The Synthesis of a Thymine Containing E-Olefinic Peptide Nucleic Acid (OPA) Monomer

Abstract

A monomeric unit of a conformationally constrained PNA analog, E-olefinic peptide nucleic acid (E-OPA) containing the base thymine was synthesized in 14 steps. The key step involved a palladium (0) catalyzed cross-coupling reaction utilizing a Reformatsky reagent as nucleophile. A protecting group regime that is compatible with solid-phase PNA and DNA chemistries was chosen.Peptide nucleic acid (PNA), reported in 1991 by Nielsen, 1 is a nucleic acid analog with remarkable pairing properties. Much work has since been invested in understanding and improving this potentially useful analog. 2 Oligomers of PNA are able to form stable duplexes with both DNA and RNA in both antiparallel and parallel orientations. Structural characterizations 3 show that when PNA is complexed with a natural nucleic acid the internal amide bond of the PNA units are uniformly aligned so that the carbonyl oxygen of the tertiary amide bond points to the carboxy terminus in an antiparallel Watson-Crick duplex. Olefinic peptide nucleic acid (OPA) monomers were designed as PNA analogs with an internal olefin of defined configuration. We reasoned that the replacement of the conformationally labile amide bond with a conformationally rigid olefin bond would allow an assessment of the role of this preorganized structural element in the duplex binding orientation observed in PNA (Scheme 1). From structural models, we anticipate that the Z-OPA isomer will bind in a parallel fashion, while the E-OPA isomer will bind in an anti-parallel orientation. The synthesis of a Z-OPA monomer has already been reported, 4 herein we report the synthesis of the thymine containing E-OPA monomer.The syntheses of OPA monomers were designed to be divergent, with both E and Z-isomers utilizing a common intermediate 1 (Scheme 2). The E-isomer is then obtained using functional group interconversion to reverse the amino acid polarity and introduce the correct nucleobase(s). The basic OPA skeleton 1 is assembled from the vinyl iodide via a palladium(0) catalyzed cross-coupling reaction utilizing an ethyl a-bromoacetate derived Reformatsky reagent as the nucleophile. 5 The geometry of the olefin is defined via a stereospecific conversion of the propargyl alcohol to the Z-iodo olefin. 6 In anticipation of assembly of this monomer into oligomers utilizing solid-phase synthesis, a strategy incorporating the monomethoxytrityl amino protecting group and acyl base protection was chosen. 7 This system was selected over the standard PNA (and peptide) chemistries due to the need to avoid strongly acidic conditions which would scramble the double-bond position and geometry. Furthermore, this strategy is compatible with DNA synthesis chemistry, allowing us to construct DNA/OPA chimeras.The synthesis of the thymine E-OPA amino acid 10 was begun from commercially available 3-butynol 2 (Scheme 3). The alcohol was protected as the THP acetal followed Scheme 1Downloaded by: Queen's University. Copyrighted material.

Olefinic Peptide Nucleic Acids (OPAs): New Aspects of the Molecular Recognition of DNA by PNA

“…The constitution of the complexed chalcone 4 a was elucidated unambiguously by a selectively 1 H-decoupled 13 C NMR experiment, and thus, a Meyer ± Schuster rearrangement could be ruled out. [7] Remarkably, the chalcones are formed with excellent trans selectivity ( 3 J 16 Hz), indicating a thermodynamically controlled double bond formation.…”

“…While we have already reported on the synthesis of the monomeric (E)-and (Z)-OPA building blocks containing the base thymine, [13,14] we describe here the synthesis of (E)-and (Z)-OPA oligomers as well as preliminary studies on pairing with complementary DNA.…”

Diastereoselective Access to 3-Nitro-4-vinylidenetetrahydrofurans and 3-Nitro-4-vinylidenetetrahydropyrans and Their Conversion into 3,6-Dihydro-1,2-oxazines by Reverse Cope Elimination of Hydroxylamine Precursors

“…5‐(Tetrahydropyran‐2‐yloxy)pent‐2‐yn‐1‐ol (4c): 63 53% yield. − R f = 0.20 (diethyl ether/ petroleum ether = 70:30).…”

Ene-nucleic acids: a different paradigm to DNA chemistry

“…In the case of a 10 mer PNA, containing a cis-or trans-olenic PNA modication in the center of the sequence, the complexes with cDNA were destabilized by 14 C and 6.5 C, respectively. 9 We further studied multiple modications in the sequence containing a continuous stretch of cis-thymine units so that the modied units could be inserted continuously or alternately in the sequence. The destabilization was about 8 C per modication when the thymine units were continuously substituted and $5 C per modication when they were alternately substituted.…”

“…1, E/Z OPAs) were synthesized to delineate the ambiguity regarding rotameric conformations and to elucidate the structural and electronic role of the tertiary amide group in PNA. 9 This design prompted us to visualize an acyclic enenucleic acid (Fig. 2, ene-NA) in which the nucleobase attachment is to a planar double bonded structure through a methylene group, having the same number of bonds as a natural ribose sugar and a constraint of double bond unsaturation instead of the sugar ring.…”