A matrix of 3,4-diaminobenzophenone for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Pharmacokinetic Studies of Antisense Oligonucleotides Using MALDI-TOF Mass Spectrometry

Cardiac diseases are the most frequent causes of death in industrialized countries. Pathological remodeling of the heart muscle is caused by several etiologies such as prolonged hypertension or injuries that can lead to myocardial infarction and in serious cases also the death of the patient. The micro-RNA miR-132 has been identified as a master-switch in the development of cardiac hypertrophy and adverse remodeling. In this study, MALDI-TOF mass spectrometry (MS) was utilized to establish a robust and fast method to sensitively detect and accurately quantify anti-microRNA (antimiR) oligonucleotides in blood plasma. An antimiR oligonucleotide isolation protocol containing an ethanol precipitation step with glycogen as oligonucleotide carrier as well as a robust and reproducible MS-analysis procedure has been established. Proteinase K treatment was crucial for releasing antimiR oligonucleotides from plasma- as well as cellular proteins and reducing background derived from biological matrices. AntimiR oligonucleotide detection was achieved from samples of studies in different animal models such as mouse and pig where locked nucleic acids-(LNA)-modified antimiR oligonucleotides have been used to generate pharmacokinetic data.

Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices

RATIONALE

For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS analysis, matrix selection is critical and a new matrix could enable more efficient and rapid structural analysis.

METHODS

We hypothesized that nucleobase derivatives could act as matrices more efficiently than the currently used matrices for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrices, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide analysis.

RESULTS

Six of the 16 nucleobase derivatives acted as matrices for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed.

CONCLUSIONS

Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrices in oligonucleotide sequencing.

Identifying Specific and Differentially Linked Glycosyl Residues in Mammalian Glycans by Targeted LC-MS Analysis

Glycans, which are widespread in nature, consist of a large number of monosaccharides linked via glycosidic bonds. Due to the complex nature of glycan structures on glycoproteins, assessing the configuration and positions of the glycosidic linkages of a glycan is a subject of considerable interest. In this study, a method for accomplishing this using partially O-methylated alditols (PMAs) from glycans combined with LC-MS analysis is reported. N-Glycans were first per-methylated with methyl iodide, and the levels of methylation were further confirmed by MALDI-TOF. PMAs were then produced via complete hydrolysis and reduction. PMAs derived from Fetuin N-glycan and Lewis^a antigen carbohydrates were successfully detected by LC-MS analysis. This analysis can be performed without the need for an additional derivatization step for GC analysis, and should be suitable for use in conjunction with a LC-MS-based analysis platform.

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H]^-) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. Graphical Abstract ᅟ.

Development of a hydrophilic interaction liquid chromatography coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging platform for N-glycan relative quantitation using stable-isotope labeled hydrazide reagents

In this work, the capability of newly developed hydrophilic interaction liquid chromatography (HILIC) coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging (MALDI-MSI) platform for quantitative analysis of N-glycans has been demonstrated. As a proof-of-principle experiment, heavy and light stable-isotope labeled hydrazide reagents labeled maltodextrin ladder were used to demonstrate the feasibility of the HILIC-MALDI-MSI platform for reliable quantitative analysis of N-glycans. MALDI-MSI analysis by an Orbitrap mass spectrometer enabled high-resolution and high-sensitivity detection of N-glycans eluted from HILIC column, allowing the re-construction of LC chromatograms as well as accurate mass measurements for structural inference. MALDI-MSI analysis of the collected LC traces showed that the chromatographic resolution was preserved. The N-glycans released from human serum was used to demonstrate the utility of this novel platform in quantitative analysis of N-glycans from a complex sample. Benefiting from the minimized ion suppression provided by HILIC separation, comparison between MALDI-MS and the newly developed platform HILIC-MALDI-MSI revealed that HILIC-MALDI-MSI provided higher N-glycan coverage as well as better quantitation accuracy in the quantitative analysis of N-glycans released from human serum. Graphical abstract Reconstructed chromatograms based on HILIC-MALDI-MSI results of heavy and light labeled maltodextrin enabling quantitative glycan analysis.

MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry

microRNA (miRNA) are short endogenous non-coding RNA that play a crucial role in post-transcriptional gene regulation and have been implicated in the initiation and progression of 160+ human diseases. Excellent analytical methods have been developed for the measurement of miRNA by mass spectrometry. However, interpretation of mass spectrometric data has been an incapacitating bottleneck in miRNA identification. This study details the development of MicroRNA MultiTool, a software for the identification of miRNA from mass spectrometric data. The software includes capabilities such as miRNA search and mass calculator, modified miRNA mass calculator, and miRNA fragment search. MicroRNA MultiTool bridges the gap between experimental data and identification of miRNA by providing a rapid means of mass spectrometric data interpretation.

UV-Light-Induced Improvement of Fluorescence Quantum Yield of DNA-Templated Gold Nanoclusters: Application to Ratiometric Fluorescent Sensing of Nucleic Acids

The use of DNA as a template has been demonstrated as an effective method for synthesizing different-sized silver nanoclusters. Although DNA-templated silver nanoclusters show outstanding performance as fluorescent probes for chemical sensing and cellular imaging, the synthesis of DNA-stabilized gold nanoclusters (AuNCs) with high fluorescence intensity remains a challenge. Here a facile, reproducible, scalable, NaBH4-free, UV-light-assisted method was developed to prepare AuNCs using repeats of 30 adenosine nucleotides (A30). The maximal fluorescence of A30-stabilized AuNCs appeared at 475 nm with moderate quantum yield, two fluorescence lifetimes, and a small amount of Au(+) on the surface of the Au core. Results of size-exclusion chromatography revealed that A30-stabilized AuNCs were more compact than A30. A series of control experiments showed that UV light played a dual role in the reduction of gold-ion precursors and the decomposition of citrate ions. A30 also acted as a stabilizer to prevent the aggregation of AuNCs. In addition, single-stranded DNA (ssDNA) consisting of an AuNC-nucleation sequence and a hybridization sequence was utilized to develop a AuNC-based ratiometric fluorescent probe in the presence of the double-strand-chelating dye SYBR Green I (SG). Under conditions of single-wavelength excitation, the combination of AuNC/SG-bearing ssDNA and perfectly matched DNA emitted fluorescence at 475 and 525 nm, respectively. The formed AuNC/SG-bearing ssDNA enabled the sensitive, selective, and ratiometric detection of specific nucleic acid targets. Finally, the AuNC-based ratiometric probes were successfully applied to determine specific nucleic acid targets in human serum.

In vitro interactions between 17β-estradiol and DNA result in formation of the hormone-DNA complexes

Beyond the role of 17β-estradiol (E2) in reproduction and during the menstrual cycle, it has been shown to modulate numerous physiological processes such as cell proliferation, apoptosis, inflammation and ion transport in many tissues. The pathways in which estrogens affect an organism have been partially described, although many questions still exist regarding estrogens' interaction with biomacromolecules. Hence, the present study showed the interaction of four oligonucleotides (17, 20, 24 and/or 38-mer) with E2. The strength of these interactions was evaluated using optical methods, showing that the interaction is influenced by three major factors, namely: oligonucleotide length, E2 concentration and interaction time. In addition, the denaturation phenomenon of DNA revealed that the binding of E2 leads to destabilization of hydrogen bonds between the nitrogenous bases of DNA strands resulting in a decrease of their melting temperatures (Tm). To obtain a more detailed insight into these interactions, MALDI-TOF mass spectrometry was employed. This study revealed that E2 with DNA forms non-covalent physical complexes, observed as the mass shifts for app. 270 Da (Mr of E2) to higher molecular masses. Taken together, our results indicate that E2 can affect biomacromolecules, as circulating oligonucleotides, which can trigger mutations, leading to various unwanted effects.

Quantitative detection of single base mutation by combining PNA hybridization and MALDI-TOF mass analysis

Peptide nucleic acid (PNA) probes were designed to bind to the internal reference sequence and the single base mutation sequence within PCR-amplified DNA templates. PNAs hybridized to the target sequences on DNA were analyzed using MALDI-TOF mass spectrometry. Accurate quantification of the relative amount of mutant DNA was reproducibly demonstrated.

