Highly selective single nucleotide polymorphism recogniton by a chiral (5S) PNA beacon

Abstract

A chiral peptide nucleic acid (PNA) beacon containing a C-5 modified monomer based on L-lysine was synthesized. The terminal amino group of the lysine side chain was linked to a spacer for future applications on surfaces. The PNA beacon bears a carboxyfluorescein fluorophore and a dabcyl quencher at opposite ends. The DNA binding properties were compared with those of a homologous PNA beacon containing only achiral monomers. Both beacons underwent a fluorescence increase in the presence of complementary DNA, with higher efficiency and higher selectivity (evaluated using single mismatched DNA sequences) observed for the chiral monomer containing PNA. Ion exchange (IE) HPLC with fluorimetric detection was used in combination with the beacon for the selective detection of complementary DNA. A fluorescent peak corresponding to the PNA beacon:DNA duplex was observed at a very low detection limit (1 nM). The discriminating capacity of the chiral PNA beacon for a single mismatch was found to be superior to those observed with the unmodified one, thus confirming the potency of chirality for increasing the affinity and specificity of DNA recognition.

Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids

“…The use of modified PNA residues in PNA oligomers can also affect the binding affinity and selectivity to nucleic acids through backbone rigidification and preorganization [25–27], increase solubility [28], provide a handle for further conjugation or ligand display [29] or increase cellular uptake [30]. Recent work with diethylene glycol γ-substituted PNA residues afforded oligomers that had both higher binding affinity to DNA and increased aqueous solubility [31].…”

Effect of chirality in gamma-PNA: PNA interaction, another piece in the picture

“…15,16,17 It was demonstrated by our group that g-PNA synthesized from Lamino acids were strong inducer of righthandedness of PNA:PNA duplexes;…”

Synthesis of Enantiopure γ-Glutamic Acid Functionalized Peptide Nucleic Acid Monomers

“…1 Recently, a number of modifications of the basic PNA monomeric units have been reported in order to improve the binding stability to the complementary nucleic acid and the specificity of complexation. [2][3][4][5] Among them, one of the most distinct modification is the introduction of stereogenic center at γ-carbon atom of the N-aminoethylglycine unit. 5 Compared to unmodified normal PNAs, the γ-substituted PNAs have several advantages of improved solubility, less self-aggregation, increased stability of PNA-DNA duplexes, and opportunities of further functionalization.…”

“…[2][3][4][5] Among them, one of the most distinct modification is the introduction of stereogenic center at γ-carbon atom of the N-aminoethylglycine unit. 5 Compared to unmodified normal PNAs, the γ-substituted PNAs have several advantages of improved solubility, less self-aggregation, increased stability of PNA-DNA duplexes, and opportunities of further functionalization. 5,6 Also, it was reported that chiral PNAs have shown promising abilities in DNA recognition.…”

“…5 Compared to unmodified normal PNAs, the γ-substituted PNAs have several advantages of improved solubility, less self-aggregation, increased stability of PNA-DNA duplexes, and opportunities of further functionalization. 5,6 Also, it was reported that chiral PNAs have shown promising abilities in DNA recognition. In the case of γ-substituted PNAs, especially, L-isomer is more favored because D-isomer does not allow them to bind efficiently to DNA or RNA due to the geometric efficiency for α-helical duplex formation.…”