Acyclic oligonucleotide analogues

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

“…Peng and Roth have also reported an acyclic artificial nucleic acid, 1′,2′‐seco‐DNA. These two acyclic analogues could not form a stable homoduplex 28. 29 A too‐flexible interior linker of the methylene chain and an ether bond between the base and main chain might reduce the stability of these duplexes.…”

“…These two acyclic analogues could not form a stable homoduplex. [28,29] A too-flexible interior linker of the methylene chain and an ether bond between the base and main chain might reduce the stability of these duplexes. It has also been reported that oligomers fully modified with acyclic analogues could not form a stable duplex with DNA and RNA.…”

Primitive Genetic Polymers

“…Subsequently, the Benner laboratory synthesized oligonucleotides containing these linkages and found that each substitution within a DNA oligonucleotide resulted in significantly depressed duplex stability, and complementary thirteen-base oligonucleotides containing eleven FNA thymine residues failed to hybridize to a DNA template (Schneider and Benner 1990). Later work by Merle and colleagues showed weak interaction of FNA oligomers with DNA-the strongest pairing being observed for a homo-FNA-adenine oligomer with the homo-dT complement, although this pairing was still depressed relative to the analogous DNA-DNA duplex (Merle et al 1995). Thus, in addition to being well-accommodated in a Watson-Crick duplex, the conformational preorganization of ribose nucleosides is clearly an important component of duplex stability.…”

Bautechnik aktuell 11/2014

“…This implies that just being abundant in a prebiotic scenario does not guarantee that these pentuloses can become part of an informational system; the selection of the sugar portion takes place at the level of base‐paring of an oligomer and not at the monomer level. Examining the pentulose‐NA closely, juxtaposed with its corresponding acyclic counterpart (an isomer of glycerolNA, called isoGNA18) and performing the same comparison, in terms of base‐pairing propensities, for RNA with its acyclic counterpart (FNA),16a,d revealed a hitherto overlooked important role for the cyclic ring structure of ribose in RNA (Figure 3). In the pentulose nucleic acids, the furanose‐ring structure orients and holds the nucleobases in such a way (anti‐conformation) that it directs the Watson‐Crick hydrogen bonding face (represented by the blue parenthesis in Figure 3) towards the same side of the sugar‐phosphate backbone, thus placing the phosphates much closer to each other in a duplex (when compared to an RNA duplex).…”