Antisense oligonucleotides (AONs) hold promise for therapeutic correction of many genetic diseases via exon skipping, and the first AON-based drugs have entered clinical trials for neuromuscular disorders. However, despite advances in AON chemistry and design, systemic use of AONs is limited because of poor tissue uptake, and recent clinical reports confirm that sufficient therapeutic efficacy has not yet been achieved. Here we present a new class of AONs made of tricyclo-DNA (tcDNA), which displays unique pharmacological properties and unprecedented uptake by many tissues after systemic administration. We demonstrate these properties in two mouse models of Duchenne muscular dystrophy (DMD), a neurogenetic disease typically caused by frame-shifting deletions or nonsense mutations in the gene encoding dystrophin and characterized by progressive muscle weakness, cardiomyopathy, respiratory failure and neurocognitive impairment. Although current naked AONs do not enter the heart or cross the blood-brain barrier to any substantial extent, we show that systemic delivery of tcDNA-AONs promotes a high degree of rescue of dystrophin expression in skeletal muscles, the heart and, to a lesser extent, the brain. Our results demonstrate for the first time a physiological improvement of cardio-respiratory functions and a correction of behavioral features in DMD model mice. This makes tcDNA-AON chemistry particularly attractive as a potential future therapy for patients with DMD and other neuromuscular disorders or with other diseases that are eligible for exon-skipping approaches requiring whole-body treatment.

Oligoribonucleotides (RNA) and modified oligonucleotides were subjected to low-energy collision-induced dissociation in a hybrid quadrupole time-of-flight mass spectrometer to investigate their fragmentation pathways. Only very restricted data are available on gas-phase dissociation of oligoribonucleotides and their analogs and the fundamental mechanistic aspects still need to be defined to develop mass spectrometry-based protocols for sequence identification. Such methods are needed, because chemically modified oligonucleotides can not be submitted to standard sequencing protocols.In contrast to the dissociation of DNA, dissociation of RNA was found to be independent of nucleobase loss and it is characterized by cleavage of the 5=-POO bond, resulting in the formation of c-and their complementary y-type ions. To evaluate the influence of different 2=-substituents, several modified tetraribonucleotides were analyzed. Oligoribonucleotides incorporating a 2=-methoxy-ribose or a 2=-fluoro-ribose show fragmentation that does not exhibit any preferred dissociation pathway because all different types of fragment ions are generated with comparable abundance. To analyze the role of the nucleobases in the fragmentation of the phosphodiester backbone, an oligonucleotide lacking the nucleobase at one position has been studied. Experiments indicated that the dissociation mechanism of RNA is not influenced by the nucleobase, thus, supporting a mechanism where dissociation is initiated by formation of an intramolecular cyclic transition state with the 2=-hydroxyl proton bridged to the 5=-phosphate oxygen. A ntisense oligonucleotides are nucleic acids of about 12 to 20 nucleobases, which are designed to hybridize to a complementary messenger RNA (mRNA) sequence, thus, inhibiting gene expression [1][2][3]. Therefore, they are of great interest in human cancer therapy and for diagnostic applications. Besides the high binding specificity of antisense oligonucleotides to their target mRNA, affinity, bioavailability, and biostability are of foremost importance. However, a major drawback of the application of unmodified phosphodiester DNA or RNA oligonucleotides is that these structures are subjected to rapid nuclease degradation under physiological conditions. To improve these factors, oligonucleotide analogs, exhibiting chemical modifications of the phosphodiester backbone, of the ribose, and, to a limited extent, also of the nucleobases, are evaluated.Mechanisms of inhibition of gene expression by antisense oligonucleotides involve mRNA degrading enzymes such as RNase H, blockade of translation initiation, or modulation of splicing [4][5][6][7]. These mechanisms allow the application of new chemical modifications to increase the binding affinity and the nuclease resistance. Possible positions of the modifications are the phosphodiester backbone, the sugar unit and the nucleobases. Introduction of a phosphorothioate backbone increases nuclease resistance of antisense oligonucleotides and simultaneously serves as a very efficient su...

Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:483-523, 2016.

