The Ultraviolet Photochemistry of Deoxyuridylyl (3′→5′) Deoxyuridine

Helleiner, C. W.; Pearson, Mark; Johns, H. E.

doi:10.1073/pnas.50.4.761

Cited by 34 publications

(6 citation statements)

References 7 publications

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“…We propose that the commonly observed tailing effect is due to pyrimidine dimer reactions reaching photostationary state, as described in early UV photolysis literature. 25,26 The reason tailing was observed in region B of MS2 after the same UV 254 dose as region A may be due to the greater number of neighboring uracil bases in the sequence (32 in region B, 19 in region A, SI Table S2). Further research will be necessary to characterize the extent of dimer reversion in different nucleic acids with varied sequences and structures.…”

Section: ■ Results and Discussionmentioning

confidence: 98%

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Zhong

Chang

et al. 2018

Environ. Sci. Technol.

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Determining the influence of higher order structure on UVC photolysis will help inform predictions of nucleic acid fate and microorganism inactivation. We measured the direct UV photolysis kinetics of four model viral genomes composed of single-stranded and double-stranded RNA (ssRNA and dsRNA, respectively), as well as single-stranded and double-stranded DNA (ssDNA and dsDNA, respectively), in ultrapure water, in phosphate buffered saline (PBS), and encapsidated in their native virus particles. The photolysis rate constants of naked nucleic acids measured by qPCR (RT-qPCR for RNA) and normalized by the number of bases measured in a particular sequence exhibited the following trend: ssDNA > ssRNA ≈ dsDNA > dsRNA. In PBS, naked ssRNA bases reacted, on average, 24× faster than the dsRNA bases, whereas naked ssDNA bases reacted 4.3× faster than dsDNA bases. Endogenous indirect photolysis involving O and ·OH was ruled out as a major contributing factor in the reactions. A comparison of our measured rate constants with rate constants reported in the literature shows a general agreement among the nucleic acid UV direct photolysis kinetics. Our results underscore the high resistance of dsRNA to UVC photolysis and demonstrate the role that nucleic acid structure and solution chemistry play in photoreactivity.

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Section: ■ Results and Discussionmentioning

confidence: 98%

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Zhong

Chang

et al. 2018

Environ. Sci. Technol.

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“…CPD are the primary form of UV-induced damage in dT 17 with small amounts of the pyrimidine-pyrimidinone photoproduct also forming, whereas CPD and photohydrates are formed in almost equal amounts in rU 17 (1,(26)(27)(28)(29)(30) under anoxic conditions. The quantum yields (/) for these processes are /50.044 for CPD formation in poly-dT and / 5 0.012 and / 5 0.015 for photohydrate and CPD formation, respectively, in poly-rU (1).…”

Section: Resultsmentioning

confidence: 99%

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶

Yarasi

McConachie

Loppnow

2005

Photochem Photobiol

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Molecular beacons (MB) are becoming more common as sequence-selective detectors of nucleic acids. Although they can easily detect single-base mismatches, they have never been used to directly detect DNA or RNA damage. To measure the degree of ultraviolet (UV) light damage in oligonucleotides, we report a novel MB approach for general detection of photoproducts in UV-irradiated rU17 and dT17 oligonucleotides. With monochromatic UV light irradiation at ca 280 nm under anoxic conditions, the oligonucleotide absorption decays with a single-exponential time constant of 123+/-1 min for rU17 and with double-exponential time constants of 78+/-0.5 min (99%) and 180+/-5 min (0.05%) for dT17 oligonucleotides. Under the same conditions, the MB fluorescence decays more quickly, with single-exponential time constants of 19+/-2 and 26+/-3 min for rU17 and dT17, respectively. Similar kinetics were observed with broadband UV light irradiation of oligonucleotides. The differences in the UV damage kinetics of dT17 and rU17 and their detection by absorption and fluorescence techniques will be discussed in the context of differential instabilities introduced in the nucleic acid-MB duplex by the different photoproducts formed.

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“…Target dT 17 and rU 17 were used because their photochemistry is well known. CPD are the primary form of UV‐induced damage in dT 17 with small amounts of the pyrimidine‐pyrimidinone [6–4] photoproduct also forming, whereas CPD and photohydrates are formed in almost equal amounts in rU 17 (1,26–30) under anoxic conditions. The quantum yields (φ) for these processes are φ= 0.044 for CPD formation in poly‐dT and φ= 0.012 and 4pH = 0.015 for photohydrate and CPD formation, respectively, in poly‐rU (1).…”

Section: Resultsmentioning

confidence: 99%

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides^¶

Yarasi

McConachie

Loppnow

2005

Photochem & Photobiology

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Molecular beacons (MB) are becoming more common as sequence-selective detectors of nucleic acids. Although they can easily detect single-base mismatches, they have never been used to directly detect DNA or RNA damage. To measure the degree of ultraviolet (UV) light damage in oligonucleotides, we report a novel MB approach for general detection of photoproducts in UV-irradiated rU17 and dTI7 oligonucleotides. With monochromatic UV light irradiation at ca 280 nm under anoxic conditions, the oligonucleotide absorption decays with a singleexponential time constant of 123 * 1 min for rU17 and with double-exponential time constants of 78 f 0.5 min (99%) and 180 +-5 min (0.05%) for dT17 oligonucleotides. Under the same conditions, the MB fluorescence decays more quickly, with single-exponential time constants of 19 f 2 and 26 f 3 min for rUI7 and dT17, respectively. Similar kinetics were observed with broadband UV light irradiation of oligonucleotides. The differences in the UV damage kinetics of dTI7 and rUI7 and their detection by absorption and fluorescence techniques will be discussed in the context of differential instabilities introduced in the nucleic acid-MB duplex by the different photoproducts formed.

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The Ultraviolet Photochemistry of Deoxyuridylyl (3′→5′) Deoxyuridine

Cited by 34 publications

References 7 publications

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides^¶

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The Ultraviolet Photochemistry of Deoxyuridylyl (3′→5′) Deoxyuridine

Cited by 34 publications

References 7 publications

Nucleic Acid Photolysis by UV254 and the Impact of Virus Encapsidation

Nucleic Acid Photolysis by UV254 and the Impact of Virus Encapsidation

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶

Contact Info

Product

Resources

About

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Nucleic Acid Photolysis by UV₂₅₄ and the Impact of Virus Encapsidation

Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides^¶