A Simple Glycol Nucleic Acid

Abstract

We here wish to disclose a novel nucleic acid analogue which displays exceptional structural simplicity and atom economy while supporting stable duplex formation. The discovered glycol nucleic acid (GNA) uses the canonical Watson-Crick base pairing scheme combined with an acyclic three-carbon propylene glycol phosphodiester backbone (Figure 1).Groundbreaking studies of the Eschenmoser group on the chemical etiology of nucleic acid structure have demonstrated that Watson-Crick base pairing can be supported by sugars in the backbone that differ from RNA or DNA. 1-3 Most surprisingly, a nucleic acid derived from a tetrose sugar (TNA) was found to be capable of antiparallel duplex formation and crosspairing with DNA and RNA (Figure 1). 4 Our laboratory is interested in structurally simplified nucleic acid backbones in order to improve synthetic accessibility of artificial duplexes. Inspired by Eschenmoser's TNA structure, we envisioned that acyclic glycol nucleosides could be synthesized just by regioselective and stereospecific nucleophilic ring opening of a "spring-loaded" epoxide. 5,6 Accordingly, commercially available (R)-(+)-and (S)-(-)-glycidol were tritylated to 1 following a standard protocol and successfully ring opened with the unprotected nucleobases thymine and adenine in the presence of substoichiometric amounts of NaH, yielding 2 and 3, respectively ( Figure 2). 7 The thymine derivative was directly transformed into the final phosphoramidite 4, whereas the adenine derivative was first benzoylated at the exocyclic amino group, followed by the formation of the final phosphoramidite 5 for the automated solid-phase oligonucleotide synthesis. With 4 and 5 in hand, we synthesized seven 18mer oligonucleotides consisting entirely out of either enantiomer of the acyclic glycol nucleotides (Table 1) (Figure 1). . (R)-(+)-glycidol yields (S)-GNA, and (S)-(-)-glycidol yields (R)-GNAFirst, we investigated duplex formation of GNA with temperature-dependent UV spectroscopy at 260 nm. Figure 3 displays the results with (S)-GNA. Mixtures (1:1) of two complementary strands, 6:7 and 8:9, yield characteristic sigmoidal melting curves with melting points (T M ) of 63°C each, thus indicating cooperative melting of GNA duplexes. No sigmoidal melting and weaker hyperchromicities were observed with the single strands alone (Figure 3a,b) or with two strands 8:10 that are complementary in a parallel fashion (Figure 3c), indicating the requirement for antiparallel duplex formation of GNA. To reassure that the duplex relies on proper Watson-Crick base pairing, we also investigated the UV melting behavior of an 18mer duplex 8:11 which contains one T:T mismatch. The stability of this duplex decreases significantly, yielding a T M of only 55°C for the single mismatched duplex. Furthermore, a duplex 8:12 with two mismatches (one T:T and one A:A) is further destabilized with a T M of only 44°C ( Figure 3c). Identical results were obtained with the enantiomeric (R)-GNA strands.For subsequent analysis, we investigated duplex forma...

Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template

“…7). These results suggest that this GNA dodecamer cannot form a stable antiparallel duplex with DNA, consistent with the previous study (18).…”

“…1). The S isomer of GNA can form stable antiparallel duplexes with itself and RNA, but not with DNA of the sequence 3Ј-taa aat tta tat tat taa-2Ј (lowercase type denotes the GNA sequence) (18). These properties suggested that direct sequence information exchange between GNA and DNA might not be possible.…”

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

“…The first selfreplicating macromolecules must not necessarily have been RNA. Derivatives of RNA, especially with altered backbones, have been suggested as predecessors of RNA owing to more favorable chemistries/stabilities for spontaneous generation and persistence of oligomerization at the presumed planetary conditions (Joyce et al 1987;Schöning et al 2000;Zhang et al 2005;Powner et al 2009;Robertson and Joyce 2012;Neveu et al 2013). …”

Non-nucleosidic analogs of nucleic acids

“…Moreover, the stability was only slightly higher in comparison to the unmodified DNA double strand. As an alternative, DNA nucleoside (Zhang et al, 2005) substitute containing (S)-1-amino-1,3-propanediol was incorporated into the oligonucleotide strand. Duplex sets modified with ethidium (18) and phenothiazine (19) derivatives showed very similar stabilities.…”