Conformational Control of Dual Emission by Pyrrolidinyl PNA-DNA Hybrids (original) (raw)
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Biochemical and Biophysical Research Communications, 2008
Molecular dynamics (MD) simulations and experimental measurements of the stability of a novel pyrrolidinyl PNA binding to DNA (PNAÁDNA) in both parallel and antiparallel configurations were carried out. For comparison, simulations were also performed for the DNAÁDNA duplex. The conformations of the three simulated systems were found to retain well-defined base pairing and base stacking as their starting B-like structure. A large gas-phase energy repulsion of the two negatively charged sugar-phosphate backbones of the DNA strands was found to reduce the stability of the DNAÁDNA duplex significantly compared with that of the PNAÁDNA complexes, especially in the antiparallel binding configuration. In addition, the antiparallel PNAÁDNA was observed to be less solvated than that of the other two systems. The simulated binding free energies and the experimental melting temperatures for the three investigated systems are in good agreement, indicating that the antiparallel PNAÁDNA is the most stable duplex.
α-PNA: A Novel Peptide Nucleic Acid Analogue of DNA
The Journal of Organic Chemistry, 1997
Peptide nucleic acid (PNA) analogues of DNA have attracted interest as potential pharmacological regulators of gene expression since they have the capacity to invade duplex DNA forming Watson-Crick base paired PNA:DNA heteroduplexes. Unfortunately, strand invasion is limited to homopurine and homopyrimidine sequences and there is the need to explore further PNA analogues for the purpose of expanding the strand invasion alphabet. Accordingly, we have designed a true peptide mimic of DNA (designated R-PNA) involving novel L-R-amino acids, with side chains comprising the four DNA bases attached via an ethylene linkage, interspaced with glycine. The four base-containing amino acids have been synthesized from N-Boc-L-homoserine, via alkylation of the appropriate base with the key intermediate (S)-2-(N-Boc-amino)-4-bromobutyric acid methyl ester followed by hydrolysis. These amino acids have been incorporated into R-PNA oligomers using both solution and solid phase methods.
Peptide Nucleic Acids with a Conformationally Constrained Chiral Cyclohexyl-Derived Backbone
Chemistry - A European Journal, 1997
Peptide nucleic acid (PNA) is an achiral nucleic acid mimic with a backbone consisting of partly flexible aminoethyl glycine units. By replacing the aminoethyl portion of the backbone by an amino cyclohexyl moiety. either in the (S , S) or the (R,R) configuration, we havc synthesized conformationally constrained PNA residues. PNA oligomers containing (S,S)-cyclohexyl residues were able to form hybrid complexes with DNA or RNA, with little effect on the thermal stability (AT,, = * I "C per (S,S) unit, depending on their number and the sequence). I n contrast. incorporation of the (R,R) isomer resulted in a drastic decrease in the stability of the PNA-DNA (or
Bioconjugate Chemistry, 2013
A methodology for the site-specific attachment of fluorophores to the backbone of pyrrolidinyl peptide nucleic acids (PNAs) with an α/β-backbone derived from D-prolyl-(1S,2S)-2aminocyclopentanecarboxylic acid (acpcPNA) has been developed. The strategy involves a postsynthetic reductive alkylation of the aldehyde-containing labels onto the acpcPNA that was previously modified with (3R,4S)-3-aminopyrrolidine-4-carboxylic acid on the solid support. The reductive alkylation reaction is remarkably efficient and compatible with a range of reactive functional groups including Fmoc-protected amino, azide, and alkynes. This allows further attachment of readily accessible carboxyl-, alkyne-, or azidecontaining labels via amide bond formation or Cu-catalyzed azide− alkyne cycloaddition (CuAAC, also known as click chemistry). The label attached in this way does not negatively affect the affinity and specificity of the pairing of the acpcPNA to its DNA target. Applications of this methodology in creating self-reporting pyrene-and thiazole orange-labeled acpcPNA probes that can yield a change in fluorescence in response to the presence of the correct DNA target have also been explored. A strong fluorescence enhancement was observed with thiazole orange-labeled acpcPNA in the presence of DNA. The specificity could be further improved by enzymatic digestion with S1 nuclease, providing a 9-to 60-fold fluorescence enhancement with fully complementary DNA and a less than 3.5-fold enhancement with mismatched DNA targets.
