Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50？g of Boc anhydride to give 31？g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. 1. Introduction Peptide nucleic acid (PNA) [1] has recently emerged as a promising alternative to the native nucleic acids DNA and RNA (Figure 1) for a wide variety of applications including antisense therapy [2] and gene diagnostics [3]. The key advantages of PNA over DNA and RNA are its resistance to degradation by cellular nucleases [4] and its relatively higher binding affinity and mismatch selectivity in duplex formation [5]. PNA can be generated by Fmoc- or Boc-solid phase peptide synthesis [6], and Fmoc-protected monomers bearing each of the four canonical nucleobases are commercially available. Recently, the incorporation of modified nucleobases into PNA has been shown to enable synthesis of nucleic acids having unique physicochemical properties [7]. However, PNA monomers bearing modified nucleobases are not commercially available, and must instead be synthesized in the laboratory. Suitable reactions have been reported for preparation of modified nucleobases and coupling of these nucleobase acetic acids to the PNA backbone (Figure 2) [7–9]. However, to our knowledge, a scalable and cost-effective synthesis for the protected N-[2-(Fmoc)aminoethyl]glycine benzyl ester (Fmoc-AEG-OBn) backbone 1 has yet to be reported. Synthesis of the Fmoc-protected carboxylic acid backbone Fmoc-AEG-OH has been reported [10], and coupling of nucleobase acetic acids with Fmoc-AEG-OH has been described in the patent literature [11]. However, this coupling reaction provides moderate-to-low yields of PNA monomer [12, 13]. Here, we describe a synthesis of 1 that proceeds in four steps with an overall yield of 32%, utilizes inexpensive reagents, and can be scaled to produce large quantities of final product in a single batch with only minimal purification. Figure 1: Chemical structure of DNA, RNA, and PNA. Figure 2: Synthesis of Fmoc-protected PNA monomers. 2. Materials and Methods 2.1. General Methods Unless otherwise noted, all starting materials were