Toward Building a Database of Bifunctional Probes for the MS3D Investigation of Nucleic Acids Structures

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dc.contributor.authorZhang, Qingrong
dc.contributor.authorYu, Eizadora T.
dc.contributor.authorKellersberger, Katherine A.
dc.contributor.authorCrosland, Elizabeth
dc.contributor.authorFabris, Daniele
dc.contributor.departmentEmeritusen_US
dc.date.accessioned2017-09-27T20:16:18Z
dc.date.available2017-09-27T20:16:18Z
dc.date.issued2006-11
dc.description.abstractThis report illustrates the approaches employed to investigate critical aspects of the activity of crosslinking reagents toward nucleic acid substrates, which should be evaluated to identify candidate probes for mass spectrometric 3D (MS3D) investigations of biomolecules and macromolecular complexes. Representative members of different classes of bifunctional reagents were taken into consideration, including bikethoxal and phenyl-diglyoxal [bis-(1,2-dicarbonyls)], cisplatin (coordinative binding agents), chlorambucil and nitrogen mustard [bis-(2-chloroethyl)amines], and sym-triazine trichloride (triazines). Nanospray-Fourier transform mass spectrometry (FTMS) was applied without desalting or separation procedures to characterize the covalent products obtained by probing dinucleotide and trinucleotide substrates under a variety of experimental conditions in vitro. The carefully controlled composition of these substrates enabled us to obtain valid comparisons of probe activity toward individual nucleotides and evaluate possible base-specific effects, including the stability of the different adducts in solution under the selected reaction conditions. The gas-phase behavior of the observed products was investigated using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) to obtain valuable information for guiding the design of sequencing experiments and helping the data interpretation. Structured RNA substrates, such as HIV-1 stemloop 1, were finally employed to investigate the structural determinant of adduct formation and highlight the different nature of the spatial information provided by the various candidate probes.en_US
dc.description.urihttps://ezproxy.stevenson.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=edb&AN=22938650&site=eds-live&scope=siteen_US
dc.format.extent11 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/M2ZS2KD6B
dc.identifier.citationZhang, 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. Journal Of The American Society For Mass Spectrometry, 17(11), 1570. doi:10.1016/j.jasms.2006.06.002en_US
dc.identifier.issn10440305
dc.identifier.urihttp://hdl.handle.net/11603/5653
dc.language.isoen_USen_US
dc.publisherJournal of the American Society for Mass Spectrometryen_US
dc.titleToward Building a Database of Bifunctional Probes for the MS3D Investigation of Nucleic Acids Structuresen_US
dc.typeTexten_US

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