Nucleic‐Acid Analogs with Restricted Conformational Flexibility in the Sugar‐Phosphate Backbone (‘Bicyclo‐DNA’). Part 5. Synthesis, Characterization, and Pairing Properties of Oligo‐α‐D‐(bicyclodeoxynucleotides) of the Bases Adenine and Thymine (α‐Bicyclo‐DNA)

Abstract

Dedicated to Professor A . Eschenmoser on the occasion of his 70th birthday (9.X.95) A conformational analysis of the (3'S,5'R)-2'-deoxy-3',5'-ethano-a-~-ribonucleosides (a-D-bicyclodeoxynucleosides) based on the X-ray analysis of N4-benzoyl-a-~-(bicyclodeoxycytidine) 6 and on 'H-NMR analysis of the a-D-bicyclodeoxynucleoside derivatives 1-7 reveals a rigid sugar structure with the furanose units in the l'-exo/T-endo conformation and the secondary OH groups on the carbocyclic ring in the pseudoequatorial orientation. Oligonucleotides consisting of a -D-bicyclothymidine and a-o-bicyclodeoxyadenosine were successfully synthesized from the corresponding nucleosides by phosphoramidite methodology on a DNA synthesizer. An evaluation of their pairing properties with complementary natural RNA and DNA by means of UV/melting curves and CD spectroscopy show the following characteristics: i) a-bcd(A,,) and a-bcd(T,,) ( a = short form of a-D) efficiently form complexes with complementary natural DNA and RNA. The stability of these hybrids is comparable or slightly lower as those with natural B-d(AIo) orD-d(T,,) @ = short form ofp-o). i i ) The strand orientation in a-bicycIo-DNA/,fl-DNA duplexes is parallel as was deduced from UV/melting curves of decamers with nonsymmetric base sequences. iii) CD Spectroscopy shows significant structural differences between a-bicyclo-DNA/fl-DNA duplexes compared to a-DNA/B-DNA duplexes. Furthermore, a-bicyclo-DNA is ca. 100-fold more resistant to the enzyme snake-venom phosphodiesterase with respect toB-DNA and about equally resistant as &-DNA.

Synthesis and Pairing Properties of α‐Tricyclo‐DNA

“…[34] Because only a-bc-oligonucleotides with adenine and thymine as bases were investigated, only a very general comparison is possible. We find the same trend in that homo-backbone duplexes are less stable than hetero-backbone duplexes, but the differences are much more pronounced in the case of atc-DNA.…”

Bicyclic nucleosides and conformational restriction of oligonucleotides

“…16 Conformational analysis of the β-configured monomers, both in the solid state and in solution, revealed them to exist in a south (C1Ј-exo, 1 E) type conformation with a pseudorotational angle P of 128Њ. 16 Protection at the secondary hydroxy group by conversion into the DMT (4,4Ј-dimethoxytrityl) ether (the thymine derivatives shown as examples) and phosphitylation at the tertiary hydroxy group of the bicyclic nucleosides 12 and 14 resulted in building blocks suitable for incorporation of monomers 12p and 14p into β-17-21 as well as α-oligonucleotides, 22 respectively, on a DNA synthesiser. The incorporation of the β-nucleoside derivatives (monomer 12p) into oligonucleotides (bicycloScheme 1 16 Reagents and conditions: i) (EtO) 2 P(O)CH 2 COOEt, NaH, THF, 0 ЊC, then rt (88%); ii) DBU, CH 2 Cl 2 (97%); iii) MCPBA, CH 2 Cl 2 , 0 ЊC to rt (77%); iv) hog-liver esterase, 0.1 M NaH 2 PO 4 , pH 7.75 (53%); v) LiAlH 4 , Et 2 O, Ϫ30 ЊC then reflux (61%, 97% ee); vi) 1,1,1-triacetyl-1,1-dihydro-1λ 5 ,2-benziodoxol-3(1H)-one, CH 2 Cl 2 , rt (91%); vii) a. H 2 O/IR-120(H ϩ ), 50 ЊC, b. Ac 2 O, pyridine, DMAP, 0 ЊC to rt (93%); viii) thymine, HMDS, TMSCl, SnCl 4 , MeCN, 0 to 55 ЊC (73%); ix) NaOH, THF, MeOH, H 2 O, 0 ЊC (94%); x) TBDMSOTf, pyridine, 0 ЊC (28% α, 62% β); xi) Bu 4 NFؒ3H 2 O (12: 69%, 14: 77%).…”

“…The thermal stability of duplexes towards DNA or RNA complements is comparable to, or slightly lower than, those of the corresponding natural reference duplexes. 22 As a consequence of the introduction of the 3Ј,5Ј-ethano linker, the 5Ј-hydroxy group of, e.g., nucleoside 12 is fixed into a unnatural orientation. Thus, the torsional angle C3Ј-C4Ј-C5Ј-O5Ј is restricted to the anticlinical range (ϩac).…”

Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates

“…(3,4) Based on these findings, our laboratory (5–7) and others (8–11) have focused on the synthesis of novel nucleoside analogs that are biased toward one specific ring pucker as potential therapeutic agents. The concept of ‘locking’(12) the furanose ring pucker by various synthetic manipulations began about 13 years ago and gave rise to a range of different analogs (7,10,13,14). Notable examples in the field derive from the bridged nucleic acids (BNAs) concept (8), where analogs contain an added ring that bridges two atoms of the furanose.…”