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Article ; Online: Celebrating the remarkable career of Prof. Catherine Fenselau.

Fabris, Daniele

2024

Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Editorial
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.21875
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Article ; Online: Investigating the Merits of Microfluidic Capillary Zone Electrophoresis-Mass Spectrometry (CZE-MS) in the Bottom-Up Characterization of Larger RNAs.

Rollo, Daniele / Kulkarni, Aditya / Yu, Kate / Fabris, Daniele

Journal of the American Society for Mass Spectrometry

2024 Volume 35, Issue 3, Page(s) 561–574

Abstract: Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these ... ...

Abstract	Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques. An oligonucleotide ladder was initially employed to investigate the roles of fundamental analyte features and experimental parameters in determining the outcome of CZE-MS analyses. The results demonstrated the ability to fully resolve the various rungs into discrete electrophoretic peaks with full-width half-height (FWHH) resolution that was visibly affected by the overall amount of material injected into the system. Analogous results were obtained from a digestion mixture prepared by treating yeast tRNA
MeSH term(s)	Microfluidics ; RNA, Transfer, Phe ; Mass Spectrometry ; Chromatography, Liquid ; Electrophoresis, Capillary/methods
Chemical Substances	RNA, Transfer, Phe
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00411
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article ; Online: MS analysis of nucleic acids in the post-genomic era.

Fabris, D

Analytical chemistry

2011 Volume 83, Issue 15, Page(s) 5810–5816

Abstract: Alternative approaches complementing the existing technologies for analysis of nucleic acids and their assemblies are necessary to take on the new challenges posed by the postgenomic era. The versatility of MS in biopolymer analysis and its ability to ... ...

Abstract	Alternative approaches complementing the existing technologies for analysis of nucleic acids and their assemblies are necessary to take on the new challenges posed by the postgenomic era. The versatility of MS in biopolymer analysis and its ability to reach beyond sequence information are the basis of ever expanding applications aimed at the elucidation of nucleic acid structure-function relationships. This Feature summarizes the current state of MS-based approaches devised to overcome the limitations of traditional techniques and to advance different facets of nucleic acids research.
MeSH term(s)	Biopolymers/analysis ; Databases, Genetic ; Mass Spectrometry ; Nucleic Acid Conformation ; Nucleic Acids/analysis
Chemical Substances	Biopolymers ; Nucleic Acids
Language	English
Publishing date	2011-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac200374y
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Zs.A 4033: Show issues

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Article ; Online: The multifaceted roles of mass spectrometric analysis in nucleic acids drug discovery and development.

Kenderdine, Thomas / Fabris, Dan

Mass spectrometry reviews

2021 Volume 42, Issue 4, Page(s) 1332–1357

Abstract: The deceptively simple concepts of mass determination and fragment analysis are the basis for the application of mass spectrometry (MS) to a boundless range of analytes, including fundamental components and polymeric forms of nucleic acids (NAs). This ... ...

Abstract	The deceptively simple concepts of mass determination and fragment analysis are the basis for the application of mass spectrometry (MS) to a boundless range of analytes, including fundamental components and polymeric forms of nucleic acids (NAs). This platform affords the intrinsic ability to observe first-hand the effects of NA-active drugs on the chemical structure, composition, and conformation of their targets, which might affect their ability to interact with cognate NAs, proteins, and other biomolecules present in a natural environment. The possibility of interfacing with high-performance separation techniques represents a multiplying factor that extends these capabilities to cover complex sample mixtures obtained from organisms that were exposed to NA-active drugs. This report provides a brief overview of these capabilities in the context of the analysis of the products of NA-drug activity and NA therapeutics. The selected examples offer proof-of-principle of the applicability of this platform to all phases of the journey undertaken by any successful NA drug from laboratory to bedside, and provide the rationale for its rapid expansion outside traditional laboratory settings in support to ever growing manufacturing operations.
MeSH term(s)	Nucleic Acids/chemistry ; Mass Spectrometry/methods ; Proteins/chemistry
Chemical Substances	Nucleic Acids ; Proteins
Language	English
Publishing date	2021-12-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.21766
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Article ; Online: B-CePs as cross-linking probes for the investigation of RNA higher-order structure.

