Control of the Chirality and Helicity of Oligomers of Serinol Nucleic Acid (SNA) by Sequence Design

Abstract

The construction of an artificial double helix that mimics natural DNA or RNA has been one of the most challenging endeavors in chemistry. [1][2][3][4][5][6][7][8][9] Recently, Meggers and co-workers showed that even a simple acyclic propylene glycol with two carbon atoms in the main chain (see (S)-GNA in Figure 1) as a nucleobase tether could form a more stable duplex than that of native DNA or RNA. [10][11][12][13] This pioneering work prompted us to synthesize a new foldamer with three carbon atoms in the main chain, acyclic threoninol nucleic acid (aTNA), from d-threoninol. [14] We found that aTNA has the following properties: 1) duplex formation involves complementary pairing in an antiparallel fashion, as for natural DNA or RNA; 2) owing to the flexibility of the backbone, the singlestranded state does not adopt a characteristic preorganized structure; 3) the thermal stability of the duplex is far greater than that of the natural DNA or RNA duplex and even higher than that of the GNA duplex. Studies on aTNA as well as GNA and peptide nucleic acid (PNA) [15,16] have confirmed that scaffold rigidity is not a prerequisite for stable duplex formation as previously thought. However, unlike PNA, with an acyclic scaffold, aTNA can not cross-hybridize with either natural DNA or natural RNA. Although A 15 of (S)-GNA can hybridize with U 15 , the incorporation of several GC pairs severely destabilizes the duplex with RNA. [11] Thus, there are no artificial nucleic acids comprising a fully acyclic backbone with a phosphodiester linkage that can cross-hybridize with DNA or RNA without sequence limitation. We hypothesize that the threoninol scaffold is still not flexible enough to form a duplex with natural DNA or RNA.Herein, we propose a new artificial nucleic acid, serinol nucleic acid (SNA, see Figure 1 a), with a 2-amino-1,3propanediol (serinol) scaffold, which is even more flexible than threoninol. In comparison with aTNA (Figure 1 a), the only structural difference is the lack of a methyl group next to the amino group. However, this small change affords the SNA oligomer a unique stereochemical property: since this methyl group provides chirality, its absence makes the scaffold achiral as well as flexible. Accordingly, the chirality of the "pure" SNA oligomer synthesized from four SNA monomers (or the helicity of its duplex) depends only on its sequence (see below). This property is specific to the SNA oligomer; DNA, RNA, and previously synthesized aTNA all have chirality (or helicity) that is inherently determined by the chirality of the scaffold. [17] In the present study, we first demonstrated this unique stereochemical property and then cross-hybridized the SNA oligomer, which was found to recognize both DNA and RNA sequence specifically.The chemical structure of the SNA oligomer is shown in Figure 1 a. Serinol (2-amino-1,3-propanediol), which, like DNA, has three carbon atoms in its backbone, is an achiral diol. However, modification of the two hydroxy groups with different functional groups to form an SNA mon...

Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds

“…ty of the SNA oligomer syn-thesized from l-serine depends only on its sequence as described previously. [18] As shown in Figure 3 a, S8 a/S8 b (blue solid line) displayed symmetrical positive and negative Cotton effects at around 260 nm, thus indicating that S8 a/ S8 b formed a right-handed helix. Conversely, S8 c/S8 d, the enantiomer of S8 a/S8 b, showed precisely the opposite CD signals (blue broken line), which is indicative of the formation of a left-handed helix.…”

“…The T m values listed in Table 1 and Figure S2 of the Supporting Information include previously reported values as well as newly measured ones for comparison. [17,18] The T m values of native DNA (D8 a/D8 b) and RNA duplexes (R8 a/R8 b) were 29.0 and 38.9 8C, respectively. The homoduplex of aTNA with the same sequence (T8 a/ T8 b) had a much higher T m (62.7 8C).…”

“…aTNA and SNA formed only antiparallel duplexes, whereas PNA forms not only an antiparallel duplex but also a stable parallel duplex. [17,18,21] On the basis of the remarkable thermal stability of the aTNA duplex, we further investigated the stability of aTNA duplexes with fewer residues, T6 a/T6 b, T5 a/T5 b, and T4 a/ T4 b. As shown in Figure 2 a, these duplexes had distinct sigmoidal melting curves with T m values of 41.8, 33.7, and 13.2 8C, respectively ( Table 1).…”

“…Keywords: DNA · helical structures · melting temperature · nucleic acids · thermodynamics spired by acyclic GNA, we have synthesized two novel artificial nucleic acids: acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA), [17,18] with acyclic d-threoninol and l-serinol as backbones, respectively ( Figure 1). These nucleic acids should be more flexible than GNA due to the additional methylene chain.…”

“…SNA forms stable heteroduplexes with both DNA and RNA; aTNA does not crosshybridize with either DNA or RNA. [17,18] Peptide nucleic acids (PNAs) are another artificial nucleic acid with an acyclic scaffold. [19,20] The extremely high stabilities of PNA/PNA, PNA/DNA, and PNA/RNA duplexes are generally ascribed to the absence of electrostatic repulsion between the two strands due to the lack of negative charge on PNA.…”