Synthesis of Amino- and Guanidino-G-Clamp PNA Monomers

Ausín, Cristina; Ortega, José-Antonio; Robles, Jordi; Grandas, Anna; Pedroso, Enrique

doi:10.1021/ol026815p

Cited by 47 publications

(34 citation statements)

References 25 publications

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“…Preparation of the tC O nucleoside for standard automated solid-phase methods using β-cyanoethyl phosphoramidite was carried out by dimethoxytritylation at the 5′-OH group (49) and phosphitylation of the 3′-OH group (Supplementary Material) to afford the dimethoxytrityl-protected phosphoramidite monomer suitable for oligonucleotide synthesis. The potassium salt of 1,3-diaza-2-oxophenoxazin-3-yl acetic acid, KtC O , was obtained by saponification of the tert-butyl ester that was synthesized following the procedures of Rajeev et al (51) and Ausín et al (52). …”

Section: Methodsmentioning

confidence: 99%

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

Sandin

Börjesson

et al. 2007

Nucleic Acids Research

142

195

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This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tCO, is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tCO is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (ε = 9000 M−1 cm−1) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tCO shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tCO, on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tCO a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).

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Section: Methodsmentioning

confidence: 99%

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

Sandin

Börjesson

et al. 2007

Nucleic Acids Research

142

195

View full text Add to dashboard Cite

show abstract

“…For the ethyl- and propyl-derivatives, this method resulted in poor yields, even after long reaction times, presumably because of the lower reactivities of ethyl and propyl bromides. Instead, the alkylations were performed by treatment with the corresponding bromides in presence of K 2 CO 3 in DMSO (47). This procedure afforded the mono- as well as the dialkylated products, which were separated by column chromatography to yield N1-ethyl- (2b) and N1-propyl- (2c) 5-bromouracil in moderate yields.…”

Section: Resultsmentioning

confidence: 99%

Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç

Shelke

Sigurdsson

2011

Nucleic Acids Research

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The influence of structural changes of an abasic site in duplex DNA on noncovalent and site-directed spin labeling (NC-SDSL) of the spin label ç were examined with electron paramagnetic resonance (EPR) spectroscopy. The binding affinities of ç to sixteen different DNA duplexes containing all possible sequences immediately flanking the abasic site were determined and the results showed that the binding of ç is highly flanking-sequence dependent. In general, a 5′-dG nucleotide favors the binding of the spin label. In particular, 5′-d(G__T) was the best binding sequence whereas 5′-d(C__T) showed the lowest affinity. Changing the structure of the abasic site linker from a tetrahydrofuran analog (F) to the anucleosidic C3-spacer (C3) does not appreciably affect the binding of ç to the abasic site. For efficient binding of ç, the abasic site needs to be located at least four base pairs away from the duplex end. Introducing a methyl substituent at N3 of ç did not change the binding affinity, but a decreased binding was observed for both N3-ethyl and -propyl groups. These results will guide the design of abasic site receptors and spin label ligands for NC-SDSL of nucleic acids.

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“…Pedroso and coworkers have prepared benzyloxycarbonylprotected Fmoc monomers of the G-clamp and guanidino G-clamp derivative [32]. The guanidino derivative is of interest because it is expected to make an additional H-bond with the N7-atom of guanine, Fig.…”

Section: Analogs Of Thymine and Cytosinementioning

confidence: 99%

Nucleobase Modifications in Peptide Nucleic Acids

Wojciechowski

Hudson

2007

CTMC

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Peptide nucleic acid (PNA) is an oligonucleotide mimic originally designed upon a repeating N-(2-aminoethyl)glycine polyamide backbone to which nucleobase heterocycles are attached through a methylene carbonyl linkage to the alpha-amino group. These molecules possess remarkable hybridization properties with DNA or RNA forming complexes with high stability and with excellent sequence discrimination despite the substantial structural divergence from natural nucleic acids. Since the disclosure of PNA, a vibrant research community with interest in the chemistry and applications of polyamide-based nucleic acid analogs has developed. This has led to the synthesis and evaluation of a wide variety of modified polyamide nucleic acids. The focus of this report is a comprehensive review of nucleobase modifications in aminoethylglycine (aeg) PNA with reference, where appropriate, to the same modification in DNA or RNA.

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Synthesis of Amino- and Guanidino-G-Clamp PNA Monomers

Cited by 47 publications

References 25 publications

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç

Nucleobase Modifications in Peptide Nucleic Acids

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