Site-Specific Discrimination of Cytosine and 5-Methylcytosine in Duplex DNA by Peptide Nucleic Acids

Okamoto, Akimitsu; Tanabe, Kazuhito; Saito, Isao

doi:10.1021/ja0264955

Cited by 44 publications

(18 citation statements)

References 11 publications

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“…Indeed, we have demonstrated here that once the DNA duplex boundary is produced, regular mixed-base PNA oligomers become capable of delivering various assays for duplex DNA similar to those which have previously been developed by us and others utilizing the ability of homopyrimidine bis-PNAs or pcPNAs to strand invasion into dsDNA (8,22,24,25,52,63). …”

Section: Resultsmentioning

confidence: 71%

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes

Smolina

Demidov²,

Soldatenkov³

et al. 2005

Nucleic Acids Research

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Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine–homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA–DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.

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Section: Resultsmentioning

confidence: 71%

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes

Smolina

Demidov²,

Soldatenkov³

et al. 2005

Nucleic Acids Research

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“…Nowadays, various methods are available to assess the DNA methylation pattern of specific DNA regions and important progress has been made toward completing a large‐scale analysis of DNA methylation . Classical methods for the detection of DNA methylation mainly include bisulfite conversion of DNA, methylation‐sensitive restriction enzyme cleavage assay , and methylation‐specific polymerase chain reaction . These methods, although effective in profiling DNA methylation statuses, often require time‐consuming and complicated procedures and are confined to limited recognition sequences of restriction enzymes or associated with false‐positive and significant inaccuracy .…”

Section: Introductionmentioning

confidence: 99%

Electrochemical Sensing of Cancer‐related Global and Locus‐specific DNA Methylation Events

Campuzano

Pingarrón

2018

Electroanalysis

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Specific DNA methylation changes, both genome‐wide and at specific gene loci in tissues and in biological fluids, have great potential as biomarkers for early detection, diagnosis, prognosis and therapeutic stratification of cancer. Although current classical methods are effective in studying DNA methylation patterns, they exhibit relatively low sensitivity and high false positive rates and require expensive instruments and complicated and time‐consuming protocols. Here, we review basic information about relevance of DNA methylation in cancer, limitations of the conventional methodologies and promising features offered by electrochemical sensors to allow the determinations of methylated biomarkers in a straightforward, simple, sensitive, fast, portable and cost‐effective way through highlighting selected examples described so far for sensing of cancer‐related DNA methylation biomarkers. Major technical and biological challenges to be solved are also pointed out.

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“…Several conventional methods have been used for the evaluation of the methylation status in genes, such as cleavage assay with methylation‐insensitive restriction enzymes , the bisulfite‐sequencing method , the use of bipyridine ligands for the direct detection of 5‐mC and other chemical approaches . Photochemical ligation methods using 5‐vinyl‐2′‐deoxyuridine derivatives or 3‐cyanovinylcarbazole nucleoside have achieved remarkable successes in the detection of the C‐5 methylation of cytosine in single‐stranded target‐DNA .…”

Section: Introductionmentioning

confidence: 99%

Novel Photodynamic Effect of a Psoralen‐Conjugated Oligonucleotide for the Discrimination of the Methylation of Cytosine in DNA

Yamayoshi

Matsuyama

Kushida

et al. 2014

Photochem & Photobiology

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DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C-5-methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen-conjugated oligonucleotide (PS-oligo) for the discrimination of 5-methylcytosine (5-mC) in DNA. The cross-linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross-linking efficiency of psoralen with cytosine would be changed with or without C-5 methylation. We found that the cross-linking efficiency of PS-oligo with target-DNA containing 5-mC was greatly increased compared to the case of target-DNA without 5-mC, approximately seven-fold higher. Here we report a new aspect of the photocross-linking behavior of psoralen with 5-mC that is applicable to a simple, sequence-specific and quantitative analysis for the discrimination of 5-mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.

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Site-Specific Discrimination of Cytosine and 5-Methylcytosine in Duplex DNA by Peptide Nucleic Acids

Cited by 44 publications

References 11 publications

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes

Electrochemical Sensing of Cancer‐related Global and Locus‐specific DNA Methylation Events

Novel Photodynamic Effect of a Psoralen‐Conjugated Oligonucleotide for the Discrimination of the Methylation of Cytosine in DNA

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