glycol and acidic aqueous solution (below pH 3), while the polymers having uracil and thymine moieties are soluble in DMSO, DMF and alkaline aqueous solution (above pH 10). 

By using this reaction, copolymers of acrylic add and N-p-(methaeryloyloxy)ethyl derivative of uracil or thymine, and also those of methacrylic add and the methacrylate of pyrimidine bases are successfully prepared. The molecular weights of poly-(aerylie acid) and poly(methacrylic acid) used here were about 15,(WO. 

Poly-9-(p-methacryloylaminoethyl)adenine (polyMAEA, 39a), poly-1 -(fi-methacry-loylaminoethyl)uracil (polyMAEU, 41 a), poly-9-(j3-acryloylaminoethyl)adenine (polyAAEA, 39b) and poly-l-(fj-acryloylaminoethyl)uracil (polyAAEU, 41 b) were prepared by the usual free-radical polymerization of the corresponding monomers45"4 (Scheme 12). 

With thymine and uracil derivatives, graft reactions proceed almost quantitatively while in the case of the adenine derivative, its activated ester hardly reacts with poly-L-lysine, and only the copolymer with low adenine content is obtained, probably owing to the instability of the activated ester. Hypochromidty of the copolymer based... 

From these facts, it is concluded that the polymer complexes are formed by specific base pairing between pendant adenine and thymine or uracil units of poly-L-lysine derivatives retaining their helical conformations (Fig. 26). The lowering of the base content in the polymers results in the decrease of the helical structure and also in the decrease of interactions with the complementary polymer. 

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