Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches.

Expansion of a GGGGCC/CCCCGG repeat sequence in the first intron of the C9ORF72 gene is a leading cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this combined disorder, called c9FTD/ALS, the expansion is bidirectionally transcribed into sense and antisense repeat RNA associated with disease. To better understand the role of C9ORF72 repeat RNA in molecular disease pathology, we determined crystal structures of a [(CCCCGG)3(CCCC)] model antisense repeat RNA to 1.

Digital quantitation of potential therapeutic target RNAs.

Accurate determination of the amount of a given RNA within a cell is necessary to gain a full understanding of the RNA's function and regulation. Typically, the abundance of RNA is measured by quantitative polymerase chain reaction (qPCR). With qPCR, however, absolute quantification is not possible unless an adequate reference standard curve is generated.

Transcriptional silencing by hairpin RNAs complementary to a gene promoter.

Double-stranded RNAs can target gene promoters and inhibit transcription. To date, most research has focused on synthetic RNA duplexes. Transcriptional silencing by hairpin RNAs would facilitate a better understanding of endogenous RNA-mediated regulation of transcription within cells.

Electrogenerated chemiluminescence of triazole-modified deoxycytidine analogues in N,N-dimethylformamide.

Triazole-modified deoxycytidines have been prepared for incorporation into single-stranded deoxyribonucleic acid (ssDNA). Electrochemical responses and electrogenerated chemiluminescence (ECL) of these deoxycytidine (dC) analogues, 1-4, were investigated as the monomers. Cyclic voltammetry and differential pulse voltammetry techniques were used to determine the oxidation and reduction potentials of 1-4, along with the reversibility of their electrochemical reactions.

Hydrogelation abilities of nucleobase-modified cytidines possessing substituted triazoles.

Nucleoside-derived hydrogelators have been sought for their potential biomedical applications, such as are found in tissue engineering and drug delivery. By judiciously adding a degree of hydrophobicity certain analogues are able to form micelles, bi-layers and gels in water. Research in this area has yet to lay down solid ground rules for the rational design of novel nucleoside gelators making further studies necessary.

Peptide nucleic acid Pt(II) conjugates: a preliminary study of antisense effects in Xenopus laevis.

The avid hybridization of peptide nucleic acid (PNA) to DNA and RNA, coupled with the analogue's stability toward enzymatic degradation, has led to its investigation as an antigene/antisense agent. PNA targeted toward the 5'-UTR of an mRNA transcript can effect efficient silencing; however, if targeted to an area within the coding region, the PNA can be displaced by the moving ribosome and be an ineffective antisense agent. Platinum-appended and standard PNAs antisense to an area within the open-reading frame of the gene noggin, were injected into Xenopus laevis embryos.

Blue fluorescent deoxycytidine analogues: convergent synthesis, solid-state and electronic structure, and solvatochromism.

We report the synthesis and photospectroscopic characterisation of intrinsically fluorescent triazole-appended cytidines. Fluorescence was found to be highly dependent on solvent conditions. X-Ray crystallographic data show the proton of the exocyclic amine of the nucleobase and the triazole N(3) engaged in a H-bond.

Cellular localization and allele-selective inhibition of mutant huntingtin protein by peptide nucleic acid oligomers containing the fluorescent nucleobase [bis-o-(aminoethoxy)phenyl]pyrrolocytosine.

Peptide nucleic acid (PNA) is a successful DNA/RNA mimic. A major challenge for research is to invent chemically modified PNAs that retain the favorable properties of the parent compound while improving biological recognition. Here, we test modified PNAs containing [bis-o-(aminoethoxy)phenyl]pyrrolocytosine bases designed to engage guanine with an additional hydrogen bond.

Gamma-radiation induced interstrand cross-links in PNA:DNA heteroduplexes.

Peptide nucleic acids (PNAs) efficiently hybridize with DNA and are promoted as versatile gene-targeting analytical tools and pharmaceuticals. However, PNAs have never been exploited as radiopharmaceuticals, and radiation-induced physicochemical modifications of PNA:DNA heteroduplexes have not been studied. Drug- and radiation-induced creation of covalent cross-links in DNA obstruct crucial cell survival processes such as transcription and replication and are thus considered genotoxic events with a high impact in anticancer therapies.

Analysis and purification of peptide nucleic acids by denaturing PAGE.

A flexible and convenient protocol for the analysis and purification of peptide nucleic acid (PNA) oligomers and PNA-peptide chimeras by denaturing PAGE is described. Vertical slab gel electrophoresis, 26% in polyacrylamide and 8 M urea at pH 3, was suitable for analysis of oligomers ranging in size from tetramers (4-mers) to tetradodecamers (24-mers). Single-base resolution of oligomers was achieved and separations are generally superior to those given by standard RP-HPLC techniques.