Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection

Elskens, Joke; Madder, Annemieke

doi:10.1039/d0cb00236d

Cited by 13 publications

(13 citation statements)

References 99 publications

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“…Molecular modeling studies indicated that photochemical [2 + 2] cycloaddition is facilitated with the orientation of the vinyl group of CNV K to be stacked onto the C5–C6 double bond of pyrimidine nucleobases located at the −1 position on the complementary strand (see above). 104,111 Overall, crosslinking stabilizes the oligonucleotide duplexes. 14,108,111 The impacts of the photoconvertible groups on duplex stabilities before crosslinking reaction were also investigated by the Fujimoto group.…”

Section: Photochemical Modifications For Dna/rna Oligonucleotidesmentioning

confidence: 99%

“…Although psoralen is widely used as a thymine-selective photo-crosslinker in biological studies, there are limitations such as requiring a TpA step in the sequence and causing photodamage to DNA by forming pyrimidine photodimers upon cycloreversion that uses UV-C (254 nm). 104,106 To alleviate these issues, Fujimoto et al, reported 3-cyanovinylcarbazole nucleoside ( CNV K) as a reversible photo-crosslinker that can photo-crosslink to pyrimidine base located 5 0 to the complementary base through [2 + 2] cycloaddition with 385 or 365 nm irradiation (Fig. 12).…”

Section: Carbazolementioning

confidence: 99%

“…The photo-crosslinking has been widely used to stabilize complexes with DNA by a covalent-bond formation. 104,105 For instance, photo-crosslinkers such as psoralen (a member of furocoumarin family, related to coumarin, Fig. 11 ) can produce DNA inter-strand crosslinks via [2 + 2] cycloaddition reaction when irradiated by UV-A (365 nm) either via their furan or pyrone photoreactive site.…”

Section: Photochemical Modifications For Dna/rna Oligonucleotidesmentioning

confidence: 99%

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Photochemical modifications for DNA/RNA oligonucleotides

Tavakoli

Min

2022

RSC Adv.

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Section: Photochemical Modifications For Dna/rna Oligonucleotidesmentioning

confidence: 99%

Section: Carbazolementioning

confidence: 99%

Section: Photochemical Modifications For Dna/rna Oligonucleotidesmentioning

confidence: 99%

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Photochemical modifications for DNA/RNA oligonucleotides

Tavakoli

Min

2022

RSC Adv.

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“…The cross-linked dumbbell ODNs were developed as potential decoy molecules with an NF-κB binding ability . In addition, various types of cross-linking reactions to the native RNA have been developed to form the stable complex, inhibit the gene expression, − capture the target RNA, − and fluorescently label RNA. − As other applications, the cross-linking reaction was utilized in the DNA-encoded dynamic library and DNA origami. − …”

Section: Introductionmentioning

confidence: 99%

Rapid Alkene–Alkene Photo-Cross-Linking on the Base-Flipping-Out Field in Duplex DNA

et al. 2022

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Specific chemical reactions by enzymes acting on a nucleobase are realized by flipping the target base out of the helix. Similarly, artificial oligodeoxynucleotides (ODNs) can also induce the base flipping and a specific chemical reaction. We now report an easily prepared and unique structure-providing photo-cross-linking reaction by taking advantage of the base-flipping-out field formed by alkene-type base-flipping-inducing artificial bases. Two 3-arylethenyl-5-methyl-2-pyridone nucleosides with the Ph or An group were synthesized and incorporated into the ODNs. We found that the two Ph derivatives provided the cross-linked product in a high yield only by a 10 s photoirradiation when their alkenes overlap each other in the duplex DNA. The highly efficient reaction enabled forming a cross-linked product even when using the duplex with a low T m value.

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“… 13 − 15 If a probe modified using a CNV-K is cross-linked with a target nucleic acid, the probe can maintain its binding state with the target nucleic acid even after the dissociation of hydrogen bonds. 16 This technology enables the use of washing procedures using denaturing agents and surfactants to remove nonspecific adsorbents. It also prevents the loss of target nucleic acids due to dissociation from the probe during magnetic separation and processes other than washing.…”

Section: Introductionmentioning

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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Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection

Abstract: Crosslinker-modified nucleic acid probes are promising substitutes for regular oligonucleotide probes in hybridization-based assays, as they allow a more selective and efficient detection of nucleic acid targets and nucleic acid biomarkers.

Cited by 13 publications

References 99 publications

Photochemical modifications for DNA/RNA oligonucleotides

Photochemical modifications for DNA/RNA oligonucleotides

Rapid Alkene–Alkene Photo-Cross-Linking on the Base-Flipping-Out Field in Duplex DNA

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

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