Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications

Morpholino-based peptide oligomers: Synthesis and DNA binding properties

The chemical structure of oligonucleotide analogues dictates the conformation of oligonucleotide analogue oligomers, their ability to hybridize complementary DNA and RNA, their stability to degradation and their pharmacokinetic properties. In a study aimed at investigating new analogues featuring a neutral backbone, we explored the ability of oligomers containing a morpholino-peptide backbone to bind oligonucleotides. Circular Dichroism studies revealed the ability of our oligomers to interact with DNA, molecular modelling studies revealed the interaction responsible for complex stabilization.

Lipid-based Vehicles for siRNA Delivery in Biomedical Field

BACKGROUND

Genetic drugs have aroused much attention in the past twenty years. RNA interference (RNAi) offers novel insights into discovering potential gene functions and therapies targeting genetic diseases. Small interference RNA (siRNA), typically 21-23 nucleotides in length, can specifically degrade complementary mRNA. However, targeted delivery and controlled release of siRNA remain a great challenge.

METHODS

Different types of lipid-based delivery vehicles have been synthesized, such as liposomes, lipidoids, micelles, lipoplexes and lipid nanoparticles. These carriers commonly have a core-shell structure. For active targeting, ligands may be conjugated to the surface of lipid particles.

RESULTS

Lipid-based drug delivery vehicles can be utilized in anti-viral or anti-tumor therapies. They can also be used to tackle genetic diseases or discover novel druggable genes.

CONCLUSION

In this review, the structures of lipid-based vehicles and possible surface modifications are described, and applications of delivery vehicles in biomedical field are discussed.

KIF9‑AS1, LINC01272 and DIO3OS lncRNAs as novel biomarkers for inflammatory bowel disease

Long non-coding RNAs (lncRNAs) are a novel group of non-coding RNAs that are associated with inflammation and tumorigenesis. At present, the diagnostic efficacy of lncRNAs in inflammatory bowel disease (IBD) is unclear. The present study aimed to identify lncRNAs that may be used as potential biomarkers for IBD. The mRNA expression levels of various lncRNAs (KIF9-AS1, LINC01272 and DIO3OS) were detected in tissue and plasma samples from patients with IBD by reverse transcription-quantitative polymerase chain reaction. The results indicated that the mRNA expression levels of KIF9-AS1 and LINC01272 were significantly upregulated in tissue and plasma samples from patients with IBD compared with in the healthy controls; conversely, the mRNA expression levels of DIO3OS were significantly downregulated in tissue and plasma samples from patients with IBD compared with in the healthy controls. Subsequently, the specificity and sensitivity of KIF9-AS1, LINC01272 and DIO3OS were determined using a receiver operating characteristic (ROC) curve analysis. The results indicated that KIF9-AS1, LINC01272 and DIO3OS had potential diagnostic value for the detection of IBD. Furthermore, there were significantly positive correlations in KIF9-AS1, LINC01272 and DIO3OS expression between IBD tissue and plasma samples. Therefore, the present study indicated that KIF9-AS1, LINC01272 and DIO3OS may be potential diagnostic biomarkers for IBD.

The influence of liposomal formulation on the incorporation and retention of PNA oligomers

Liposomal formulations composed of phospholipids with different unsaturation degrees, head groups and at different cholesterol content have been tested for the encapsulation of Peptide Nucleic Acid (PNA) oligomers. The best loading capability (177μg, ER%=87.2) was obtained for pure liposomes of phosphatidylglycerol (DOPG) with negatively charged head group. The insertion of a 10-20% of cholesterol in DOPG based liposomes provides a slight decrease (∼160μg) of the PNA loading. On the other hand, the cholesterol addition (20-30%) slows down the PNA's release (∼27%) in fetal bovine serum from the liposomal formulation. Based on the encapsulation and the release properties, PEGylated DOPG liposomes with a percentage of cholesterol of 10-20% are the optimal formulation for the loading of PNA-a210.

Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide

Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA12) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.

Incorporation of Naked Peptide Nucleic Acids into Liposomes Leads to Fast and Efficient Delivery

The delivery of peptide nucleic acids (PNAs) to cells is a very challenging task. We report here that a liposomal formulation composed of egg PC/cholesterol/DSPE-PEG2000 can be loaded, according to different encapsulation techniques, with PNA or fluorescent PNA oligomers. PNA loaded liposomes efficiently and quickly promote the uptake of a PNA targeting the microRNA miR-210 in human erythroleukemic K562 cells. By using this innovative delivery system for PNA, down-regulation of miR-210 is achieved at a low PNA concentration.

Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure

The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.