Effect of locked nucleic acid modifications on the thermal stability of noncanonical DNA structure

Long non-coding RNA-targeting therapeutics: discovery and development update

INTRODUCTION

lncRNAs are major players in regulatory networks orchestrating multiple cellular functions, such as 3D chromosomal interactions, epigenetic modifications, gene expression and others. Due to progress in the development of nucleic acid-based therapeutics, lncRNAs potentially represent easily accessible therapeutic targets.

AREAS COVERED

Currently, significant efforts are directed at studies that can tap the enormous therapeutic potential of lncRNAs. This review describes recent developments in this field, particularly focusing on clinical applications.

EXPERT OPINION

Extensive druggable target range of lncRNA combined with high specificity and accelerated development process of nucleic acid-based therapeutics open new prospects for treatment in areas of extreme unmet medical need, such as genetic diseases, aggressive cancers, protein deficiencies, and subsets of common diseases caused by known mutations. Although currently wide acceptance of lncRNA-targeting nucleic acid-based therapeutics is impeded by the need for parenteral or direct-to-CNS administration, development of less invasive techniques and orally available/BBB-penetrant nucleic acid-based therapeutics is showing early successes. Recently, mRNA-based COVID-19 vaccines have demonstrated clinical safety of all aspects of nucleic acid-based therapeutic technology, including multiple chemical modifications of nucleic acids and nanoparticle delivery. These trends position lncRNA-targeting drugs as significant players in the future of drug development, especially in the area of personalized medicine.

Amplifying gene expression with RNA-targeted therapeutics

Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.

Characterization of DNA G-quadruplex Topologies with NMR Chemical Shifts

G-quadruplexes are nucleic acid motifs formed by stacking of guanosine-tetrad pseudoplanes. They perform varied biological roles, and their distinctive structural features enable diverse applications. High-resolution structural characterization of G-quadruplexes is often time-consuming and expensive, calling for effective methods. Herein, we develop NMR chemical shifts and machine learning-based methodology that allows direct, rapid, and reliable analysis of canonical three-plane DNA G-quadruplexes sans isotopic enrichment. We show, for the first time, that each unique topology enforces a specific distribution of glycosidic torsion angles. Newly acquired carbon chemical shifts are exquisite probes for the dihedral angle distribution and provide immediate and unambiguous backbone topology assignment. The support vector machine learning methodology aids resonance assignment by providing plane indices for tetrad-forming guanosines. We further demonstrate the robustness by successful application of the methodology to a sequence that folds in two dissimilar topologies under different ionic conditions, providing its first atomic-level characterization.

Bridged Nucleic Acids Reloaded

Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.

Double duplex invasion of DNA induced by ultrafast photo-cross-linking using 3-cyanovinylcarbazole for antigene methods

New photoresponsive antigene probes containing^CNVK and^CNU have a high double-duplex invasion capability upon photoirradiation because of the inhibition of photo-cross-linking between the probes.

Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides

This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability

We present the synthesis and characterization of 2′-N-guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligo-DNA that forms a stable triplex (ΔT_m +9.5 °C) with exceptional nuclease stability.

Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain

Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects.

Hepatitis C virus gene-specific locked nucleic acid enzyme significantly inhibits C gene expression in vitro

AIM: To investigate the inhibitory effects of locked nucleic acid enzyme targeting the hepatitis C virus (HCV) C gene on HCV RNA replication and expression in HepG2.9706 cells.

METHODS: The sequences encoding DNAzyme, thiolmodificated DNAzyme and LNAzyme targeting the HCV C gene were designed and synthesized. The following experimental groups were set up: lipo-DNAzyme, lipo-S-DNAzyme, lipo-LNAzyme, blank control, empty liposomes, and lipo-random-LNAzyme. Transfection was performed using cationic liposomes. The level of HCV RNA and luciferase gene expression in supernatants were tested by real-time fluorescent quantitative PCR and chemiluminescence technique 24, 48 and 96 h after treatment, respectively. Cytotoxicity of LNAzyme was evaluated by MTT assay.

RESULTS: Significant down-regulation of HCV RNA replication and luciferase gene expression was noted in the lipo-LNAzyme group, lipo-DNAzyme group and lipo-S-DNAzyme group compared with the control group (P < 0.05 for all). Relative to the lipo-DNAzyme group and lipo-S-DNAzyme group, the average inhibition rates in the lipo-LNAzyme group were 47.55% and 52.44%, respectively. With the prolongation of the treatment time, the inhibition rate increased. At 96 h, HCR RNA replication and fluorescent protein expression were significantly lower than those before treatment in the lipo-LNAzyme group (P < 0.01 for both), and the average inhibition rates were 79.40% and 84.05%, respectively. No obvious toxicity was observed.

