The base discriminating potential of pyrrolidinyl PNA demonstrated by magnetic Fe(x)O(y) particles

Selective enrichment of zein gene of maize from cereal products using magnetic support having pyrrolidinyl peptide nucleic acid probe

Here, we describe DNA enrichment of the zein gene from maize using pyrrolidinyl peptide nucleic acid (PNA) immobilized on a magnetic solid support as a capture element. Magnetite nanoparticles (MNP) with a capacity of 373 pmolPNA/mg and coated with poly(N-acryloylglycine) (PNAG) showed a good response to magnetic field. The PNA probe immobilized on the MNP discriminated between non-complementary and complementary DNA using fluorophore-tagged DNA as a model. We applied this system for the enrichment of the zein gene from maize in eight cereal product samples. After DNA desorption from the MNP, and its amplification via polymerase chain reaction (PCR), gel electrophoresis indicated that only cereal samples containing the zein gene from maize yielded positive results, indicating a high binding specificity between the PNA used and the complementary DNA. This PNA-functionalized MNP is potentially useful as an effective nano-solid support for DNA enrichment from other samples.

Poly(acrylic acid)-grafted magnetite nanoparticle conjugated with pyrrolidinyl peptide nucleic acid for specific adsorption with real DNA

Magnetite nanoparticle conjugated with pyrrolidinyl peptide nucleic acid (MNP@PNA) was synthesized for use as both a magnetic nano-support and a probe for specific adsorption with complementary deoxyribonucleic acid (DNA). MNP@PNA with the size ranging between 120 and 170 nm in diameter was prepared via a free radical polymerization of acrylic acid in the presence of acrylamide-grafted MNP to obtain negatively charged magnetic nanoclusters, followed by ionic adsorption with PNA. According to fluorescence spectrophotometry and gel electrophoresis, this MNP@PNA can differentiate between fully matched, single-base mismatched and fully mismatched synthetic DNAs tagged with different fluorophores. UV-vis spectrophotometry and gel electrophoresis indicated that MNP@PNA can be used for specific adsorption with real DNA (zein gene of maize) having complementary sequence with the PNA probe. This novel anionic MNP conjugated with the PNA probe might be potentially applicable for use as a magnetic support for DNA base discrimination and might be a promising tool for testing genetic modification.

Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications

The specific pairing between two complementary nucleobases (A·T, C·G) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric α/β-dipeptide backbone derived from nucleobase-modified proline and cyclic β-amino acids. The conformational constraints dictated by the pyrrolidine ring and the β-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools.