PNA-DNA chimeras containing 5-alkynyl-pyrimidine PNA units. Synthesis, binding properties, and enzymatic stability.
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.
Bajor
Zoltán
Z
Chemical Research Center, Institute of Chemistry, Hungarian Academy of Sciences, Budapest, Hungary.
Sági
Gyula
G
Tegyey
Zsuzsanna
Z
Kraicsovits
Ferenc
F
D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism*; D019281:Dimerization; D004795:Enzyme Stability; D006868:Hydrolysis; D015394:Molecular Structure; D009691:Nucleic Acid Denaturation; D020135:Peptide Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism*; D011743:Pyrimidines / Q000737:chemistry*; D013696:Temperature
D020135:Peptide Nucleic Acids; D011743:Pyrimidines; D004247:DNA; C030986:pyrimidine