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

Fujimoto, Kenzo; Asuka, Yamada; Yoshimura, Y.; Tsukaguchi, Tadashi; Shimoyama, Takashi

doi:10.1021/ja406965f

Cited by 94 publications

(56 citation statements)

References 33 publications

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“…The presence of binding was confirmed by electrophoresis that revealed a second band of higher molecular weight above the migration band of the TS-ds (Fig 6A) and of the C-rich ss TS but not with G-rich ss TS (Fig 6B). As expected from the EMSA experiment, a binding band was also observed with Pu27 without CNV K. Since the crosslink with CVN K is stable even at high temperature [66] we were able to verify the binding using one way PCR with primers designed to recognize each strand of the double strand target. Fig 6C shows an agarose gel run with the PCR products, “Fw” is for the primer reading the C-rich strand and “Rev” for the primer reading the G-rich.…”

Section: Resultssupporting

confidence: 56%

“…The cross-linker [3-cyanovinylcarbazole ( CNV K = K)] is a photoactive nucleoside analogue originally described by Yoshimura et.al. [65, 66], that was incorporated in Pu27 sequence (at the position 1 = PuK1 or position 12 = PuK12). Pu27, PuK1 and PuK12 were hybridized to the target sequence double stranded (TS-ds) previously used in EMSA assay for the binding study, or with the C-rich and G-rich single strands of the same sequence (C-r ss, G-r ss), then exposed to UV light for crosslinking in order to create a covalent bond (CxL).…”

Section: Resultsmentioning

confidence: 99%

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Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression

et al. 2016

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G-quadruplex forming sequences are particularly enriched in the promoter regions of eukaryotic genes, especially of oncogenes. One of the most well studied G-quadruplex forming sequences is located in the nuclease hypersensitive element (NHE) III1 of the c-MYC promoter region. The oncoprotein c-MYC regulates a large array of genes which play important roles in growth regulation and metabolism. It is dysregulated in >70% of human cancers. The silencer NHEIII1 located upstream of the P1 promoter regulates up-to 80% of c-MYC transcription and includes a G-quadruplex structure (Pu27) that is required for promoter inhibition. We have identified, for the first time, a family of seventeen G-quadruplex-forming motifs with >90% identity with Pu27, located on different chromosomes throughout the human genome, some found near or within genes involved in stem cell maintenance or neural cell development. Notably, all members of the Pu27 family interact specifically with NHEIII1 sequence, in vitro. Crosslinking studies demonstrate that Pu27 oligonucleotide binds specifically to the C-rich strand of the NHEIII1 resulting in the G-quadruplex structure stabilization. Pu27 homologous sequences (Pu27-HS) significantly inhibit leukemic cell lines proliferation in culture. Exposure of U937 cells to the Pu27-HS induces cell growth inhibition associated with cell cycle arrest that is most likely due to downregulation of c-MYC expression at the RNA and/or protein levels. Expression of SOX2, another gene containing a Pu27-HS, was affected by Pu27-HS treatment as well. Our data suggest that the oligonucleotides encoding the Pu27 family target complementary DNA sequences in the genome, including those of the c-MYC and SOX2 promoters. This effect is most likely cell type and cell growth condition dependent. The presence of genomic G-quadruplex-forming sequences homologous to Pu27 of c-MYC silencer and the fact that they interact specifically with the parent sequence suggest a common regulatory mechanism for genes whose promoters contain these sequences.

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Section: Resultssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression

et al. 2016

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“…So far neither unsubstituted nor substituted pyrimidine nucleosides have ever been applied as components of coumarin photoswitches. [35,36] This feature would be one of the important milestones for the photoswitchable DNA interstrand cross-linking. The photochromic behavior of these compounds was observed via gel electrophoresis analysis followed by UV photo-irradiation.…”

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confidence: 99%

Photoswitchable Formation of a DNA Interstrand Cross‐Link by a Coumarin‐Modified Nucleotide

et al. 2014

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A coumarin-modified pyrimidine nucleoside (1) has been synthesized using Cu(I)-catalyzed click reaction and incorporated into oligodeoxynucleotides (ODNs). Interstrand cross-links are produced upon irradiation of ODN containing 1 at 350 nm. Cross-linking occurs via [2+2] cycloaddition reaction with the opposing thymidine, 2′-deoxycytidine, or 2′-deoxyadenosine. A much higher reactivity was observed with dT than dC or dA. Irradiation of the dT-1 and dC-1 cross-linked products at 254 nm leads to a reversible ring-opening reaction, while such phenomenon was not observed with dA-1 adducts. The reversible reaction is ultrafast and complete within 50 s – 90 s. Consistent photoswitching behavior was observed over 6 cycles of irradiation at 350 nm and 254 nm. To the best of our knowledge, this is the first example of photoswitchable interstrand cross-linking formation induced by a modified pyrimidine nucleoside. Compound 1 is a novel tool for developing reversible DNA photoswitches which will lead to new applications in chemistry, biology, and nanotechnology.

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“…As advanced sequencing technology has become available, there is an urgent need for chemical tools that are suitable for a variety of investigations on structure and function of RNA. These include site-specific alkylation (19–21), photo-affinity labeling (22,23), site-specific chemical labeling of long RNA molecules (24), chemically modified ribozymes (25) and random acylation of the 2′-hydroxyl group of RNA for profiling (26), among others (27). To attain biological functions through the modification of RNA, it is desirable for a method to be utilized in situ .…”

Section: Introductionmentioning

confidence: 99%

Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

et al. 2014

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Modified nucleosides in natural RNA molecules are essential for their functions. Non-natural nucleoside analogues have been introduced into RNA to manipulate its structure and function. We have recently developed a new strategy for the in situ modification of RNA based on the functionality transfer reaction between an oligodeoxynucleotide probe and an RNA substrate. 2′-Deoxy-6-thioguanosine (6-thio-dG) was used as the platform to anchor the transfer group. In this study, a pyridinyl vinyl ketone moiety was newly designed as the transfer group with the expectation that a metal cation would form a chelate complex with the pyridinyl-2-keto group. It was demonstrated that the (E)-pyridinyl vinyl keto group was efficiently and specifically transferred to the 4-amino group of the opposing cytosine in RNA in the presence of NiCl2 with more than 200-fold accelerated rate compared with the previous system with the use of the diketo transfer group. Detailed mechanistic studies suggested that NiCl2 forms a bridging complex between the pyridinyl keto moiety and the N7 of the purine residue neighboring the cytosine residue of the RNA substrate to bring the groups in close proximity.

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

Cited by 94 publications

References 33 publications

Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression

Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression

Photoswitchable Formation of a DNA Interstrand Cross‐Link by a Coumarin‐Modified Nucleotide

Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

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