Synthesis and properties of PNA/DNA chimeras

Homopyrimidine PNAs form PNA-DNA-PNA triplexes with dsDNA by displacing one DNA strand. The nucleobase interactions follow Watson-Crick and Hoogsteen base pairing rules. This finding has led to the development of bis-PNAs consisting of a strand anti-parallel to the target DNA for Watson-Crick recognition and a second covalently linked strand which is designed to bind the target DNA by Hoogsteen base pairing. These bis-PNAs show a higher mismatch discrimination due to the two-fold recognition process.

Moreover, binding of DNA–PNA chimeras to double-stranded DNA to form triple helices was studied.

The objective of this study was to evaluate the effects of inserting PNA oligonucleotide sequences into the protein-binding surface of an immobilized 4WJ. As expected, the CD amplitude for each hybrid 4WJ was diminished (and blue-shifted) versus J1 due to the presence of the achiral PNA strand. A similar CD profile is generated by chimeric PNA-DNA duplexes., With regard to specific spectroscopic features of each hybrid, 4WJ-PNA1 did not undergo a clear transition between an open-x and stacked-x conformation in the presence of magnesium ions. The divergent CD spectra for 4WJ-PNA1 may reflect the inability of this substrate to acquire a stacked conformation. A similar CD pattern was observed for mobile 4WJs in the presence of MgCl2.57

Solid phase synthesis of DNA-3′-PNA chimeras by …

These PNA monomers were used for the preparation of several DNA–PNA chimeras and their hybridization properties are described.

Despite its name, PNA is neither a nucleic acid nor a peptide. As a result, PNA is stable against enzymatic degradation by both proteases and nucleases. In combination with the high DNA- and RNA-binding affinity, PNA's increased biostability has stimulated research into its potential as an antisense or antigene drug. It is able to inhibit transcription by blocking RNA polymerase as demonstrated for a T-octamer PNA by Nielsen and co-workers. In contrast to other antisense agents like phosphorothioates, PNA does not induce RNase H-mediated cleavage of the RNA strand but acts via steric blocking of either RNA processing, transport into cytoplasm, or translation.,,, Besides PNA, PNA-DNA-chimeras have been investigated as potential antisense agents. These chimeras can stimulate RNase H as well as RNase L activity and are therefore more effective antisense agents than pure PNA. PNA-DNA chimeras can also act as substrates for other oligonucleotide related enzymes like DNA-polymerases and reverse transcriptases. Both PNA and PNA-DNA-chimeras suffer from low cellular uptake. Several attempts to circumvent this problem have been made. Cationic liposomes have been used as carriers to deliver PNAs to the cytoplasm. Attaching antibodies to PNA also improves their ability to enter cells. Another way of enhancing cellular uptake is the coupling to a delivery peptide that accelerates cellular uptake significantly. Other peptide sequences, including a 35 residue peptide from HIV Tat, appear to have the same properties.

phase synthesis of APNA-PNA chimeras and APNA homopolymers ..

PNA oligomers that carry six histidine residues can be used to purify target nucleic acids by nickel affinity chromatography (24). Moreover, PNAs linked to biotin in combination and streptavidin-coated magnetic beads can be used to purify genomic DNA of Chlamydia trachomatis directly from urine samples. This "purification by hybridization" approach offers a number of advantages over traditional purification methods. One drawback, however, is that it requires knowledge of a target sequence and a dedicated capture oligomer must be synthesized for each different target nucleic acid. Short pyrimidine PNAs form unprecedently stable triplexes with complementary nucleic acids. Because being short means that their target sequence is prevalent in large nucleic acids, such short PNAs can be used as generic capture probes to purify large nucleic acids. It has been shown that a biotin-tagged PNA-thymine heptamer purifies human genomic DNA efficiently from whole blood by a simple and rapid procedure.

Solid phase synthesis of DNA-3'-PNA chimeras by ..

The association process of DNG/PNA chimera with single strand DNA and strand invasion of longer ds-DNA is faster than the association of PNA, with the same DNA targets, as evident by thermal hysteresis and gel retardation under isothermal conditions.

Synthesis and Properties of PNA/DNA Chimeras.

The binding of DNG/PNA chimera with guanidinium linkages on both ends, with single strand length-matched complementary DNA under thermal melt conditions and with longer double strand DNA under isothermal conditions is sequence specific.