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Abstract

b ) Departement Chemie, ETH Hˆnggerberg, CH-8093 Z¸rich Chimeric DNA molecules containing four different linking groups, the natural phosphate, 5'-methylenephosphonate, bis(methylene)phosphinate, and bis(methylene) sulfone (see Fig. 1), were directly compared for their ability to form duplexes with complementary DNA and DNA chimeras. From melting temperatures for analogous complementary sequences, general conclusions about the impact of geometric distortion of the internucleotide linkage around the two PÀOÀC bridges were drawn, as were conclusions about the impact on duplex stability that arises from the removal of the negative charge in the linking group. Each structural perturbation diminished the melting temperature, by ca. À 2.58 per modification for the 5'-methylenephosphonate, À 3.58 per modification for the bis(methylene)phosphinate, and À 4.58 per modification for the bis(methylene) sulfone linker. These results have implications for DNA chemistry including the design of −antisense× candidates and the proposal of alternative genetic materials in the search for non-terrean life.Upon expanding the size of the oligosulfones beyond the dinucleoside level, however, major differences in the physicochemical behavior compared with natural DNA emerged. Particularly remarkable was the oligosulfone r(ASO 2 USO 2 GSO 2 GSO 2 U-SO 2 CSO 2 ASO 2 U) [5] (SO 2 corresponds to CH 2 SO 2 CH 2 instead of OP(O)(O À )O). The molecule displayed an extraordinary thermal denaturation curve, melting at ca. 808. Upon melting, a large hyperchromicity was observed (> 200%; 25% is typical for the melting of a DNA duplex). The sequence was not, in the Watson-Crick sense, selfcomplementary. Thus, it was concluded that this oligosulfone folded to a rather stable conformation, indeed one of the most stable single-stranded −RNA× structures known. Richert et al. have subsequently examined the conformation of sulfone-linked oligonucleotide analogs, establishing details of the folding [5].The results of these and other experiments suggested that each oligosulfone has its own unique properties and reactivity. Different oligosulfones differing (in some cases) by only one nucleobase displayed different levels of solubility, aggregation behavior, folding, chemical reactivity, and Watson-Crick base-pairing ability. Their properties were often influenced dramatically by adding a single charge to one end of the molecule [6].These results suggested that removing all the phosphate groups of an oligonucleotide introduces such a big change in the molecule×s physicochemical behavior that the effect cannot easily be interpreted. We, therefore, set out to synthesize chimeric sequences were the phosphate groups were replaced one at a time. We hoped to gain a more quantitative understanding of the influence of charge neutralization on duplex stability and conformation, which then would enable us by extrapolation to better understand the unexpected properties of the oligosulfones.The results with these chimeras were again surprising. The incorporation of one ...

Modified internucleoside linkages for nuclease-resistant oligonucleotides

“…Thermal stability experiments (T m evaluations) with complementary ODN were conducted along with resistance evaluation against SVPDE. The presence of VP linkages destabilized the duplexes formed with the complementary (d(A 14 )) by À3 1C per modification (comparable to the EtP linkage 203 ). Nuclease digestion experiments showed that the VP linkage, as the EtP one, 202 is totally resistant to SVPDE over 20 min.…”

“…The repulsion between the nucleobase and the hydrogen atom(s) at the C6 0 -position induces deleterious effects on the duplex formation as demonstrated on EtP and VP internucleoside linkages. 203,204 The authors synthetized EP linked thymidine dinucleotides having either two natural riboses or one LNA modified nucleoside (Fig. 11).…”

Current Developments in HIV Chemotherapy

“…Indeed, Benner and co‐workers have studied the physical and chemical effects of sulfone analogues of oligonucleotides extensively 109. 110 In contrast to the approach of Benner, Gervay‐Hague et al. have used a unique disulfone/diphosphonate reagent 16 (Figure 18) to synthesize a large number of highly functionalized geminal disulfone‐containing compounds through Horner–Emmons–Wadsworth (HEW) olefination chemistry 111.…”

Carbohydrate Chemistry for RNA Interference: Synthesis and Properties of RNA Analogues Modified in Sugar-Phosphate Backbone

“…Although the crystal structure of dinucleoside analog r(G SO2 C) reveals an only slightly distorted Watson-Crick miniduplex [83], all sulfone-linked octamers do not base pair with complementary oligonucleotides but self-associate and form very stable self-folded structures instead [80,84]. The authors conclude that the absence of the negative charge greatly facilitates formation of the self-structures and that any genetic molecule using Watson-Crick base pairing template must have a charged backbone [85,86].…”