A Constrained Tricyclic Nucleic Acid Analogue of α-l-LNA: Investigating the Effects of Dual Conformational Restriction on Duplex Thermal Stability

Abstract

A constrained tricyclic analogue of α-L-LNA (2), which contains dual modes of conformational restriction about the ribose sugar moiety, has been synthesized and characterized by X-ray crystallography. Thermal denaturation experiments of oligonucleotide sequences containing this tricyclic α-L-LNA analogue (α-L-TriNA 2, 5) indicate that this modification is moderately stabilizing when paired with complementary DNA and RNA, but less stabilizing than both α-L-LNA (2) and α-L-TriNA 1 (4).

Alternative Syntheses of (S)-cEt-BNA: A Key Constrained Nucleoside Component of Bioactive Antisense Gapmer Sequences

“…To the best of our knowledge, and except for the original Imanishi report, previous approaches to the synthesis of LNA-related nucleosides utilized appropriate carbohydrate molecules as starting materials. − In particular, this strategy allowed the stereocontrolled introduction of a given nucleobase to give the β- d -4′-branched ribonucleoside, which was then elaborated further to incorporate the 2′,4′-oxamethylene bridge via an S N 2 displacement reaction. Inspired by the Imanishi synthesis of LNA starting with uridine, we envisaged that the 2′,4′-ether bridge in ( S )-cEt-BNA can be formed via S N 2 displacement of an appropriate leaving group by the 2′ alcohol of nucleoside A (Scheme ).…”

“…Inspired by the Imanishi synthesis of LNA starting with uridine, we envisaged that the 2′,4′-ether bridge in ( S )-cEt-BNA can be formed via S N 2 displacement of an appropriate leaving group by the 2′ alcohol of nucleoside A (Scheme ). This approach has been successfully applied in the synthesis of complex nucleosides bearing the protected 3′-OH. , In the case of the diol group in A , we would face a 4-exotet vs 5-exotet cyclization both favored by Baldwin’s rules, hoping that the formation of the four-membered ring oxetane to be less favored due to ring strain in the [2.1.1]dioxabicycloheptane core structure. With this strategy in mind, the stereoselective addition of a methyl group to the corresponding aldehyde to obtain the ( R )-alcohol B required particular attention.…”

The Medicinal Chemistry of Therapeutic Oligonucleotides

“… One dual constrained analogue based on the α-L-LNA scaffold indeed showed enhanced RNA affinity, while a second analogue was slightly destabilizing relative to α-L-LNA (Figure ). In the β-D-LNA series, one dual constrained analogue showed LNA-like binding affinity for RNA while a second analogue was less stabilizing . Examination of structural models suggested that the six-membered carbocyclic may experience tighter contact with the sugar–phosphate backbone in analogues which showed lower affinity in both series …”

Synthesis and Biophysical Properties of C5-Functionalized LNA (Locked Nucleic Acid)

“…The development of novel conformationally restricted nucleotides is a vibrant area of research. , Efforts are driven by the interesting properties of oligodeoxyribonucleotides (ONs) modified with classic examples of conformationally restricted nucleotides such as homo-DNA, hexitol nucleic acid (HNA), cyclohexane nucleic acid (CeNA), bicyclo DNA, tricyclo DNA, or locked nucleic acid (LNA), , which is also known as bridged nucleic acid (BNA) . ONs comprising these building blocks display high affinity toward complementary DNA/RNA often due to reduced entropic binding penalties and are accordingly in high demand for a wide range of nucleic acid targeting applications in molecular biology, biotechnology, and pharmaceutical science .…”

“…Many analogues of LNA have been synthesized with the aim of further improving the binding affinity/specificity, enzymatic stability and pharmokinetic characteristics of LNA. ,, The vast majority of these efforts have focused on modifying the oxymethylene bridge spanning the C2′/C4′-positions and/or introducing minor-groove-oriented substituents on the bridge. These structural perturbations have resulted in improved enzymatic stability and altered biodistribution and/or toxicity profiles but have generally not resulted in major improvements in binding affinity and specificity.…”