In most studies, the alcohol marker phosphatidylethanol (PEth) was used to differentiate social drinking from alcohol abuse. This study investigates PEth's potential in abstinence monitoring by performing a drinking study to assess the detection window of PEth after ingesting a defined amount of alcohol. After 2 weeks of abstinence, 16 volunteers ingested a single dose of alcohol, leading to an estimated blood alcohol concentration (BAC) of 1 g/kg. In the week after drinking, blood and urine samples were taken daily; in the second week, samples were taken every other day. PEth 16:0/18:1 and 16:0/18:2 were analyzed in blood by online-SPE-LC-MS/MS. Ethyl glucuronide and ethyl sulfate were determined in urine for abstinence monitoring. Prior to start of drinking, PEth 16:0/18:1 exceeded 30 ng/mL in blood samples of five volunteers despite the requested abstinence period. Positive PEth values resulted from drinking events prior to this abstinence period. After the start of drinking, maximum BACs were reached after 2 h with a mean of 0.80 ± 0.13 g/kg (range: 0.61-1.11 g/kg). PEth 16:0/18:1 increased within 8 h to maximum concentrations (mean: 88.8 ± 47.0 ng/mL, range: 37.2-208 ng/mL). After this event, PEth was detectable for 3 to 12 days with a mean half-life time of approximately 3 days. PEth has a potential in abstinence monitoring, since PEth could be detected for up to 12 days after a single drinking event. Further investigations are necessary, to establish cut-off levels for PEth as diagnostic marker for the determination of drinking habits like abstinence, social drinking, or risky alcohol consumption.

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w-and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c-and y-ions. (J Am Soc Mass Spectrom 2002, 13, 936 -945)

Gender-specific elimination of 5FU is supported by the present data and may partly explain the gender-specific association between DPYD risk variants and 5FU-specific toxicity.

An efficient synthetic approach to construct a fully substituted benzo[1,2-b:4,5-b']difuran (BDF) 2a via base-catalyzed double annulations is presented. Compound 2a can readily undergo Suzuki, Heck, and Sonogashira coupling reactions to afford in good yields a manifold of extended pi-conjugated BDF derivatives, e.g., with pyridine termini (4-6) and with different spacers. These are highly luminescent materials that undergo two reversible one-electron oxidations. Remarkably, their photophysical and electrochemical properties can be largely tuned by methylation or protonation. Consequently, they can function as pH-dependent fluorescence switches. Finally, the observed electronic properties are explained on the basis of density functional theory.

The chemotherapeutic drug 5‐fluorouracil (5‐FU) is widely used for treating solid tumors. Response to 5‐FU treatment is variable with 10–30% of patients experiencing serious toxicity partly explained by reduced activity of dihydropyrimidine dehydrogenase (DPD). DPD converts endogenous uracil (U) into 5,6‐dihydrouracil (UH2), and analogously, 5‐FU into 5‐fluoro‐5,6‐dihydrouracil (5‐FUH2). Combined quantification of U and UH2 with 5‐FU and 5‐FUH2 may provide a pre‐therapeutic assessment of DPD activity and further guide drug dosing during therapy. Here, we report the development of a liquid chromatography–tandem mass spectrometry assay for simultaneous quantification of U, UH2, 5‐FU and 5‐FUH2 in human plasma. Samples were prepared by liquid–liquid extraction with 10:1 ethyl acetate‐2‐propanol (v/v). The evaporated samples were reconstituted in 0.1% formic acid and 10 μL aliquots were injected into the HPLC system. Analyte separation was achieved on an Atlantis dC18 column with a mobile phase consisting of 1.0 mm ammonium acetate, 0.5 mm formic acid and 3.3% methanol. Positively ionized analytes were detected by multiple reaction monitoring. The analytical response was linear in the range 0.01–10 μm for U, 0.1–10 μm for UH2, 0.1–75 μm for 5‐FU and 0.75–75 μm for 5‐FUH2, covering the expected concentration ranges in plasma. The method was validated following the FDA guidelines and applied to clinical samples obtained from ten 5‐FU‐treated colorectal cancer patients. The present method merges the analysis of 5‐FU pharmacokinetics and DPD activity into a single assay representing a valuable tool to improve the efficacy and safety of 5‐FU‐based chemotherapy. Copyright © 2012 John Wiley & Sons, Ltd.