Detection of the phosphorothioate oligonucleotide fomivirsen using a ligase detection reaction with polymerase chain reaction.

This study aimed to develop a simple and sensitive detection method for fomivirsen, a 21-nucleotide phosphorothioate oligonucleotide used as a nucleic acid medicine, using a ligase detection reaction. A ligation probe was designed to hybridize with fomivirsen and polymerase chain reaction (PCR) primers, with a deoxyuridine part between the primer binding sites. The probe was ligated to a circular product by Taq DNA ligase, and the resulting product was converted to a linear form through the removal of the uracil base using uracil DNA glycosylase. The linear product was then quantified using real-time PCR. The developed method could detect 0.025-6.4 nM of fomivirsen in water and HeLa genomic DNA solutions and 0.6-160 nM of fomivirsen in mouse serum in combination with an extraction method based on alkalinization and neutralization. This method could be useful for not only detecting fomivirsen but also other functional oligonucleotides composed of phosphorothioate oligonucleotides. In summary, this study presents a practical and effective approach to the detection of the nucleic acid medicine fomivirsen.

Dynamic Ordering in High-χ Block Copolymer Lamellae Based on Cross-Sectional Orientational Alignment.

Further development of next-generation block copolymer (BCP) lithography processes is contingent on comprehensive studies of the ordering dynamics of high-χ BCPs that can form sub-10 nm features on thin films. However, quantitative analyses of the degree of ordering on the surface and cross sections of thin films have been difficult to execute. To tackle this challenge, we employ a perpendicular lamella-forming high-χ BCP, poly(polyhedral oligomeric silsesquixone-block-2,2,2-trifluoroethyl methacrylate) (PMAPOSS-b-PTFEMA), and reveal that the high-χ PMAPOSS-b-PTFEMA requires three times the activation energy (Ea) compared to that of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) for defect annihilation, at Ea = 2600 ± 420 kJ mol-1, and a transition from a fast ordering regime with a growth exponent of Φ = 0.30 at lower orientational order parameters (ψ2 < 0.36) to a slow ordering regime with Φ < 0.05 at ψ2 > 0.36, where well-aligned lamellae restrict defect annihilations to enthalpically unfavorable glide mechanisms that require BCP intermixing.