Structure of Hybrid Backbone Methylphosphonate DNA Heteroduplexes:  Effect of R and S Stereochemistry^,

Abstract

Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R(p) and S(p) diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate, d(Cp(Me)Cp(Me)Ap(Me)Ap(Me)Ap(Me)Cp(Me)A), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R(p) stereoisomer) or RpRpRpSpRpRp (S(p) stereoisomer, although only one of the six methylphosphonate centers has the S(p) stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the DNA strand. Substitution of one chiral center from R(p) to S(p) has a profound effect on the hybridization ability of the methylphosphonate strand. Sugars in the phosphodiester strand exhibit C(2)(') endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C(4)(') endo puckering. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5' to the S(p) chiral center shows A-form sugar puckering, with a C(3)(')-endo conformation. Minor groove width in the R(p) stereoisomer is considerably wider, particularly at the R(p) vs S(p) site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove.

Watson–Crick Base‐Pairing Properties of Nucleic Acid Analogues with Stereocontrolled α and β Torsion Angles (α,β‐D‐CNAs)

“…The molecular dynamics results indicate that the overall B conformation of the double helix remains mostly intact, but at the price of a noticeable bending in the helical axis primarily caused by the propagation of this structural distortion along the phosphodiester backbone and base-sugar network. Importantly, in contrast to, for example, methylphosphonate linkages, [28] the disposition of the dioxaphosphorinane linker on the surface of the duplex is not expected to induce significant steric hindrance differences. Indeed, the two modified duplexes position the ethylene bridge of the linker away from the major and minor grooves and directly toward the solvent (D, Figure 3).…”

The Effect of a Single Boranophosphate Substitution With Defined Configuration on the Thermal Stabiltiy and Conformation of a Dna Duplex

“…[7] The binding affinity order, Sp borano > Rp borano, was contrary to that observed for methylphosphonate substitution, where the Rp diastereomers always formed more stable complexes with the complementary DNA than their Sp counterparts. [8,9] For the phosphorothioate modification, the situation is more complicated-the Rp diastereomers could form DNA duplexes that were more stable, less stable, or with the same stability compared to the Sp analogues. [4,10 -13] A recent thermodynamic study with DNA duplexes containing stereoregular all-Rp, all-Sp, and nonstereoregular ''mix'' phosphorothioate ODNs of different sequences concluded that the relative stability depended on the sequence rather than the phosphorus configuration.…”

Synthesis and properties of nucleic acid methylene carboxamide mimics derived from morpholine nucleosides

“…They are normally used as a racemic mixture without separating into isomers [8]. The properties of these diastereomers differ dramati cally [9] and this can be a factor determining the effi cacy of interactions with nucleic acids, such as the for mation of complementary complexes and other more complicated structures [10].…”