Hybridization potential of oligonucleotides comprising 3′-O-methylated altritol nucleosides

Abstract

Abstract:A series of 3'-O-methylated D-altrohexitol nucleoside analogs (MANA) was synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. These monomers were incorporated into While the specificity of these new synthons is slightly lower compared to mismatches within RNA double strands, it is similar to the discrimination potential of other hexitol modifications (HNA and ANA) which already proved their biologic interest, highlighting the potential of MANA constructs in antisense and in siRNA applications.3

Hybridisation Potential of 1',3'-Di-O-methylaltropyranoside Nucleic Acids

“…Where the natural RNA duplex displayed a Tm of 40.6 °C, the DMANA construct still paired albeit with slightly lower affinity (−0.3 °C/modification). The different hexitol constructs on the other hand strongly increased the affinity for the RNA complement as documented before [23,34]. It hence can be concluded that the DMANA analogues are different from the previous hexitol series of compounds with a constrained 6-membered ring conformation fit for pairing to RNA.…”

“…The selective O - vs . N -methylation mainly depends upon the dielectric constant of the solvent [23,25] and the stability of sodium-enolate chelation [26]. Hence, low dielectric constant and high chelation stabilizing capacity of THF afforded a higher O -selectivity compared to DMF.…”

“…As on average the DMNA pairing affinity to RNA was not advantageous nor really detrimental, we further studied their mismatch behavior within the same RNA nonamer constructs (5'-GCGU-X*-UGCG/5'-CGCAYACGC; Figure 2) in comparison to different constructs. The graphical chart displays the destabilization in relation to the respective matched sequence as obtained for DMANA building blocks in comparison to discrimination properties for HNA and MANA ([23] and within dsRNA duplexes. Analogous discrimination properties were noted, and especially for dmanaC very selective pairing to guanosine was obtained with −22 °C to −24 °C of destabilization for the different mismatches.…”

“…Several biological studies have been undertaken with both HNA and ANA [22,35,36] and interesting results were obtained more recently regarding their use as xeno-nucleic acids [37,38]. Highest affinities so far however were obtained with MANA building blocks [23]. We therefore started to study the influence of DMANA analogues carrying an additional methoxy substituent on the 6-membered ring system.…”

“…Addition of a supplementary hydroxyl at the 3'-α-position resulted in d -altritol nucleic acid (ANA, Figure 1) analogs with increased affinity for RNA strands [18,22]. More recently, we finally reported on the 3'- O -methylated ANA congeners (MANA, Figure 1) resulting in a further increase of 0.5 °C/modification when evaluating melting temperatures (T m ) upon hybridisation to RNA [23]. Herein, both the heterocyclic base and the 3'- O -methyl moiety are located in an axial position with a 4 C 1 conformation.…”