Synthesis and Properties of 7-Deazapurine- and 8-Aza-7-deazapurine-Locked Nucleic Acid Analogues: Effect of the Glycosidic Torsion Angle

Convenient Synthesis of 3-Deazapurine Nucleosides (3-Deazainosine, 3-Deazaadenosine and 3-Deazaguanosine) Using Inosine as a Starting Material

A convenient synthetic method for preparing 3-deazapurine nucleosides (3-deazainosine, 3-deazaadenosine, and 3-deazaguanosine) from inosine via a 5-ethynyl-1-β-D-ribofuranosylimidazole-4-carboxamide (EICAR) derivative, which is a key intermediate, is described. A large-scale synthesis of an EICAR derivative starting from inosine was achieved in six steps via dinitrophenylation at the N¹ position followed by ring opening, iodination of the resulting 5-amino group, and a palladium-catalyzed cross-coupling reaction. The resulting EICAR derivative was then converted into 3-deazainosine, 3-deazaadenosine, and 3-deazaguanosine. This route enabled us to synthesize 3-deazapurine nucleosides conveniently in good yields. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 5-ethynyl-1-β-D-ribofuranosylimidazole-4-carboxamide (EICAR) derivative 6 Basic Protocol 2: Preparation of 3-deazapurine nucleosides 8, 11, and 14.

Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties

7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. K_Taut values calculated from H₂O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H₂O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.

Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative

We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).

anti-syn Unnatural Base Pair Enables Alphabet-Expanded DNA Self-Assembly

Self-assembly properties and diversity in higher-order structures of DNA enable programmable tools to be used to construct algorithms at the molecular level. However, the utility of DNA-based programmable tools is hampered by the low orthogonality to natural nucleic acids, especially in complex molecular systems. To address this challenge, we report here the orthogonal regulation of DNA self-assembly by using an unnatural base pair (UBP) formation. Our newly designed UBP An^N:Sy^N is formed in combination with anti and unusual syn glycosidic conformation with high thermal stability and selectivity. Furthermore, An^C worked as a pH-sensitive artificial nucleobase, which forms a strong base pair with cytosine under a weak acidic condition (pH 6.0). The orthogonal An^N:Sy^N base pair functioned as a trigger for hybridization chain reaction to provide long nicked double-stranded DNA (ca. 1000 base pairs). This work represents the first example of the orthogonal DNA self-assembly that is nonreactive to natural four-letter alphabets DNA trigger and expands the types of programmable tools that work in a complex environment.

Enhancement of exon skipping activity by reduction in the secondary structure content of LNA-based splice-switching oligonucleotides

PAGE and UV melting analysis revealed that longer LNA-based splice-switching oligonucleotides (SSOs) formed secondary structures by themselves, reducing their effective concentration. To avoid such secondary structure formation, we introduced 7-deaza-2'-deoxyguanosine or 2'-deoxyinosine into the SSOs. These modified SSOs, with fewer secondary structures, showed higher exon skipping activities.

Synthesis and thermal stabilities of oligonucleotides containing 2'-O,4'-C-methylene bridged nucleic acid with a phenoxazine base

We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes.

Antiviral effect of hepatitis B virus S gene-specific anti-gene locked nucleic acid in hepatitis B virus transgenic mice

AIM

To investigate the antiviral effect of hepatitis B virus (HBV) S gene-specific anti-gene locked nucleic acid (LNA) in transgenic mice.

METHODS

Thirty HBV transgenic mice were randomly divided into 5 groups (n = 6 each): blank control group, negative control group (unrelated sequence), lamivudine group, antisense-LNA treatment group, and anti-gene LNA treatment group. LNA was injected into transgenic mice via the tail vein, and lamivudine was given by gavage. Serum HBV DNA was tested by real-time PCR; serum hepatitis B surface antigen (HBsAg) was determined by ELISA; the mRNA level of HBV S gene was detected by RT-PCR; and the positive rate of HBsAg in liver cells was detected by immunohistochemistry.

RESULTS

On 3, 5, and 7 d after anti-gene LNA treatment, HBV DNA was reduced by 37.18%, 50.27%, and 61.46%, respectively, and HBsAg was reduced by 30.17%, 44%, and 57.76%, respectively; there was a significant difference in HBV DNA and HBsAg compared with those before administration (P < 0.05) or compared with control groups (blank control, negative control, lamivudine, and antisense-LNA) (P < 0.05). The mRNA level of HBV S gene (0.33) and the HBsAg positive rate of liver cells (31%) were significantly reduced compared with control groups (P < 0.05). The function of liver and kidney tests and tissue HE staining showed no abnormal changes.

CONCLUSION

Anti-gene LNA targeting the S gene has a strong inhibitory effect on HBV replication and expression in HBV transgenic mice, and this provides experimental basis for gene therapy of HBV.