Oxy-peptide Nucleic Acids Research Articles

Quantification of the orientations of pyrrolidine-based oxypeptide nucleic acid–DNA hybrid duplexes

We describe the fluorescence quenching-based quantification of complementary parallel and antiparallel hybrids of DNAs with pyrrolidine-based oxypeptide nucleic acids (POPNAs). When BODIPY-modified DNAs as fluorescent probe formed hybrids with complementary POPNAs, fluorescence of the BODIPY was effectively quenched by the guanine unit and the Lys unit on the POPNAs. The orientations of hybrids of POPNA with DNA were estimated by the quenching efficiencies of two BODIPY-modified DNAs. As a result, we clarified that configurations of POPNAs affect the extent of orientation of the hybrid duplexes.

Antisense effect of pyrrolidine-based oxy-peptide nucleic acids in Escherichia coli

To investigate the antisense effect of a pyrrolidine-based oxy-peptide nucleic acid (POPNA), we carried out the LacZ reporter assay using a 12-mer trans-l-POPNA conjugated with a cell-penetrating peptide (antisense reagent). The antisense effect of the conjugated POPNA (inhibition of LacZ activity) was comparable to that shown by a Nielsen-type peptide nucleic acid. Furthermore, the conjugated POPNA could switch the LacZ activity over a wide range of ambient temperatures.

Synthesis of pyrrolidine-based oxy-peptide nucleic acids carrying four types of nucleobases and their transport into cytoplasm

We synthesized 16 pyrrolidine-based oxy-peptide nucleic acid (POPNA) monomers carrying four different nucleobases onto four different stereoisomers of pyrrolidine rings. Using these monomers, we prepared POPNA oligomers, which formed sequence-specific hybrids with DNAs. The oligomer configurations influenced the hybrid stability. The oligomers were not taken into CHO cells. However, they could enter the cell cytoplasm when mixed with the influenza virus hemagglutinin peptide–arginine heptamer conjugate.

ChemInform Abstract: Synthesis of δ-Amino Acids with an Ether Linkage in the Main Chain and Nucleobases on the Side Chain as Monomer Units for Oxy-Peptide Nucleic Acids.

Abstract Syntheses of four N -Fmoc δ-amino acids with an ether linkage in the main chain and four different nucleobases on the side chain, Fmoc-NH-C ∗ H(CH 2 -CH 2 -B)-CH 2 -O-CH 2 -COOH (B =thymine, uracil, N 4 -benzoylcytosine, and N 2 -isobutyrylguanine) are described. The δ-amino acids were prepared through 8–12 step synthesis starting from l -homoserine and could be linked together to form novel peptide nucleic acids (oxy-PNAs = OPNAs).

Synthesis of a Novel Pyrrolidine-based Peptide Nucleic Acid that Contains Tertiary Amines in the Main Chain and Its Internalization into Cells

Abstract A novel thymine monomer of pyrrolidine-based peptide nucleic acid that contains tertiary amines in the main chain (pyrrolidine-based amino peptide nucleic acid = PAPNA) was synthesized. A mixed oligomer of two PAPNA(T) units and seven units of pyrrolidine-based oxypeptide nucleic acid (POPNA), was synthesized by a solid-phase method. The mixed oligomer was internalized into CHO cells more readily than the previous version of POPNA oligomers.

Configurational preference of pyrrolidine‐based oxy‐peptide nucleic acids as hybridization counterparts with DNA and RNA

A new series of oxy-peptide nucleic acids (pyrrolidine-based oxy-peptide nucleic acids = POPNAs) of four different stereoisomeric forms (cis-L, cis-D, trans-L, trans-D) have been synthesized. To find a favorable stereoisomer of POPNA for hybridization with DNA or RNA, thermodynamic parameters and conformations of the hybrids between the four stereoisomers with 9 adenine bases [po(A(9))s] and dT(9) or rU(9) were investigated from ultraviolet (UV) melting curves and circular dichroism (CD) spectra. The cis-L-po(A(9)) formed the most stable hybrid with dT(9), because of the smallest entropy loss, despite the smallest enthalpy gain. In contrast, trans-L-po(A(9)) formed the most stable hybrid with rU(9), because of the largest enthalpy gain, despite the largest entropy loss. The hybrid stability of trans-L-po(A(9)) with rU(9) was significantly improved as compared with a previous version of oxy-peptide nucleic acid (OPNA) that lacks the pyrrolidine ring.

Fluorescence Detection of Hybrid Formation between Pyrrolidine-based Oxy-peptide Nucleic Acid and DNA

Abstract When an oxy-peptide nucleic acid that contains pyrrolidine rings (pyrrolidine-based oxy-PNA = POPNA) hybridized with its complementary DNA, a fluorophore, DiSC2(5), bound specifically to the hybrid in aqueous solution. Free DiSC2(5) did not fluoresce by itself, but the bound DiSC2(5) showed strong fluorescence. The fluorescence was observed only on a fully-matched POPNA–DNA hybrid, but not on hybrids with even single mismatches. This finding provides bases for highly sensitive and highly specific detection of single nucleotide polymorphisms.