CONCLUSION: LNAzyme has a significant inhibitory effect on HCV C gene replication and expression in vitro, which is stronger than that of the thiolmodificated DNAzyme.

A self-assembling short oligonucleotide duplex suitable for pretargeting

Monoclonal antibodies (mAbs) have naturally evolved as suitable, high affinity and specificity targeting molecules. However, the large size of full-length mAbs yields poor pharmacokinetic properties. A solution to this issue is the use of a multistep administration approach, in which the slower clearing mAb is administered first and allowed to reach the target site selectively, followed by administration of a rapidly clearing small molecule carrier of the cytotoxic or imaging ligand, which bears a cognate receptor for the mAb. Here, we introduce a novel pretargetable RNA based system comprised of locked nucleic acids (LNA) and 2'O-Methyloligoribonucleotides (2'OMe-RNA). The duplex shows fast hybridization, high melting temperatures, excellent affinity, and high nuclease stability in plasma. Using a prototype model system with rituximab conjugated to 2'OMe-RNA (oligo), we demonstrate that LNA-based complementary strand (c-oligo) effectively hybridizes with rituximab-oligo, which is slowly circulating in vivo, despite the high clearance rates of c-oligo.

Hybridization potential of oligonucleotides comprising 3'-O-methylated altritol nucleosides

A series of 3'-O-methylated-d-altrohexitol nucleoside analogs (MANA) was synthesized comprising all four base moieties, adenine, cytosine, uracil, and guanine. These monomers were incorporated into oligonucleotides (ONs) by automated solid phase synthesis and the thermal and thermodynamic stability of all new modified constructs were evaluated. Data were compared with results obtained for both anhydrohexitol (HNAs) and 3'-O-altrohexitol-modified ONs (ANAs). We hereby demonstrate that ONs modified with MANA monomers have an improved thermal and thermodynamic stability compared to RNA, ANA, or HNA containing ONs of which the extent depends on the number of incorporated moieties and their position in the sequence. Thermodynamic analysis afforded comparable or even improved results in comparison with the incorporation of locked nucleic acids. While the specificity of these new synthons is slightly lower compared to mismatches within RNA double strands, it is similar to the discrimination potential of other hexitol modifications (HNA and ANA) which already proved their biologic interest, highlighting the potential of MANA constructs in antisense and in siRNA applications.

Antiviral effects of locked nucleic acid antisense oligonucleotides targeting the HBV preS1 gene in HepG2 2.2.15 cells

AIM: To investigate the inhibitory effects of locked nucleic acid (LNA) antisense oligonucleotides targeting the purine region of the hepatitis B virus (HBV) preS1 gene in HepG2 2.2.15 cells, and to screen effective LNA anti-gene oligonucleotides.

METHODS: LNA anti-gene oligonucleotides of different lengths that were complementary to the purine-abundant regions (2 941-2 962 nt, 3 015-3 036 nt and 3 089-3 110 nt) of the HBV preS1 gene were designed, synthesized, and introduced into HepG2 2.2.15 cells by cationic liposome-mediated transfection. Hepatitis B surface antigen (HBsAg) and HBV DNA levels in cell supernatants were tested by time-resolved fluorescence immune assay (TRFIA) and fluorescent quantitative polymerase chain reaction (FQ-PCR) 1, 3, 5 and 7 d after transfection. The cell toxicity of LNA anti-gene oligonucleotides was detected by methyl thiazolyl tetrazolium (MTT) assay.

RESULTS: LNA anti-gene oligonucleotides targeting the HBV preS1 gene showed strong inhibitory effects on HBV DNA replication and HBsAg expression in vitro, and the effects were time-dependent. Seven days after transfection, the reduced rates of HBV DNA and HBsAg levels were 64.32% and 67.51%, respectively. The inhibitory effects were significantly different between each experimental group and control group (all P < 0.05). The inhibitory effect of the LNA anti-gene oligonucleotide targeting the region 2 941-2 962 nt was most strong. The optimal length of LNA anti-gene oligonucleotides ranges from 20 to 30 bases. No obvious cell toxicity was observed with LNA anti-gene oligonucleotides.

CONCLUSION: LNA anti-gene oligonucleotides targeting the HBV preS1 gene showed strong inhibitory effects on HBV replication in vitro. The inhibitory effect of the LNA anti-gene oligonucleotide targeting the region 2 941-2 962 nt was most strong, and the optimal length of LNA anti-gene oligonucleotides ranges from 20 to 30 bases.

Cleavage of oligonucleotides containing a P3'→N5' phosphoramidate linkage mediated by single-stranded oligonucleotide templates

Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3'→N5' phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids.