Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand

Fujimoto, Kenzo; Konishi-Hiratsuka, Kaoru; Shimoyama, Takashi

doi:10.3390/ijms14035765

Cited by 13 publications

(9 citation statements)

References 24 publications

(18 reference statements)

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“…UPLC analysis after the photosplitting reaction, the peak having the same retention time and the same molecular mass of ORN(Ψ) was appeared (Figure S3). Thus, we concluded that the photocrosslinking reaction to the ORN(Ψ) is photoreversible, the same as the case of U and other unmodified pyrimidine bases in our previous report . This is the first report about the site‐specific chemical reaction toward Ψ in RNA strands.…”

Section: Resultssupporting

confidence: 84%

Geometric Effect on the Photocrosslinking Reaction between 3‐Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex

Fujimoto¹,

Kishi

Shimoyama

2013

Photochem & Photobiology

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To clarify the geometric effect of the ultra-fast photocrosslinking reaction of photoreactive oligodeoxyribonucleotide containing 3-cyanovinylcarbazole nucleoside ((CNV)K) on uridine in complementary RNA strands, pseudouridine (Ψ), which is an isomer of uridine with a C5-C1' glycosidic bond, was introduced to the photocrosslink site of (CNV)K in complementary RNA instead of U. The photoreactivity of (CNV)K toward Ψ was two-fold lower than that of U, suggesting that the geometry between the vinyl moiety on (CNV)K and the reactive double bond in the pyrimidine base has a large affect on the photoreactivity of (CNV)K. Contrary to the case of U, the reactivity of the (CNV)K toward Ψ was decreased by the decrease of reaction temperature below the Tm of heteroduplex, suggesting that the flexible structure of the duplex is advantageous for the photocrosslinking reaction with Ψ, whose reactive double bond possesses unfavorable geometry for the photocrosslinking reaction with (CNV)K. These basic findings might contribute to the development of a geometry selective photocrosslinking reaction. This is the first example of a sequence specific photocrosslinking reaction toward Ψ, which is the most abundant posttranscriptionally modified nucleoside.

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Section: Resultssupporting

confidence: 84%

Geometric Effect on the Photocrosslinking Reaction between 3‐Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex

Fujimoto¹,

Kishi

Shimoyama

2013

Photochem & Photobiology

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“…As the signal at 170 ppm can be assigned as C4 carbon of thymidine, we assigned signals at 50 and 52 ppm as the carbons attached with Ha or Hc. As the signal at 50 and 52 ppm has the cross peak with 3.8 and 4.4 ppm in 1 H− 13 C HSQC spectrum (Figure S7, Supporting Information), protons having the signal at 3.8 and 4.4 ppm can be assigned as Ha or Hc. Together with 1 H− 1 H NOESY experiment as shown in Figure 3b; i.e., the proton at 3.8 ppm has cross peaks with phenyl proton (2H and 4H) on carbazole ring and the proton at 4.4 ppm did not; we successfully assigned the protons on cyclobutane ring as shown in Figure 3b,c.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping

Fujimoto¹,

Asuka²,

Yoshimura³

et al. 2013

J. Am. Chem. Soc.

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To clarify the cis-trans isomeric effect on the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside ((CNV)K) in the DNA duplex, which gives a single photodimer on the reversed-phase HPLC chromatogram, the kinetics of the cis-trans photoisomerization of (CNV)K in double-stranded DNA was evaluated. Since the photoisomerization rate constant for cis to trans isomerization in double-stranded DNA was significantly larger than that for trans to cis isomerization, and the thermodynamic stability of the trans isomer was higher than that of the cis isomer, it was strongly suggested that the trans isomer of (CNV)K is a reactive species of the photo-cross-linking reaction. (1)H-(1)H NOESY analysis of the photoadduct consisting of (CNV)K and T also supported the trans-mediated photo-cross-linking reaction of (CNV)K. By using this ultrafast photo-cross-linking reaction for the molecular beacon-based SNPs typing, four individual Japanese rice strains were clearly distinguishable with simple photoirradiation and fluorescence imaging using double-stranded target DNAs.

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“… 13 The photo-cross-linking efficiency between the photo-cross-linkable probe and the target nucleic acid is affected by the amount of energy of the irradiated light. 14 Turbidity is generated in the reaction solution when PPMPs are used, which may reduce the photo-cross-linking reaction rate.…”

Section: Resultsmentioning

confidence: 99%

Photo-Cross-Linked Probe-Modified Magnetic Particles for the Selective and Reliable Recovery of Nucleic Acids

et al. 2022

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Polymerase chain reaction (PCR) assays are used to diagnose various infectious diseases such as Coronavirus disease 2019 by detecting the nucleic acids of the pathogen. However, in practice, the yield of the extraction process and the inhibition of the reverse transcription reaction and PCR by foreign substances reduce the sensitivity and may yield false negative results. The sensitivity of the PCR test can be improved by using technologies that can reliably capture the target nucleic acid and remove foreign substances. In this study, we developed photo-cross-linkable probe-modified magnetic particles (PPMPs) for the sequence-specific recovery of target nucleic acids using photo-cross-linkable artificial nucleic acid probes and magnetic particles. Nucleic acid probes modified with photo-cross-linkable artificial nucleic acids can hybridize with the target nucleic acids in a sequence-specific manner and then securely capture the target nucleic acids by UV irradiation-mediated covalent bonding. Then the target nucleic acid is detected by trapping the target-bound probe on the surface of the magnetic particles and subjecting these collected magnetic particles to PCR. Recovery of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N gene pseudo-DNA (120 bp) was performed using PPMPs. We confirmed that the PPMPs captured the target consistently even after washes were done with denaturing agents and surfactants. Even in the presence of foreign DNA fragments, PPMPs were able to specifically recover the target DNA. This method allows for a more accurate detection by recovering only the target DNA for PCR. Hence, PPMPs can be successfully used for PCR-mediated detection of SARS-CoV-2 and other pathogens whose nucleic acid sequences are known.

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Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand

Cited by 13 publications

References 24 publications

Geometric Effect on the Photocrosslinking Reaction between 3‐Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex

Geometric Effect on the Photocrosslinking Reaction between 3‐Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex

Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping

Photo-Cross-Linked Probe-Modified Magnetic Particles for the Selective and Reliable Recovery of Nucleic Acids

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