Daniele Fabris - Publications

  • Lippens, J.L.; Ranaganathan, S.; D’Esposito, R.J.; and Fabris, D. “Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry” Analyst (2016), DOI: 10.1039/C6AN00453A, in press.
  • Rose, R.E.; Pazos, M.A. II; Curcio, J.; and Fabris, D. “Global profiling of RNA post-transcriptional modifications as an effective tool for investigating the epitranscriptomics of stress response” Mol. Cell. Proteomics 15(3), 932-44 (2016) DOI: 10.1074/mcp.M115.054718.
  • Frecentese, F.; Sosic, A.; Saccone, I.; Gamba, E.; Link, K.; Miola, A.; Cappellini, M.; Cattelan, M.G.; Severino, B.; Fiorino, F.; Magli, E.; Corvino, A.; Perissutti, E.; Fabris, D.; Gatto, B.; Caliendo, G.; Santagada, V. “Synthesis and in vitro screening of new series of 2,6-dipeptidyl-anthraquinones: influence of side chain length on HIV-1 nucleocapsid inhibition” J. Med. Chem. 59(5), 1914-24 (2016) DOI: 10.1021/acs.jmedchem.5b01494.
  • Murray, B.; Sorci, M.; Rosenthal, J.; Lippens, J.; Isaacson, D.; Das, P.; Fabris, D.; Li, S.; Belfort, G. “A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure and LTP inhibition” Proteins: Structure, Function, and Bioinformatics 4(4), 488-500 (2016) DOI: 10.1002/prot.24995.
  • Ribaudo, G.; Scalabrin, M.; Pavan, V.; Fabris, D.; Zagotto, G. “Constrained bisanthrene derivatives as G-quadruplex binders” ARKIVOC, 3, 145-160 (2016).
  • Lippens, J.L.; Mangrum, J.B.; McIntyre, W.; Redick, B.; and Fabris, D. “A simple heated-capillary modification improves the analysis of non-covalent complexes by Z-spray electrospray ionization” Rapid Comm. Mass Spectrom. 30, 773-783 (2016) DOI: 10.1002/rcm.7490.
  • Sosic, A.; Sinigaglia, L.; Cappellini, M.; Carli, I.; Parolin, C.; Zagotto, G.; Sabatino, G.; Rivero, P.; Fabris, D.; and Gatto, B. “Mechanisms of HIV-1 nucleocapsid protein inhibition by lysyl-peptidyl-anthraquinone conjugates” Bioconj. Chem. 27(1), 247-56 (2016) DOI10.1021/acs.bioconjchem.5b00627.
  • Tosoni, E.; Frasson, I.; Scalabrin, M.; Perrone, P.; Butovskaya, E.; Nadai, M.; Palù, G.; Fabris, D.; Richter, S. “Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription” Nucl. Acids Res. 43(18), 8884-97 (2015) DOI:10.1093/nar/gkv897.
  • Rose, R. E.; Quinn, R.; Sayre, J. L.; and Fabris, D. “Profiling ribonucleotide modifications at full-transcriptome level: a step towards MS-based epitranscriptomics” RNA, 21, 1-14 (2015) DOI:10.1261/rna.049429.114.
  • Sosic, A.; Cappellini, M.; Sinigaglia, L.; Jacquet, R.; Deffieux, D.; Fabris, D.; Quideau, S.; Gatto, B. “Polyphenolic C-glucosidic ellagitannins present in oak-aged wine inhibit HIV-1 nucleocapsid protein ” Tetrahedron, 71, 3020-3026 (2015). DOI:10.1016/j.tet.2015.01.035
  • Asare-Okai, P. N.; Agustin, E.; Fabris, D.; Royzen, M. “Site-specific fluorescence labelling of RNA using bio-orthogonal reaction of trans-cyclooctene and tetrazine” Chem. Commun., 50 (58), 7844 -7847 (2014).
  • Scalabrin, M.; Siu, Y.; Asare-Okai, P. N.; Fabris, D. “Structure-specific ribonucleases for MS-based elucidation of higher-order RNA structure” J. Am. Soc. Mass Spectrom., 25 (7), 1136–45 (2014), DOI: 10.1007/s13361-014-0911-2.
