Backbones

The backbones are one of the important building blocks for synthesizing peptide nucleic acid (PNA) monomer.

Introduction

PNA is an oligonucleotide analog linked by peptide bond, which uses N - (2-aminoethyl) glycine skeleton instead of sugar phosphate skeleton as a repeating structural unit.

PNA has some physical and chemical properties of polypeptide and nucleic acid due to its unnatural backbones structure, but it is different from polypeptide and nucleic acid molecules. The backbones of polyamides synthesized by PNA have almost no charge, while DNA and RNA molecules have more negative charges due to the strong polarity of polysaccharide and phosphoric acid molecules in the backbones structure. PNA molecules can effectively resist the degradation of nuclease and protease, showing a high degree of biological stability. Even if PNA molecules are incubated with S1 nuclease or DNase I, no degradation will occur. PNA can be chemically modified, for example, it can combine with biotin, fluorescein and other molecules to form marker molecules, or it can combine with DNA, polypeptide and other molecules to form chimeric molecules.

• Synthesis

There are three common methods for synthesizing backbones.

1. Alkylation reaction
   With ethylenediamine or aminoacetonitrile as raw material, alkylation reaction is carried out with haloacetic acid derivatives. Applicable protection groups include 9-fluoromethoxycarbonyl (Fmoc), 4-methoxyphenyldiphenylmethyl (Mmt) and tert-butyloxycarbonyl (Boc).
2. Reduction reaction of schiff base
   Although the Schiff base formed by reducing glycine ester and protected aminoacetaldehyde is only applicable to Boc protecting group, this method can be used to synthesize various PNA monomers with side chains with slight modification. For example, the Schiff base can be formed by reducing ethylenediamine and glyoxylic acid to obtain N - (2-aminoethyl) glycine, and then glycine can selectively connect appropriate protective groups, including Fmoc and Mmt. Or glycine is reduced to Boc aminoacetaldehyde, and then reacted with glycine ester.
3. Mitsunobu reaction
   PNA backbones can be synthesized by Mitsunobu reaction between Boc protected aminoethanol and glycine ester protected by p-nitrophenyl methanesulfonyl (o-NBS).