Sosic, Alice / Göttlich, Richard / Fabris, Dan / Gatto, Barbara

Nucleic acids research

2021 Volume 49, Issue 12, Page(s) 6660–6672

Abstract: Elucidating the structure of RNA and RNA ensembles is essential to understand biological functions. In this work, we explored the previously uncharted reactivity of bis-chloropiperidines (B-CePs) towards RNA. We characterized at the molecular level the ... ...

Abstract	Elucidating the structure of RNA and RNA ensembles is essential to understand biological functions. In this work, we explored the previously uncharted reactivity of bis-chloropiperidines (B-CePs) towards RNA. We characterized at the molecular level the different adducts induced by the fast reacting compound B-CeP 1 with RNA. Following an approach based on solution thermal melting coupled with ESI mass spectrometry (STHEM-ESI), we proved the ability of B-CePs to induce inter-molecular cross-links between guanines in double stranded RNA. These results open the possibility of using B-CePs as structural probes for investigating higher-order structures, such as the kissing loop complex established by the dimerization initiation site (DIS) of the HIV-1 genome. We confirmed the potential of B-CePs to reveal the identity of RNA structures involved in long-range interactions, expecting to benefit the characterization of samples that are not readily amenable to traditional high-resolution techniques, and thus promoting the elucidation of pertinent RNA systems associated with old and new diseases.
MeSH term(s)	Cross-Linking Reagents/chemistry ; Guanine/chemistry ; HIV-1/genetics ; Nucleic Acid Conformation ; Piperidines/chemistry ; RNA/chemistry ; RNA, Double-Stranded/chemistry ; RNA, Viral/chemistry ; Spectrometry, Mass, Electrospray Ionization
Chemical Substances	Cross-Linking Reagents ; Piperidines ; RNA, Double-Stranded ; RNA, Viral ; bis-3-chloropiperidine ; Guanine (5Z93L87A1R) ; RNA (63231-63-0)
Language	English
Publishing date	2021-06-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab468
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Zs.A 1067: Show issues

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Article ; Online: Catherine Fenselau: A distinguished career dedicated to biomedical mass spectrometry.

van Breemen, Richard B / Hathout, Yetrib / Fabris, Daniele

Journal of mass spectrometry : JMS

2020 Volume 55, Issue 2, Page(s) e4500

MeSH term(s)	Biochemistry/history ; Biochemistry/methods ; Biochemistry/organization & administration ; Female ; History, 20th Century ; History, 21st Century ; Humans ; Mass Spectrometry/history ; Mass Spectrometry/methods ; Proteomics ; United States
Language	English
Publishing date	2020-03-08
Publishing country	England
Document type	Editorial ; Historical Article
ZDB-ID	1221763-3
ISSN	1096-9888 ; 1076-5174
ISSN (online)	1096-9888
ISSN	1076-5174
DOI	10.1002/jms.4500
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Zs.A 4254: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 220: Show issues

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Article ; Online: In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction.

Sosic, Alice / Olivato, Giulia / Carraro, Caterina / Göttlich, Richard / Fabris, Dan / Gatto, Barbara

International journal of molecular sciences

2022 Volume 23, Issue 2

Abstract: After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem-bulge-loop domain of ... ...

Abstract	After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem-bulge-loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.
MeSH term(s)	HIV-1/drug effects ; HIV-1/metabolism ; Nucleic Acid Conformation ; Nucleocapsid Proteins/metabolism ; Piperidines/chemistry ; Piperidines/pharmacology ; RNA, Viral/chemistry ; RNA, Viral/drug effects ; RNA, Viral/metabolism
Chemical Substances	Nucleocapsid Proteins ; Piperidines ; RNA, Viral ; bis-3-chloropiperidine
Language	English
Publishing date	2022-01-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23020582
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Article ; Online: Ion Mobility Mass Spectrometry Reveals Rare Sialylated Glycosphingolipid Structures in Human Cerebrospinal Fluid.

Sarbu, Mirela / Fabris, Dragana / Vukelić, Željka / Clemmer, David E / Zamfir, Alina D

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 3

Abstract: Gangliosides (GGs) represent an important class of biomolecules associated with the central nervous system (CNS). In view of their special role at a CNS level, GGs are valuable diagnostic markers and prospective therapeutic agents. By ion mobility ... ...