  • Quinn, R.; Basanta-Sanchez, M.; Rose, R. E.; Fabris, D. “Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition” J. Mass Spectrom 48 (6), 703–712 (2013), DOI: 10.1002/jms.3207. PuMed PMID: 23722961; PubMed Central PMCID: PMC3767442.
  • Stephenson, W.; Asare-Okai, P. N.; Chen, A.; Keller, S.; Santiago, R.; Tenenbaum, S.; Garcia, A. E.; Fabris, D.; Li, P.T.X. “The essential role of stacking adenines in a two-base-pair RNA kissing complex” J. Amer. Chem. Soc. 135 (15), 5602–5611 (2013), DOI: 10.1021/ja310820h. PubMed PMID: 23517345; PubMed Central PMCID: PMC3664431.
  • Doria, F.; Nadai, M.; Folini, M.; Scalabrin, M.; Germani, L; Sattin, G.; Mella, M.; Palumbo, M.; Zaffaroni, N.; Fabris, D.; Freccero, M.; and Richter, S. “Targeting Loop Adenines in G-Quadruplex by a Selective Oxirane” Chem. Eur. J. 19, 78-82 (2012), DOI: 10.1002/chem.201203097. PubMed PMID: 23212868; PubMed Central PMCID: PMC3863998.
  • Fabris, D.; Kellersberger, K.A.; Wilhide, J.A. “Higher-order structure of nucleic acids in the gas-phase: Top-down analysis of base-pairing interactions” Int. J. Mass Spectrom. 312, 155-162 (2012). PubMed PMID: 24027423; PubMed Central PMCID: PMC3767431.
  • Cantara, W. A.; Crain, P. F.; Rozenski, J.; McCloskey, J. A.; Harris, K. A.; Zhang, X.; Vendeix, F. A. P.; Fabris, D.; Agris, P. F. “The RNA modification database, RNAMDB: 2011 update” Nucleic Acids Res. 39(suppl 1), D195-D201 (2011). DOI: 10.1093/nar/gkq1028. Epub 2010 Nov 10. PubMed PMID: 21071406; PubMed Central PMCID: PMC3013656.
  • Fabris D. and Limbach P. A. “Review of the 22nd Sanibel Conference on Mass Spectrometry: From Structural Biology to Drug Discovery: New Roles for Mass Spectrometry of Nucleic Acids,” J. Am. Soc. Mass Spectrom., 7, R1-4 (2010).
  • Fabris D, Limbach PA. (2010) Review of the 22nd Sanibel Conference on Mass Spectrometry: From Structural Biology to Drug Discovery: New Roles for Mass Spectrometry of Nucleic Acids. J Am Soc Mass Spectrom. Mar 6. [Epub ahead of print]
  • Fabris D. (2010) A role for the MS analysis of nucleic acids in the post-genomics age. J Am Soc Mass Spectrom. 21(1):1-13.
  • Turner KB, Yi-Brunozzi HY, Brinson RG, Marino JP, Fabris D, Le Grice SF. (2009) SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA 15(8):1605-13.
  • Turner KB, Yi-Brunozzi HY, Le Grice SF, Fabris D, Marino JP. (2009) Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B. Brinson RG, Biochemistry. 48(29):6988-97.
  • Ramos I, Fabris D, Qi W, Fernandez EJ, Good TA. (2009) Kinetic study of beta-amyloid residue accessibility using reductive alkylation and mass spectrometry. Biotechnol Bioeng. 104(1):181-92.
  • Gapeev A, Berton A, Fabris D. (2009) Current-controlled nanospray ionization mass spectrometry. J Am Soc Mass Spectrom. 20(7):1334-41.
  • Fabris D. (2009) Special Series: advances in the investigation of the structure-function relationship in nucleic acids and their assemblies. Biopolymers. 91(6):v.
  • Fabris D. (2009) Special Series: Advances in the investigation of the structure-function relationship in nucleic acids and their assemblies. Biopolymers. 91(4):iii-iv.