Synthesis of pyrrolidine-based oxy-peptide nucleic acids that contain four bases and their properties

Adenine, guanine, thymine and cytosine monomers of oxy-peptide nucleic acid that contain a pyrrolidine ring in the main chain have been synthesized for use in the synthesis of novel peptide nucleic acid.

Oxy-peptide nucleic acid with a pyrrolidine ring that is configurationally optimized for hybridization with DNAElectronic supplementary information (ESI) available: details of synthesis and the spectral data of four stereoisomers of POPNA. See http://www.rsc.org/suppdata/cc/b4/b401057d/

Four stereoisomers of oxy-peptide nucleic acids containing ether linkages in the main chain and conformationally-restricted pyrrolidine rings (pyrrolidine-based oxy-PNA = POPNA) were newly synthesized and investigated for binding to DNA. cis-l-POPNA with 9 adenine bases formed the most stable hybrid with dT(9). The POPNA showed high sequence specificity similar to that of the Nielsen-type PNA and sharper melting behavior in hybridization with DNA than the Nielsen-type PNA.

Thermodynamic analysis of hybridization between POPNA and DNA.

We have developed a new series of oxy-peptide nucleic acids with pyrrolidine rings of four different types of structural isomers (cis L, cis D, trans L, trans D configurations; POPNAs). Melting curves of adenine nanomers of POPNAs in the presence of the complementary DNA showed the highest Tm value for cis L-POPNA, but in the case of RNA, the highest Tm value was observed for trans L-POPNA. Thermodynamic parameters (delta H and delta S) of POPNA/DNA and POPNA/RNA hybridizations were evaluated from concentration dependence of Tm values. The POPNA/DNA and POPNA/RNA hybridizations were governed by entropy and enthalpy terms, respectively.

Synthesis and DNA Binding Property of a Novel Peptide Nucleic Acid that Contains cis-4-Adeninyl-l-prolinol Unit

Abstract A novel oxy-peptide nucleic acid that contains a cis-4-adeninyl-l-prolinol unit in the main chain (PPNA) was synthesized. The peptide nucleic acid with nine adenine units [PPNA(A9)] hybridized with the complementary DNA (T9). The hybrid showed a very sharp melting curve with Tm = 34 °C.

Hybridization between oxy-peptide nucleic acids and DNAs: dependence of hybrid stabilities on the chain-lengths, types of base pairs, and the chain directions.

Oxy-peptide nucleic acids (OPNAs) of [-NH-CH(CH2-CH2-Base)-CH2-O-CH2-CO-]-type main chain with four different types of nucleobases (Base = A, G, C, and U) or with an abasic side group (X) were synthesized. Melting curves of the 1:1 hybrids of o(A(n))-d(Tn)) pairs with n = 6, 9, 12, and 15 showed very sharp transitions at high Tm values, particularly for long chains, indicating that nearly optimum matching is attained in the structure of the o(A(n))-d(Tn) hybrids. Effect of different types of base pairs on the hybrid stabilities was examined for the o(A4NA4)-d(T4N'T4) 1:1 mixtures where N is A, G, C, U, or X and N' is A, G, C, or T. In all series of the hybrids the complementary pairs showed the highest Tm values. The Tm values of the complementary pairs were about 35 degrees C when purine bases were inserted as the N group in the OPNA, but they were 20-23 degrees C when pyrimidine bases were inserted. The melting curves of the hybrids with a single mismatch were similar to those with a single X-N' pair, suggesting that the mismatch base pairs have been ignored in the hybrids. All complementary OPNA-DNA hybrids showed higher Tm values and sharper transitions than the corresponding DNA-DNA hybrids. The OPNA-DNA hybrids favor a parallel direction i.e., the N-terminal of OPNA is directed to the 5'-terminal of DNA.

Synthesis of oxy-peptide nucleic acids with mixed sequences.

Syntheses of N-Fmoc delta-amino acids with an ether linkage in the main chain and six different nucleobases on the side chain, Fmoc-NH-C*H(CH2-CH2-B)-CH2-O-CH2-COOH (B = N6-benzoyladenine, thymine, uracil, N-benzoylcytosine, guanine, and N2-isobutyrylguanine) are described. The delta-amino acids were prepared through 8-12 step synthesis starting from L-homoserine and could be linked together to form novel peptide nucleic acids (oxy-PNAs = OPNAs) by solid-phase peptide synthesis.

Synthesis of δ-amino acids with an ether linkage in the main chain and nucleobases on the side chain as monomer units for oxy-peptide nucleic acids

Syntheses of four N-Fmoc δ-amino acids with an ether linkage in the main chain and four different nucleobases on the side chain, Fmoc-NH-C ∗H(CH 2-CH 2-B)-CH 2-O-CH 2-COOH (B =thymine, uracil, N 4-benzoylcytosine, and N 2-isobutyrylguanine) are described. The δ-amino acids were prepared through 8–12 step synthesis starting from l-homoserine and could be linked together to form novel peptide nucleic acids (oxy-PNAs = OPNAs).