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[Photochemistry and UV Spectroscopy of Proteins and Nucleic Acids]. - Abstract - Europe PMC

A log phase culture of E. At various times two aliquots were removed from the culture.


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The percent recovery of tritiated DNA free of protein versus the unirradiated control aliquots is plotted against the time following the pulse of thymine-H 3. Photosensitized Crosslinks. When bacterial cells were pretreated with acridine orange or with methylene blue, and then exposed to intense visible light, survival deceased markedly, and a large amount of their DNA was crosslinked to protein. There is a correlation between the relative killing efficiency of the two dyes, and the relative production of DNA protein crosslinks Figure 3.

Figure 3. The killing of E. Stationary phase cells were washed and suspended in 0.

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Viability was determined on nutrient agar plates, and the DNA was isolated using the sodium dodecyl sulfate method see above Smith and Kaplan, ; Smith, These results may be explained by the fact that X-rays produce a significant amount of single- and double-strand breaks in DNA, and the fact that the assay depends upon the selective precipitation of large molecular weight DNA crosslinked with protein.

X-ray-induced crosslinks are observed, however, if cells are irradiated under nitrogen Barker et al. Under nitrogen, three times less DNA double-strand breaks are formed than when cells are X-irradiated under oxygen Bonura et al. Photoreactions of Nucleobases and Nucleosides with Amino Acids and Related Compounds The first amino acid shown to photochemically add to uracil was cysteine, to form 5-S-cysteinylhydrouracil Smith and Aplin, The chemical structure of the mixed photoproduct of thymine and cysteine was also determined Smith, Figure 4.

Later work showed that this compound is photochemically-produced in two diastereomeric forms, and that two other compounds, namely 5-S-cysteinylmethyluracil Varghese, and 5-S-cysteinyl-5,6-dihydrothymine Shetlar and Hom, are also produced when thymine is irradiated in the presence of cysteine. Figure 4.

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Adducts arising from the photoreactions of thymine with cysteine left and N-acetyltyrosine right. In addition to the products of the photoreactions of thymine and uracil with cysteine, photoproducts have been characterized in a number of other systems containing nucleobases or nucleosides , and amino acids or amino acid analogs reviewed in Saito and Sugiyama, For example, the reaction of thymine with the phenolic ring system contained in N-acetyltyrosine results in a compound with the structure shown in Figure 4 Shaw et al.

There is evidence that cytosine and 5-methylcytosine a minor nucleobase found in eukaryotic DNA photoreact with lysine to form adducts of a similar nature Dorwin et al. Interestingly, 5-methylcytosine also reacts with cysteine analogs e. Other recent work Shetlar et al. Early work Janion and Shugar, showed that dihydrocytosines can undergo transamination reactions in the dark, in which aliphatic amines displace the 4-amino group of the dihydro compound to form "transaminated" dihydrocytosines.

This same type of reaction also occurs with cytosine nucleoside photohydrates, in which the 5,6 bond is saturated. In particular, it has been shown that this reaction occurs when the RNA bacteriophage MS2 is irradiated, leading to crosslinking of lysine residues in coat protein to the genomic nucleic acid Budowsky et al.

These results suggest that secondary dark reactions, subsequent to the formation of primary photoproducts in DNA, may play a role in DNA-protein crosslinking. Determination of the contributions of various secondary crosslinking reactions to the total photochemistry of DNA in its cellular environment, may be a fertile field for further study.

Figure 5. Structure of the photoproduct arising from the reaction of thymidine with lysine. Other amino acids are also reactive with nucleobases and polynucleotides. The first survey performed determined the ability of the 22 common amino acids to add photochemically nm to uracil. The 11 reactive amino acids were glycine, serine, phenylalanine, tyrosine, tryptophan, cystine, cysteine, methionine, histidine, arginine and lysine.