Abstract	Gangliosides (GGs) represent an important class of biomolecules associated with the central nervous system (CNS). In view of their special role at a CNS level, GGs are valuable diagnostic markers and prospective therapeutic agents. By ion mobility separation mass spectrometry (IMS MS), recently implemented by us in the investigation of human CNS gangliosidome, we previously discovered a similarity between GG profiles in CSF and the brain. Based on these findings, we developed IMS tandem MS (MS/MS) to characterize rare human CSF glycoforms, with a potential biomarker role. To investigate the oligosaccharide and ceramide structures, the ions detected following IMS MS separation were submitted to structural analysis by collision-induced dissociation (CID) MS/MS in the transfer cell. The IMS evidence on only one mobility feature, together with the diagnostic fragment ions, allowed the unequivocal identification of isomers in the CSF. Hence, by IMS MS/MS, GalNAc-GD1c(d18:1/18:1) and GalNAc-GD1c(d18:1/18:0) having both Neu5Ac residues and GalNAc attached to the external galactose were for the first time discovered and structurally characterized. The present results demonstrate the high potential of IMS MS/MS for biomarker discovery and characterization in body fluids, and the perspectives of method implementation in clinical analyses targeting the early diagnosis of CNS diseases through molecular fingerprints.
MeSH term(s)	Adult ; Carbohydrate Sequence ; Gangliosides/cerebrospinal fluid ; Gangliosides/chemistry ; Glycosphingolipids/cerebrospinal fluid ; Glycosphingolipids/chemistry ; Humans ; Ion Mobility Spectrometry ; Isomerism ; Meningitis/cerebrospinal fluid ; Meningitis/diagnosis ; Models, Molecular ; N-Acetylneuraminic Acid/cerebrospinal fluid ; N-Acetylneuraminic Acid/chemistry ; Tandem Mass Spectrometry/methods
Chemical Substances	Gangliosides ; Glycosphingolipids ; N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2022-01-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27030743
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Zs.MO 81: Show issues

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Article ; Online: Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code.

Deng, L / Kumar, J / Rose, R / McIntyre, W / Fabris, Daniele

Mass spectrometry reviews

2022 Volume 43, Issue 1, Page(s) 5–38

Abstract: The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general ... ...

Abstract	The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
MeSH term(s)	Humans ; RNA/genetics ; Sequence Analysis, RNA/methods ; RNA Processing, Post-Transcriptional
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-09-02
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.21798
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Article ; Online: Novel flexible and conformable composite neutron scintillator based on fully enriched lithium tetraborate.

Pino, Felix / Delgado, Jessica Carolina / Carturan, Sara Maria / Mantovani, Giorgia / Polo, Matteo / Fabris, Daniela / Maggioni, Gianluigi / Quaranta, Alberto / Moretto, Sandra

Scientific reports

2023 Volume 13, Issue 1, Page(s) 4799

Abstract: Thermal neutron detection is a key subject for nuclear physics research and also in a wide variety of applications from homeland security to nuclear medicine. In this work, it is proposed a novel flexible and conformable composite thermal neutron ... ...

Abstract	Thermal neutron detection is a key subject for nuclear physics research and also in a wide variety of applications from homeland security to nuclear medicine. In this work, it is proposed a novel flexible and conformable composite thermal neutron scintillator based on a fully enriched Lithium Tetraborate preparation ([Formula: see text]Li[Formula: see text]B[Formula: see text]O[Formula: see text]) combined with a phosphorescent inorganic scintillator powder (ZnS:Ag), and is then distributed into a polydimethylsiloxane matrix. The proposed scintillator shows a good neutron detection efficiency (max. [Formula: see text] 57% with respect to the commercial EJ-420), an average light output of [Formula: see text] 9000 ph/neutron-capture, a remarkable insensitivity to [Formula: see text]-rays (Gamma Rejection Ratio <10[Formula: see text]), and an extraordinary flexibility, so as to reach extremely small curvature radii, down to 1.5 mm, with no signs of cracking or tearing. Its characteristics make it suitable to be employed in scenarios where non-standard geometries are needed, for example, to optimize the detector performance and/or maximize the detection efficiency. Finally, the response of a hybrid detector made of a plastic scintillator, wrapped with the proposed scintillator, coupled to a silicon photomultiplier array is described, and the excellent discrimination between [Formula: see text]-rays, fast and thermal neutrons resulting from data processing is demonstrated.
Language	English
Publishing date	2023-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-31675-9
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