Effect of each guanidinium group on the RNA recognition and cellular uptake of Tat-derived peptides

Wu, Cheng‐Hsun; Weng, Ming-Huei; Chang, Hsien-Chen; Li, Jhe-Hao; Cheng, Richard P.

doi:10.1016/j.bmc.2014.03.037

Cited by 10 publications

(9 citation statements)

References 49 publications

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“…The cellular uptake of a DNA duplex-binding TFO with a 2′-OMe or 2′-AE RNA backbone containing a Q base is facilitated by electroporation (27). We reason that combining the guanidine group and the flexibility of PNA backbone may facilitate the penetration (37,38,46,48–53) of the Q modified PNAs through the cell membrane. Our preliminary confocal microscopy studies (Figure 7) show that a PNA incorporating three Q residues and labeled with Cy3 dye (Supplementary Table S1) is taken by HeLa cells without any transfection agent.…”

Section: Resultsmentioning

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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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%

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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“…It is known that incorporation of the guanidinium moiety facilitates enhanced cellular uptake of various cargos including PNAs. 13,23,[38][39][40][41][42][43][44][45][46][47][48][49] We attached carboxyfluorescein to PNAs P1 (H2N-Lys-TCTCTTTC-CONH2,) and P5-3R (H2N-Lys-TRTRTTTR-CONH2) to obtain P1-CF and P5-3R-CF, respectively (Table S1), to assess how incorporation of R residues may affect cellular permeability. We incubated Sf9 cells with carboxyfluorescein-labelled P5-3R-CF and P1-CF for Our previous work shows that incorporating multiple Q but not L residues may not improve cellular permeability, 13,55 although both Q and L have a guanidine moiety (Figure 1).…”

Section: Cellular Uptake Of An R-modified Pnamentioning

confidence: 99%

“…[29][30][31][32][33][34][35][36][37] Incorporation of the guanidinium moiety facilitates enhanced cellular uptake of various cargos. 13,23,[38][39][40][41][42][43][44][45][46][47][48][49] Free guanidinium has recently been found to be tightly bound in riboswitches. 50,51 Guanidine modified aromatic moieties have been incorporated into artificial nucleic acids for the recognition of single-stranded G residues as G-clamps 52,53 or C-G pairs through Q·C-G triple (Figure 1e) or other triple formation.…”

Section: Introductionmentioning

confidence: 99%

“…Guanidinium (protonated form of guanidine) has unique hydrogen bonding and interesting stacking properties. , Guanidinium (arginine residue) is present in proteins often involved in hydrogen bonding and stacking interactions with nucleic acids. − Various compounds incorporating the guanidinium moiety show important biological activities. − Incorporation of the guanidinium moiety facilitates enhanced cellular uptake of various cargos. ,,− Free guanidinium has recently been found to be tightly bound in riboswitches. , …”

mentioning

confidence: 99%

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Incorporating G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs

et al. 2019

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Recognition of RNAs at physiological conditions is important for developing chemical probes and therapeutic ligands. Nucleobase modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner at near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, as well as in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic with unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs for facilitating enhanced molecular recognition of G-C pairs in dsRNAs and for improved bioactivity. We grafted guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of PNA R monomer is relatively simple compared to that of previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, influenza A viral panhandle duplex structure, and HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.

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“…Extensive studies have been done for facilitating the cellular uptake bioactive PNAs and other peptides and nucleic acids (32,34,(88)(89)(90)(91)(92)(93)(94)(95)(96)(97)(98)(99)(100). We focused on testing the effect of bromination of PNA on cellular uptake as previous studies suggest that fluorination of PNA T base does not significantly enhance cellular uptake of PNAs (101,102).…”

Section: Targeting Hiv-1 Ribosomal Frameshift Inducing Mrna Hairpinmentioning

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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Effect of each guanidinium group on the RNA recognition and cellular uptake of Tat-derived peptides

Cited by 10 publications

References 49 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 G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs

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

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