Proceedings of the National Academy of Sciences, 2003
Peptide nucleic acids (PNAs) are oligonucleotide analogues in which the sugar-phosphate backbone has been replaced by a pseudopeptide skeleton. They bind DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids more stable than the corresponding nucleic acid complexes. The binding affinity and selectivity of PNAs for nucleic acids can be modified by the introduction of stereogenic centers (such as D-Lys-based units) into the PNA backbone. To investigate the structural features of chiral PNAs, the structure of a PNA decamer containing three D-Lys-based monomers (namely H-GpnTpnApnGpnAdlTdlCdlApnCpnTpn-NH2, in which pn represents a pseudopeptide link and dl represents a D-Lys analogue) hybridized with its complementary antiparallel DNA has been solved at a 1.
Hybridization of Peptide Nucleic Acid
Biochemistry, 1998
The thermodynamics of hybridization and the conformations of decameric mixed purinepyrimidine sequence PNA/PNA, PNA/DNA, and DNA/DNA duplexes have been studied using fluorescence energy transfer (FET), absorption hypochromicity (ABS), isothermal titration calorimetry (ITC), and circular dichroism (CD) techniques. The interchromophoric distances determined in the FET experiments on fluorescein-and rhodamine-labeled duplexes indicate that the solution structures of the duplexes are extended helices in agreement with available NMR (PNA/DNA) and crystal X-ray data (PNA/PNA). The melting thermodynamics of the duplexes was studied with both FET and ABS. The thermodynamic parameters obtained with ABS are in good agreement with the parameters from calorimetric measurements while FET detection of duplex melting gives in most cases more favorable free energies of hybridization. This discrepancy between FET and ABS detection is ascribed to the conjugated dyes which affect the stability of the duplexes substantially. Especially, the dianionic fluorescein attached via a flexible linker either to PNA or to DNA seems to be involved in an attractive interaction with the opposite dicationic lysine when hybridized to a PNA strand. This interaction leads to an increased thermal stability as manifested as a 3-4°C increase of the melting temperature. For the PNA/DNA duplex where fluorescein is attached to the PNA strand, a large destabilization (∆T m ) -12°C) occurs relative to the unlabeled duplex, probably originating from electrostatic repulsion between the fluorescein and the negatively charged DNA backbone. In the case of the PNA/PNA duplex, the sense of helicity of the duplex is reversed upon conjugation of fluorescein via a flexible linker arm, but not when the fluorescein is attached without a linker to the PNA. FIGURE 1: Chemical structures of DNA and PNA. The deoxyribose phosphate ester backbone in DNA has been changed to N-(2aminoethyl)glycine in PNA. FIGURE 2: (a) Sequences of PNA and DNA used in this study (all lysines with L-configuration). (b) Schematic structures and notations of the fluorescently labeled PNAs and DNAs. Strands positioned in antiparallel orientation.
Role of chirality and optical purity in nucleic acid recognition by PNA and PNA analogs
Chirality, 2002
Peptide nucleic acids are DNA mimics able to form duplexes with complementary DNA or RNA strands of remarkable affinity and selectivity. Oligopyrimidine PNA can displace one strand of dsDNA by forming PNA 2 :DNA triplexes of very high stability. Many PNA analogs have been described in recent years, in particular, chiral PNA analogs. In the present article the results obtained recently using PNA derived from N-aminoethylamino acids 7 are illustrated. In particular, the dependence of optical purity on synthetic methodologies and a rationale for the observed effects of chirality on DNA binding ability is proposed. Chirality as a tool for improving sequence selectivity is also described. PNA analogs derived from D-or L-ornithine 8 were also found to be subjected to epimerization during solid phase synthesis. Modi®cation of the coupling conditions or the use of a submonomeric strategy greatly reduced epimerization. The optically pure oligothymine PNAs 8 were found to bind to RNA by forming triplexes of unusual CD spectra. The melting curves of these adducts presented two transitions, suggesting a conformational change followed by melting at high temperature.
Beilstein Journal of Organic Chemistry, 2014
DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV-vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA-DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes. 2166