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

Zhou, Chuanzheng; Chattopadhyaya, J.

doi:10.3998/ark.5550190.0010.314

Cited by 4 publications

(4 citation statements)

References 21 publications

(34 reference statements)

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“…Therefore, ( S p )-D 2 -CNA in AONs 2 − 5 and carba-LNA-6′,5′-phosphodiester modification in AONs 10 − 13 make a stacking geometry distortion in AON/RNA and AON/DNA duplexes, and it is likely that they can not be base-paired with the complementary nucleobases in the opposite strand. This conclusion is consistent with the thermal denaturation studies in that in this 15mer AON/RNA duplex, a single mismatch leads to T m decrease about −9 to −12 °C and T m decrease in this AON/RNA duplex induced by single ( S p )-D 2 -CAN modification (about −7 °C) or especially carba-LNA-6′,5′-phosphodiester modification (−10 to −12 °C) exactly fall in this range.…”

Section: Resultssupporting

confidence: 92%

Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides

2009

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Two diastereomerically pure carba-LNA dioxaphosphorinane nucleotides [(S(p))- or (R(p))-D(2)-CNA], simultaneously conformationally locked at the sugar and the phosphate backbone, have been designed and synthesized. Structural studies by NMR as well as by ab initio calculations showed that in (S(p))- and (R(p))-D(2)-CNA the following occur: (i) the sugar is locked in extreme North-type conformation with P = 11 degrees and Phi(m) = 54 degrees ; (ii) the six-membered 1,3,2-dioxaphosphorinane ring adopts a half-chair conformation; (iii) the fixed phosphate backbone delta, epsilon, and zeta torsions were found to be delta [gauch(+)], epsilon (cis), zeta [anticlinal(+)] for (S(p))-D(2)-CNA, and delta [gauche(+)], epsilon (cis), zeta [anticlinal(-)] for (R(p))-D(2)-CNA. It has been found that F(-) ion can catalyze the isomerization of pure (S(p))-D(2)-CNA or (R(p))-D(2)-CNA to give an equilibrium mixture (K = 1.94). It turned out that at equilibrium concentration the (S(p))-D(2)-CNA isomer is preferred over the (R(p))-D(2)-CNA isomer by 0.39 kcal/mol. The chemical reactivity of the six-membered dioxaphosphorinane ring in D(2)-CNA was found to be dependent on the internucleotidic phosphate stereochemistry. Thus, both (S(p))- and (R(p))-D(2)-CNA dimers (17a and 17b) were very labile toward nucleophile attack in concentrated aqueous ammonia [t(1/2) = 12 and 6 min, respectively] to give carba-LNA-6',5'-phosphodiester (21) approximately 70-90%, carba-LNA-3',5'-phosphodiester (22) approximately 10%, and carba-LNA-6',3'-phosphodiester (23) <10%. In contrast, the (S(p))-D(2)-CNA was about 2 times more stable than (R(p))-D(2)-CNA under hydrazine hydrate/pyridine/AcOH (pH = 5.6) [t(1/2) = 178 and 99 h, respectively], which was exploited in the deprotection of pure (S(p))-D(2)-CNA-incorporated antisense oligodeoxynucleotides (AON). Thus, after removal of the solid supports from the (S(p))-D(2)-CNA-modified AONs by BDU/MeCN, they were treated with hydrazine hydrate in pyridine/AcOH to give pure AONs in 35-40% yield, which was unequivocally characterized by MALDI-TOF to show that they have an intact six-membered dioxaphosphorinane ring. The effect of pure (S(p))-D(2)-CNA modification in the AONs was estimated by complexing to the complementary RNA and DNA strands by the thermal denaturation studies. This showed that this cyclic phosphotriester modification destabilizes the AON/DNA and AON/RNA duplex by about -6 to -9 degrees C/modification. Treatment of (S(p))-D(2)-CNA-modified AON with concentrated aqueous ammonia gave carba-LNA-6',5'-phosphodiester modified AON ( approximately 80%) plus a small amount of carba-LNA-3',5'-phosphodiester-modified AON ( approximately 20%). It is noteworthy that Carba-LNA-3',5'-phosphodiester modification stabilized the AON/RNA duplex by +4 degrees C/modification (J. Org. Chem. 2009, 74, 118), whereas carba-LNA-6', 5'-phosphodiester modification destabilizes both AON/RNA and AON/DNA significantly (by -10 to -19 degrees C/modification), which, as shown in our comparative CD studies, that the cyclic phos...

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Section: Resultssupporting

confidence: 92%

Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides

2009

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“…48 The positive Cotton band and the negative band at 210 nm characteristic of an A-form helical structure are most prominent in the TMO5/RNA heteroduplex and closely resemble a typical A-form RNA/RNA duplex shown in Figure S34. 49 This observation further supports the hypothesis that the increased conformational flexibility gained by inserting 2′deoxynucleotide linkages between TMO subunits imposes a more pronounced A-form conformation in its duplexes resulting in the superior binding affinity for this design.…”

Section: ■ Introductionsupporting

confidence: 73%

Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras

2020

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This Article outlines the optimized chemical synthesis and preliminary biochemical characterization of a new oligonucleotide analogue called thiophosphoramidate morpholinos (TMOs). Their rational design hinges upon integrating two well-studied pharmacophores, namely, phosphorothioates (pS) and morpholinos, to create morpholino–pS hybrid oligonucleotides. Our simple synthesis strategy enables the easy incorporation of morpholino–pS moieties and therapeutically relevant sugar modifications in tandem to create novel oligonucleotide (ON) analogues that are hitherto unexplored in the oligotherapeutics arena. Exclusively TMO-modified ONs demonstrate high stability toward 3′-exonuclease. Hybridization studies show that TMO chimeras consisting of alternating TMO and DNA–pS subunits exhibit higher binding affinity toward complementary RNA relative to the canonical DNA/RNA duplex (∼10 °C). Oligonucleotides that consist entirely of TMO linkages also show higher RNA binding affinity but do not recruit ribonuclease H1 (RNase H1). Chimeric TMO analogues demonstrate high gene silencing efficacy, comparable to that of a chimeric 2′-OMe–pS/pO control, during in vitro bioassay screens designed to evaluate their potential as microRNA inhibitors of hsa-miR-15b-5p in HeLa cells.

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“…We newly designed a boat-shaped glucopyranosyl nucleic acid (BsNA), which had a pyranose ring as the basic skeleton. The nucleobase will lean more than that of LNA owing to this unusual skeleton . We report here the synthesis of BsNA and the thermal stability of the ONs including BsNA.…”

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confidence: 99%

Design, Synthesis, and Properties of Boat-Shaped Glucopyranosyl Nucleic Acid

2011

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A boat-shaped glucopyranosyl nucleic acid (BsNA) was synthesized to investigate the possibility that the lean of a nucleobase is a factor affecting duplex-forming ability of oligonucleotides. From the crystal structure of a BsNA nucleoside and the thermal stability of duplex oligonucleotides, it was found that not only the lean of the base but also the rotation angle of the glycosidic bond axis were important factors in a stable duplex formation.

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

Cited by 4 publications

References 21 publications

Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides

Double Sugar and Phosphate Backbone-Constrained Nucleotides: Synthesis, Structure, Stability, and Their Incorporation into Oligodeoxynucleotides

Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras

Design, Synthesis, and Properties of Boat-Shaped Glucopyranosyl Nucleic Acid

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