Synthesis, Crystal Structure, and Comparative Study of a New Organic Material 3,4-Diaminobenzophenone Semihydrate

The new organic 3,4-diaminobenzophenone semihydrate (34ABPH) is grown by slow evaporation method. The compound crystallizes in the monoclinic space group: C2. The unit cell dimensions are (8) Å, (2) Å, (10) Å, andβ = 99.40 (2)° with . The crystal structure analysis reveals that the C13H12N2O molecules chains are organized into a double ribbon in the (b,c) plane. The structural components interact by N–H⋯O and O–H⋯O hydrogen bonds, building up a two-dimensional network. The presence of functional groups in the molecular structure is confirmed by the Fourier transform infrared (FT-IR) spectroscopy. Thermogravimetric analysis (TGA) confirms the presence of the water molecule.

Mutagenesis as a tool in plant genetics, functional genomics, and breeding

Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.

Applications of mass spectrometry to the study of siRNA

RNA interference (RNAi) has quickly become a well-established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double-stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field.

Mass spectrometric analysis of sulfated N- and O-glycans

Sulfated N- and O-glycans carried on a myriad of cell-surface adhesion molecules and receptors are often not detected by current approaches in mass spectrometry (MS)-based glycomic mapping of cells and tissues. This is in part due to a natural lower abundance, compounded further by their negatively charged nature, which adversely disfavors their ionization and detection amid a sea of often much more abundant, nonsulfated, sialylated glycans. However, this particular limitation can actually be taken advantage of to effect highly selective enrichment and sensitive MS screening in negative ion mode, provided the ubiquitous sialic acids can first be neutralized. It has been demonstrated that permethylation not only fulfills this role adequately but further confers better MS/MS fragmentation characteristics for more efficient structural mapping and sequencing. Protocols and general practical considerations are described here which would enable one to readily prepare permethylated sulfated glycans, fractionate them away from the more abundant nonsulfated ones in simple steps for high-sensitivity MS analysis, and sensibly interpret the initial sulfoglycomic screening data thus obtained.

Enabling techniques and strategic workflow for sulfoglycomics based on mass spectrometry mapping and sequencing of permethylated sulfated glycans

Sulfate modifications on terminal epitopes of N- and O-glycans have increasingly been implicated as critical determinants mediating a diverse range of biological recognition functions. To address these low abundance but important sulfated glycans, and the sulfoglycome in general, further development of enrichment strategies and enabling mass spectrometry (MS)-based mapping techniques are needed. In this report, we demonstrate that the sulfated glycans, with and without additional sialylation, can be successfully permethylated by the sodium hydroxide slurry method and be distinguished from phosphorylated glycans by virtue of this derivatization. In conjunction with simple microscale postderivatization fractionation steps, permethyl derivatives fully retaining the negatively charged sulfate moiety and separated from the nonsulfated ones, can be efficiently detected and sequenced de novo by advanced MS/MS in the positive-ion mode. In particular, we show that the highly sequence and linkage informative high energy collision induced dissociation (CID) MS/MS afforded by MALDI-TOF/TOF can be extended to sulfoglycomic applications. The sulfated parent ion selected for CID MS/MS was found to mostly retain the sulfate moiety and therefore allow efficient fragmentation via the usual array of glycosidic, cross ring, and concerted double cleavages. Collectively, the optimized strategy enables a high sensitivity detection and critical mapping of the sulfoglycome such as the one derived from lymph node tissues or cell lines in both negative and positive-ion modes. Novel sulfated epitopes were identified from a crude mouse lymph node preparation, which fully attested to the practical utility of the methodology developed.

3,4-diaminobenzophenone matrix for analysis of oligonucleotides by MALDI-TOF mass spectrometry

This unit contains procedures for analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry with 3,4-diaminobenzophenone (DABP) as a matrix. This new matrix has demonstrated advantages in the analysis of oligonucleotides. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation, and fewer alkali-metal ion adducts compared with results obtained using conventional matrices. Minimal fragmentation and fewer alkali-metal ion adducts were seen even at low oligonucleotide concentrations. It was also found that samples prepared with DABP are highly homogenous, therefore reducing the need to find "sweet spots" in MALDI. Finally, excellent shot-to-shot reproducibility, resolution, and signal-to-noise ratio are observed using the DABP matrix.

Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.