Synthesis, Physicochemical and Biochemical Studies of 1‘,2‘-Oxetane Constrained Adenosine and Guanosine Modified Oligonucleotides, and Their Comparison with Those of the Corresponding Cytidine and Thymidine Analogues

Abstract

We have earlier reported the synthesis and antisense properties of the conformationally constrained oxetane-C and -T containing oligonucleotides, which have shown effective down-regulation of the proto-oncogene c-myb mRNA in the K562 human leukemia cells. Here we report on the straightforward syntheses of the oxetane-A and oxetane-G nucleosides as well as their incorporations into antisense oligonucleotides (AONs), and compare their structural and antisense properties with those of the T and C modified AONs (including the thermostability and RNase H recruitment capability of the AON/RNA hybrid duplex by Michaelis-Menten kinetic analyses, their resistance in the human serum, as well as in the presence of exo and endonucleases).

New methylene-bridged hexopyranosyl nucleoside modified oligonucleotides (BHNA): synthesis and biochemical studies

“…This is very similar to what we have observed earlier with other North-type conformationally constrained systems such as oxetane 15 azitidine 16,17 or aza-ENA 12 based AONs/RNA duplexes. This can be attributed to the local conformational change from DNA•RNA type to the RNA•RNA type conformation, which is not a substrate to RNase H. This local conformational change for a stretch of 5-6 nucleotides is however not detectable either by CD spectra or by the molecular model.…”

“…) or the carbocylic chain (carba-LNA 13 and carba-ENA 13,14 ), or by a covalent linkage between C1′ and C2′ (such as oxetane 15 or azetidine 16,17 types of constraints) result in to a conformationally-constrained North-type sugar. Oligonucleotides with these types of covalently constrained nucleosides can also potentially preorganize the single-stranded oligonucleotide in to a helical form, which, in turn, show much improved affinity toward complementary RNA (3-8ºC/modification, with the exception of C1′ and C2′ constrained systems) as well as to DNA 18 ;…”

Chemical Modification of Oligonucleotides for Therapeutic, Bioanalytical and other Applications

“…Oxetane purine analogues inserted within DNA oligonucleotides show a minor destabilising effect (DT m /mod 0.0 to À0.33 8C) on DNA-RNA heteroduplexes, while oxetane pyrimidines show a significant destabilising effect on DNA-RNA heteroduplexes (DT m /mod À4.3 to À5.5 8C). [18] In addition 1',2'-azitidine modifications of pyrimidine nucleotides (14) within DNA oligonucleotides has also been explored. This DNA modification (14) stabilises DNA-RNA heteroduplexes when compared to the iso-sequential oxetane-modified oligonucleotides (13), but still shows a destabilising effect (DT m /mod À1.0 to À5.5 8C) when compared to the native DNA-RNA heteroduplex.…”

“…However, duplexes made solely from complementary GNA 15-mers show an overall increase in T m of 24 8C when compared to the iso-sequential DNA duplex. [24] More recently Sozstak and coworkers introduced N2'!P3' phosphoramidate glycerol nucleic acids (18). The npGNA showed similar properties to GNA in that npGNA formed stable duplexes with itself, which have increased overall T m values when compared to native DNA duplexes.…”

Synthesis and Biological Evaluation of 4′‐C,3′‐O‐Propylene‐Linked Bicyclic Nucleosides

“…In addition, some bicyclic nucleoside analogues containing a fused oxirane (1), [6] oxetane (2) [7] and tetrahydrofuran (3-4 [8] and 5) [9] rings ( Figure 1) have been reported to exhibit anti-HIV activity. Besides LNA and ENA, some oxygenated bicyclic nucleosides, such as 6, [10] 7, [11] 8, [12] 9 [13] and 10 14 ( Figure 2), have been incorporated into oligonucleotides and evaluated for antisense application. To the best of our knowledge, since our previous work [15] on the synthesis of the 4Ј-C,3Ј-O-propylene-bridged nucleosides 11 and 12 starting from thymidine (Scheme 1), no effort to prepare such bicyclic nucleosides has been described in the literature, with the exception of a publication by Morita et al [14] Figure 2.…”