Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

Ohkubo, Akihiro; Yamada, Kenji; Yu, I.; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Yoshio, Masaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

doi:10.1093/nar/gkv496

Cited by 43 publications

(28 citation statements)

References 29 publications

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“…The guanidine group in the Q monomer, incorporated via a two-carbon linker, is predicted to form two hydrogen bonds with the G base in a C-G pair (Figure 1D) (27,28). Thus, the incorporation of Q residues into triplex-forming PNAs may improve the binding affinity and sequence specificity to an RNA duplex with an inverted Watson–Crick C-G pair (Figure 2B and G).…”

Section: Resultsmentioning

confidence: 99%

“…Extensive research has been done to design and synthesize TFOs with modified nucleobases to enhance the recognition of C-G inversions in DNA duplexes (25–28). A guanidine functionalized C base, N 4 -(2-guanidoethyl)-5-methylcytosine (27) has been previously incorporated into relatively long TFOs (17-mer) with 2′-O-methyl (2′-OMe) and 2′-O-aminoethoxy (2′-AE) RNA backbones for TFO·DNA 2 triplex formation.…”

Section: Introductionmentioning

confidence: 99%

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Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

Toh¹,

Devi²,

Patil³

et al. 2016

Nucleic Acids Res

122

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RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson–Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

Toh¹,

Devi²,

Patil³

et al. 2016

Nucleic Acids Res

122

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“…Targeting dsRNAs through sequence-specific majorgroove triplex formation is a promising strategy and numerous chemical modifications have been developed to enhance the binding affinity and specificity of Triplex-Forming Oligonucleotides (TFOs) (14)(15)(16)(17)(18)(19). Peptide Nucleic Acids (PNAs) (20) typically have a neutral peptide-like backbone ( Figure 1) and are advantageous with strong resistance against nucleases and proteases, and enhanced binding to natural nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A–U pairs in dsRNAs

Patil

Toh

Yuan

et al. 2018

Nucleic Acids Research

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Double-stranded RNA (dsRNA) structures form triplexes and RNA-protein complexes through binding to single-stranded RNA (ssRNA) regions and proteins, respectively, for diverse biological functions. Hence, targeting dsRNAs through major-groove triplex formation is a promising strategy for the development of chemical probes and potential therapeutics. Short (e.g., 6–10 mer) chemically-modified Peptide Nucleic Acids (PNAs) have been developed that bind to dsRNAs sequence specifically at physiological conditions. For example, a PNA incorporating a modified base thio-pseudoisocytosine (L) has an enhanced recognition of a G–C pair in an RNA duplex through major-groove L·G–C base triple formation at physiological pH, with reduced pH dependence as observed for C+·G–C base triple formation. Currently, an unmodified T base is often incorporated into PNAs to recognize a Watson–Crick A–U pair through major-groove T·A–U base triple formation. A substitution of the 5-methyl group in T by hydrogen and halogen atoms (F, Cl, Br, and I) causes a decrease of the pKa of N3 nitrogen atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions. Here, we synthesized a series of PNAs incorporating uracil and halouracils, followed by binding studies by non-denaturing polyacrylamide gel electrophoresis, circular dichroism, and thermal melting. Our results suggest that replacing T with uracil and halouracils may enhance the recognition of an A–U pair by PNA·RNA2 triplex formation in a sequence-dependent manner, underscoring the importance of local stacking interactions. Incorporating bromouracils and chlorouracils into a PNA results in a significantly reduced pH dependence of triplex formation even for PNAs containing C bases, likely due to an upshift of the apparent pKa of N3 atoms of C bases. Thus, halogenation and other chemical modifications may be utilized to enhance hydrogen bonding of the adjacent base triples and thus triplex formation. Furthermore, our experimental and computational modelling data suggest that PNA·RNA2 triplexes may be stabilized by incorporating a BrUL step but not an LBrU step, in dsRNA-binding PNAs.

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“…In spite of the number of many studies for antiparallel type (Kolganova et al., ; Sasaki and Taniguchi et al., ; Taniguchi & Sasaki, ; Taniguchi, Nakamura, Senko, Nagatsugi, & Sasaki, .) and parallel type (Hari, Akabane, & Obika, ; Ohkubo et al., ; Semenyuk et al., ) triplex formations, there are no general compounds for the formation of the stable triplex DNA with a high selectivity. Therefore, it is desired to develop innovative artificial nucleic acid derivatives.…”

Section: Commentarymentioning

confidence: 99%

Synthesis of 2′‐deoxy‐4‐aminopyridinylpseudocytidine Derivatives for Incorporation Into Triplex Forming Oligonucleotides

Taniguchi

Wang

Okamura

et al. 2019

CP Nucleic Acid Chemistry

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This unit describes the detailed synthetic protocol for the preparation of the phosphoramidite units of the 2′‐deoxy‐4‐aminopyridinylpseudocytidine derivatives. These C‐nucleoside derivatives are useful units for the incorporation into triplex forming oligonucleotides (TFOs) to form the stable triplex DNA containing the CG interrupting sites. Commercially available 1‐methyl‐2′‐deoxypseudouridine is prepared from thymidine and 5‐iodo‐uracil by a simple method, that is, coupling of glycal and 5‐iodo‐1‐methyluracil by the Heck reaction, followed by desilylation and diastereoselective reduction. The carbonyl group at the 4 position of the pseudouridine derivative is activated by 3‐nitorotriazole and treated with the corresponding aromatic amine compounds to produce the 2′‐deoxy‐4‐aminopyridinylpseudocytidine derivatives. These derivatives are then successfully converted to the phosphoramidite units and incorporated into the oligodeoxynucleotides. © 2019 by John Wiley & Sons, Inc.

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Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

Cited by 43 publications

References 29 publications

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A–U pairs in dsRNAs

Synthesis of 2′‐deoxy‐4‐aminopyridinylpseudocytidine Derivatives for Incorporation Into Triplex Forming Oligonucleotides

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