title: 3-Aminopyrrolidine-4-carboxylic acid as versatile handle for internal labeling of pyrrolidinyl PNA.
abstract: Conformationally restricted pyrrolidinyl PNAs with an α/β-dipeptide backbone consisting of a nucleobase-modified proline and a cyclic five-membered amino acid spacer such as (1S,2S)-2-aminocyclopentanecarboxylic acid (ACPC) (acpcPNA) can form very stable hybrids with DNA with high Watson-Crick base pairing specificity. This work aims to explore the effect of incorporating 3-aminopyrrolidine-4-carboxylic acid (APC), which is isosteric to the ACPC spacer, into the acpcPNA. It is expected that the modification should not negatively affect the DNA binding properties, and that the additional nitrogen atom in the APC should provide a handle for internal modification. Orthogonally-protected (N(3)-Fmoc/N(1)-Boc and N(3)-Fmoc/N(1)-Tfa) APC monomers have been successfully synthesized and incorporated into the acpcPNA by Fmoc-solid-phase peptide synthesis. T(m), UV and CD spectroscopy confirmed that the (3R,4S)-APC could substitute the (1S,2S)-ACPC spacer in the acpcPNA with only slightly decreasing the stability of the hybrids formed between the modified acpc/apcPNA and DNA. In contrast, the (3S,4R) enantiomer of APC caused substantial destabilization of the hybrids. Furthermore, a successful on-solid-support internal labeling of the acpc/apcPNA via amide bond formation between pyrene-1-carboxylic acid or 4-(pyrene-1-yl) butyric acid and the pyrrolidine nitrogen atom of the APC spacer has been demonstrated. Fluorescence properties of the pyrene-labeled acpc/apcPNAs are sensitive to their hybridization states and can readily distinguish between complementary and single-mismatched DNA targets.
authors.affiliation: Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Ta-Po District, Muang, Phitsanulok 65000, Thailand.
authors.forename: Nisanath
authors.initials: N
authors.lastname: Reenabthue
authors.forename: Chalothorn
authors.initials: C
authors.lastname: Boonlua
authors.forename: Chotima
authors.initials: C
authors.lastname: Vilaivan
authors.forename: Tirayut
authors.initials: T
authors.lastname: Vilaivan
authors.forename: Chaturong
authors.initials: C
authors.lastname: Suparpprom
mesh_terms: D002264:Carboxylic Acids / Q000737:chemistry*; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011759:Pyrrolidines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: C569521:3-aminopyrrolidine-4-carboxylic acid; D002264:Carboxylic Acids; D020135:Peptide Nucleic Acids; D011759:Pyrrolidines