D-Altritol Nucleic Acids (ANA): Hybridisation Properties, Stability, and Initial Structural Analysis

Abstract

Oligonucleotides composed of a phosphorylated d-altritol backbone with nucleobases introduced in the 2'-position, hybridise strongly and sequence-selectively with RNA in an antiparallel way. The order of hybridisation strength is: dsANA b ANA:RNA b ANA:DNA. Complexes between ANA and RNA or DNA are more stable than between HNA and natural oligonucleotides. The dsANA hybrid is extremely stable. When compared with an identical dsDNA sequence, the DT m per modification is 10.2 8C for a hexamer. CD spectral analysis indicates that ANA complexes are very similar to the A-form dsRNA duplex. ANA are stable in alkaline medium up to pH 12 and, likewise, are not degraded in human serum.

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

“…Synthesis of HNA and ANA monomers was outlined before [10,30]. Assembly of ANA and HNA constructs likewise has been described previously [11,12].…”

“…The white crystal was filtered off, washed with cold DCM (2x3 mL) and dried under vacuum in a desiccator. Oligonucleotide assembly and Purification: Automated assembly was carried out at 1.0 μmol scale on an Expedite synthesizer (Applied Biosystems) mainly as described before [12]. An extended 12 min coupling step with the aid of ethyl thiotetrazole 0.25M as the catalyst and a 14-fold excess of amidite solution (200 μL of 0.07 M) was used.…”

“…Another way to address this problem is to assemble carbohydrate-modified ONs, exemplified by hexitol nucleic acids [10][11][12][13][14], 2'-O-(2-methoxy)ethyl ONs [15,16] and bicyclic ONs [17], with the LNA monomers of the Wengel group [18] showing the strongest affinity for RNA, and having many alternative structures [19]. The strong hybridization characteristics between these structures and complementary RNA are generally attributed to the formation of a preorganized conformation, fitting the A-form of dsRNA, with strong stacking interactions between the bases, adequate interaction of the latter in a Watson-Crick type geometry with their complement, and efficient hydration of the double-stranded helix [20].…”

“…The D-altritol nucleic acid (ANA) analogs [12,24,25] of HNA with a supplementary hydroxyl at the 3′-α-position have already paved the way and strong biological effects were noted for ANA containing constructs for the siRNA field. The underlying reason for the duplex stabilization effect of the supplementary OH group in an ANA:RNA hybrid has been highlighted very recently [26].…”

Structural Preorganization of Peptide Nucleic Acids: Chiral Cationic Analogues with Five- or Six-Membered Ring Structures

“…Such a structural preorganization approach using additional conformational constraint has been extremely successful in the case of DNA analogues. Prominent examples are conformationally locked nucleic acids [24] or conformationally frozen hexitol [25] and altritol nucleic acids [26] (Figure 6), which have preorganized 3Ј-endo sugar conformations as prevalent in highly stable DNA-RNA duplexes. The structural preferences of PNA in PNA/DNA or PNA-RNA complexes are not yet as well deciphered as those of DNA-DNA/RNA complexes and may also be sequence-dependent.…”