This 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. (J Am Soc Mass Spectrom 2006, 17, 1570 -1581) © 2006 American Society for Mass Spectrometry M ass spectrometric 3D (MS3D) approaches seek to obtain information about the three-dimensional structure of biomolecules using chemical crosslinking and footprinting reagents followed by MS analysis [1][2][3][4]. The very wide range of applicability offered by these techniques is rapidly advancing MS3D to the forefront of the new technologies developed for the structural elucidation of biomolecules that exceed the size accessible by NMR, or afford inadequate crystallization. Fulfilling this potential, however, will require expanding the repertoire of available probes and developing new computational tools for the interpretation and utilization of this type of information in biomolecular modeling. For this purpose, a bioinformatics infrastructure has been recently created to support the efforts of investigators engaged in the development of enabling technologies for MS3D (http://ms3d.org) [5].The MS3D investigation of nucleic acids and proteinnucleic acid complexes can count on mono-and bifunctional alkylating reagents to reveal the location of base pairs, tertiary interactions, and inter-molecular contacts [4,6,7]. The ability of such reagents to support the elucidation of complex RNA structures was recently tested by completing the determination of two ribosome-frameshifting pseu...
The combination of chemical probing and high-resolution mass spectrometry constitutes a powerful alternative for the structural elucidation of biomolecules possessing unfavorable size, solubility, and flexibility. We have developed nested Arg-specific bifunctional crosslinkers to obtain complementary information to typical Cys-and Lys-specific reagents available on the market. The structures of 1,4-phenyl-diglyoxal (PDG) and 4,4′-biphenyl-diglyoxal (BDG) include two identical 1,2-dicarbonyl functions capable of reacting with the guanido group of Arg residues in proteins, as well as the base-pairing face of guanine in nucleic acids. The reactive functions are separated by modular spacers consisting of one or two benzene rings, which confer greater rigidity to the crosslinker structure than it is afforded by typical aliphatic spacers. Analysis by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has shown that the probes provide both mono-and bifunctional products with model protein substrates, which are stabilized by the formation of diester derivatives in the presence of borate buffer. The identification of crosslinked sites was accomplished by employing complementary proteolytic procedures and peptide mapping by ESI-FTICR. The results showed excellent correlation with the solvent accessibility and structural context of susceptible residues, and highlighted the significance of possible dynamic effects in determining the outcome of crosslinking reactions. The application of nested reagents with different spacing has provided a new tool for experimentally recognizing flexible regions that may be involved in prominent dynamics in solution. The development of new bifunctional crosslinkers with diverse target specificity and different bridging spans is expected to facilitate the structure elucidation of progressively larger biomolecular assemblies by increasing the number and diversity of spatial constraints available for triangulating the position of crosslinked structures in the three dimensions. KeywordsStructural probing; structure determination; bifunctional crosslinking; bis-(1,2-dicarbonyls); Argspecific labels; ESI-FTICR mass spectrometry Chemical labeling techniques and mass spectrometric analysis constitute an ideal combination for investigating the structure and dynamics of biomolecules that exceed the size accessible by nuclear magnetic resonance, or afford inadequate crystallization [1][2][3][4]. Monofunctional footprinting targeted to specific functional groups provides valuable information about *Corresponding author: University of Maryland Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21228 USA, Tel. (410) Fax (410) 455-2608. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resu...
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