PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis, Binding Properties, and Enzymatic Stability

Abstract

Three chimeric dimer synthons (oeg_t(NH)T, oeg_up(NH)T and oeg_uh(NH)T) containing thymine (t), 5-(1-propynyl)-uracil (up) and 5-(1-hexyn-1-yl)-uracil (uh) PNA units with N-(2-hydroxyethyl)glycine (oeg) backbone were synthesized in solution and incorporated into T20 oligonucleotide analogues, using standard P-amidite chemistry. Insertion of dimer blocks led to destabilization of duplexes with dA20 target. The smallest Tm drops were found for chimeras containing oeg_up(NH)T dimers. Incorporation of the chimeric synthons into the 3'-end of T20 brought about growing resistance to 3'-exonucleolytic (SV PDE) cleavage in the order of oeg_t(NH)T < oeg_up(NH)T < oeg_uh(NH)T. Due to different endonuclease activities of 3'- and 5'-exonucleases applied, placing of five consecutive dimers at the 5'-terminus resulted in a relatively smaller, but also side-chain dependent, stabilization towards the hydrolysis by 5'-exonuclease (BS PDE). Neither exonucleases (SV and BS PDE) nor an endonuclease (Nuclease P1) could hydrolyse the unnatural phosphodiester bond linking the 3'-OH of thymidine to the terminal OH of N-(2-hydroxyethyl)glycine PNA backbone.

Alternate PNA‐DNA chimeras (PNA‐DNA)n: Synthesis, binding properties and biological activity

“…Coupling efficiencies were calculated to be >80% for PNA monomers and >90% for DNA monomers (average yields). This synthetic strategy, unlike previously reported approaches for the assembly of oligomers containing alternate PNA-DNA moieties which employs as building blocks PNA-DNA dimers activated as phosphoramidites, 15 should allow for the synthesis of mixed sequences with no need to preform the dimer in the correct combination. In our approach, all the sequences can be obtained using any PNA monomer and any DNA monomer, while in the other reported strategies a bigger effort is required to synthesize dimers in all their combinations.…”

“…In our approach, all the sequences can be obtained using any PNA monomer and any DNA monomer, while in the other reported strategies a bigger effort is required to synthesize dimers in all their combinations. 15 Cleavage of the molecules from the resin was performed by treatment with a NH 4 OH aq (37%) solution at 508C, 2 h. Oligomers were purified by HPLC on an anion exchange column, followed by desalting on Sephadex G25 prepacked column. Matrix Assisted Laser Desorption Ionization-Time Of Flight (MALDI-TOF) mass spectra of the purified chimeras confirmed the identity of the molecules.…”

Synthesis and properties of oligonucleotides that contain a triazole‐linked nucleic acid dimer

“…The total strand concentration ranged from 2.4 to 3.0 lM in 90 mM NaCl, 10 mM sodium phosphate, and 1 mM EDTA at pH 7.0. a For the DT m values, the T m of Entry I is the reference (T m ¼ 40.9 C). observed when compared to a PNA-DNA chimera that contained a PNA element at the terminal end [29].…”

Nucleobase Modifications in Peptide Nucleic Acids

“…(5) [13,14]. The PNA was incorporated by use of preformed PNA-DNA heterodimers compatible with DNA oligomerization chemistry.…”