  • Turner KB, Kohlway AS, Hagan NA, Fabris D. (2009) Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: the case of NC-mediated dimerization of genomic RNA in HIV-1. Biopolymers 91(4):283-96.
  • Yu ET, Hawkins A, Kuntz ID, Rahn LA, Rothfuss A, Sale K, Young MM, Yang CL, Pancerella CM, Fabris D. (2008) The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches. J Proteome Res., 7(11):4848-57.
  • Legiewicz M, Badorrek CS, Turner KB, Fabris D, Hamm TE, Rekosh D, Hammarskjöld ML, Le Grice SF. (2008) Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element. Proc Natl Acad Sci U S A., 105(38):14365-70.
  • Turner, K. B.; Brinson, R. G.; Yi-Brunozzi, H. Y.; Rausch, J. W.; Miller, J. T. Le Grice, S. F. J.; Marino, J. P.; Fabris, D. (2008) “Recognition of HIV-1 Polypurine Tract RNA:DNA Hybrid by Classic Nucleic Acid Ligands” Nucleic Acids Res. 36, 2799-2810.
  • Zhang, Q.; Crosland, E.; Fabris, D. (2008) “Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies” Anal Chim Acta. 627(1):117-28.
  • Yu ET, Hawkins A, Eaton J, Fabris D. (2008) MS3D structural elucidation of the HIV-1 packaging signal. Proc Natl Acad Sci USA. 105(34):12248-53.
  • Holland R, Hawkins AE, Eggler AL, Mesecar AD, Fabris D, Fishbein JC.(2008) Prospective type 1 and type 2 disulfides of Keap1 protein. Chem Res Toxicol. 21(10):2051-60.
  • Hagan, N. A. and Fabris, D. (2007) “Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1” J. Mol. Biol. 365, 396-410 .
  • Fabris, D.; Chaudhari, P.; Hagan, N. A.; Turner, K. B. (2007) “Functional Investigations of Retroviral Protein-RNA Complexes by Nanospray-FTICR Mass Spectrometry” Eur. J. Mass Spectrom. 13, 29-33 .
  • Turner, K. B.; Hagan, N. A.; Fabris, D. (2007) “Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein” J. Mol. Biol. 369, 812-828 .
  • Stephen, A. G.; Datta, S. A. K.; Worthy, K. M.; Bindu, L.; Fivash, M.J.; Turner, K. B.; Fabris, D.; Rein, A.; Fisher, R.J. (2007) “Measuring the binding stoichiometry of HIV-1 Gag to very-low-density oligonucleotide surfaces using plasmon resonance spectroscopy” J. Biomol. Tech. 18, 259-266 .
  • Turner, K. B.; Hagan, N. A..; Fabris, D. (2006) “Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Y-RNA”, Nucleic Acids Res. 34, 1305-1316 .
  • Fisher, R.J.; Fivash, M.J.; Stephen, A.G.; Hagan, N.A.; Shenoy, S.R.; Medaglia, M.V.; Smith, L.R.; Worthy, K.M.; Simpson, J.T.; Shoemaker, R.; McNitt, K.L.; Johnson, D.J.; Hixson, C.V.; Gorelick, R.J.; Fabris, D.; Henderson, L.E.; Rein, A. (2006) “Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides”, Nucleic Acids Res. 34, 472-484 .
  • Rait, V. K.; Zhang, Q.; Fabris, D.; Mason, J. T.; O’Leary, T. J. (2006) “Conversions of formaldehyde-modified 2´-deoxyadenosine 5´-monophosphate in conditions modeling formalin-fixed tissue dehydration” J. Histochem. Cytochem. 54, 301-310 .
  • Turner, K. B.; Hagan, N. A.; Kohlway, A.; Fabris, D. (2006) “Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry” J. Am. Soc. Mass Spectrom. 17, 1401-1411 , journal cover.
  • Zhang, Q.; Yu, E. T.; Kellersberger, K. A.; Crosland, E.; Fabris, D. (2006) “Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures” J. Am. Soc. Mass Spectrom. 17, 1570-1581 .