The most reactive amino acids were phenylalanine, tyrosine and cysteine. Therefore, the photochemical addition of amino acids to uracil appears to be a fairly common phenomenon Smith, A later study of the photoreactivity of polyuridylic acid indicated that all 20 amino acids were reactive, as well as a variety of glycylpeptides and other peptides Shetlar et al. When thymine was similarly screened for photochemical reactivity with 22 common amino acids, only lysine, arginine, cysteine and cystine formed heteroadducts after exposure times similar to those used for uracil. Thymine was generally less reactive than uracil with amino acids when exposed to UV radiation Schott and Shetlar, This may be due to the by shielding of carbon-5 in thymine by the methyl group at that position.

Another study used a fluorescence assay method to assess the photoreactivity of DNA and polynucleotides for the addition of various amino acids and peptides. The reactivities of the 20 amino acids commonly occurring in proteins were determined for their photochemical addition to denatured calf thymus DNA at pH 7. Fifteen amino acids were reactive, with cysteine, lysine, phenylalanine, tryptophan, and tyrosine being the most reactive. Alanine, aspartic acid, glutamic acid, serine, and threonine were unreactive Shetlar et al.


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Corresponding quantum yields were also determined for many of the glycyldipeptides e. It was found that of the peptides studied, those containing lysine, cystine, proline, histidine and the various aromatic acids phenylalanine, tyrosine, tryptophan were the most reactive glycylcysteine was not studied. Interestingly, in peptide form, all of the amino acids studied displayed some degree of reactivity.

Nucleic Acids

In almost all cases, amino acids incorporated into peptides had higher reactivities towards photoaddition than the corresponding carboxyl terminal amino acids at the same concentration. Measurements similar to those done on DNA photoreactivity were made on the photochemical reactivity of four polyribonucleotides, namely poly rA, poly rC, poly rG, and poly rT, towards the addition of glycine and the L-amino acids commonly occurring in proteins, excluding proline Shetlar et al.

Poly rA was reactive with eleven of the twenty amino acids tested, with phenylalanine, tyrosine, glutamine, lysine and asparagine being the most reactive.

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Photochemistry

Poly rG reacted with sixteen amino acids; phenylalanine, arginine, cysteine, tyrosine, and lysine displayed the largest quantum yields. Poly rC showed photoreactivity with fifteen amino acids, with phenylalanine, lysine, cysteine, tyrosine and arginine having the highest reactivities. Poly rT was reactive with fifteen of nineteen amino acids surveyed, and showed the highest quantum yields for cysteine, phenylalanine, tyrosine, lysine and asparagine.

None of the polynucleotides were reactive with aspartic acid or glutamic acid. Studies on the photoaddition of various glycyldipeptides with each of the polynucleotides indicated that they were often more reactive than the amino acids themselves. In general, poly rT was the most reactive polynucleotide towards photoaddition for most of the amino acids and peptides studied.

For example, the quantum yields for the photoaddition of phenylalanine to poly rT, poly rC, poly rA, and poly rG were in the ratio of The timescale for the photoinduced endosomal disruption a few seconds to a few minutes was much longer than the 1 O 2 lifetime 4. Thus, a process es must exist after 1 O 2 generation until endosomal disruption that requires a few seconds to a few minutes to complete. This might be a destabilization process induced by membrane lipids damaged by 1 O 2. The hidden process between 1 O 2 generation and endosomal disruption needs to be clarified by future experiments.

Labeling efficiencies of the carrier proteins were calculated by measuring the absorbance of the respective dyes. This represents a non-specific shRNA in normal mammalian cells, but contains an anti-luciferase sequence. The intensity of methylene blue in octanol was, in turn, estimated from that in ethanol 0. As a result, the 1 O 2 generation quantum yield of methylene blue in octanol was determined as 0.

The quantum yields of the dye solutions were measured using an absolute photoluminescence quantum yields measurement system, Quantaurus-QY C Hamamatsu Photonics K. After washing, the cells were visualized using a fluorescence microscope Olympus, Tokyo, Japan. One of the 1 O 2 quenchers listed below was added to the cells at the following time points; i at the same time as treatment with the complex, or ii after treatment with the complex.

How to cite this article : Ohtsuki, T.


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