The exposure of electrospray droplets to acid vapors can significantly affect protein charge state distributions (CSDs) derived from unbuffered solutions. Such experiments have been conducted by leaking acidic vapors into the counter-current nitrogen drying gas of an electrospray interface. Based on changes in protein CSDs, protein folding and unfolding phenomena are implicated in these studies. Additionally, non-covalently-bound complexes are preserved and transient intermediates observed, such as high charge state ions of holomyoglobin. CSDs of proteins containing disulfide bonds shift slightly, if at all, with acid vapor leak-in, but when these disulfide bonds are reduced in solution, charge states higher than the number of basic sites (Lys, Arg, His and N-terminus) are observed. Since there is no observed change in the CSD of buffered proteins exposed to acidic vapors, this novel multiple charging phenomenon is attributed to a pH effect. Thus, this acid vapor leak-in approach can be used to reverse ‘wrong-way-round’ nanoelectrospray conditions by altering solution pH in the charged droplets relative to the pH in bulk solution. In general, the exposure of electrospray droplets to acidic vapors provides means for altering protein CSDs independent of bulk unbuffered solution pH.

The dissociation of model RNA anions has been studied as a function of anion charge state and excitation amplitude using ion trap collisional activation. Similar to DNA anions, the precursor ion charge state of an RNA anion plays an important role in directing the preferred dissociation channels. Generally, the complementary c/y-ions from 5= P-O bond cleavage dominate at low to intermediate charge states, while other backbone cleavages appear to a limited extent but increase in number and relative abundance at higher excitation energies. The competition between base loss, either as a neutral or as an anion, as well as the preference for the identity of the lost base are also observed to be charge-state dependent. To gain further insight into the partitioning of the dissociation products among the various possible channels, model dinucleotide anions have been subjected to a systematic study. In comparison to DNA, the 2=-OH group on RNA significantly facilitates the dissociation of the 5= P-O bond. However, the degree of excitation required for a 5= base loss and the subsequent 3= C-O bond cleavage are similar for the analogous RNA and DNA dinucleotides. Data collected for protonated dinucleotides, however, suggest that the 2=-OH group in RNA can stabilize the glycosidic bond of a protonated base. Therefore, base loss from low charge state oligonucleotide anions, in which protonation of one or more bases via intramolecular proton transfer can occur, may also be stabilized in RNA anions relative to corresponding DNA anions. t has been recognized that various noncoding RNA species play important roles in cellular function [1][2][3][4]. Recently, significant effort has been focused on the identification of these noncoding RNAs. However, conventional methods are usually labor intensive and ineffective in the characterization of RNA modifications [5]. On the other hand, tandem mass spectrometry is a rapid and sensitive alternative, provided the desired structural information can be derived from the dissociation chemistry that occurs between stages of mass analysis.To develop tandem mass spectrometry-based RNA sequencing methods, an understanding of the factors that determine the nature of the structural information that can be obtained via dissociation of RNA ions is necessary. Some of the first studies on RNA dissociation were conducted with ions generated from fast atom bombardment (FAB). A variety of fragment ions, including the characteristic structural fragment c x -ion, were identified [6,7]. The combination of matrixassisted laser desorption ionization (MALDI) and electrospray ionization (ESI) with tandem mass spectrometry facilitated the study of the gas-phase dissociation of larger oligonucleotide ions. However, far more attention has been dedicated to the study of the dissociation behavior of DNA ions than to dissociation of RNA ions [8]. Using MALDI combined with a quadrupole/timeof-flight (Q/TOF) tandem mass spectrometer, Kirpekar and Krogh [9], for example, investigated the dissociation behavior of singly...

Borosilicate theta glass capillaries pulled to serve as nanoelectrospray ionization emitters are used for short time-scale mixing of protein and acid solutions during the electrospray process to alter protein charge state distributions (CSDs) without modifying the sample solution. The extent of protein CSD shifting/denaturing can be tailored by acid identity and concentration. The observed CSD(s) are protein dependent, and the short mixing time-scale enables the study of short-lived unfolding intermediates and higher charge states of noncovalent protein complexes, including those of holomyoglobin. Additionally, the theta tips provide a simple and inexpensive method for mixing nonvolatile reagents such as supercharging agents, which cannot be used with previously developed vapor leak-in techniques, with protein solutions during the electrospray process.

We studied the mechanism of action of 3,5-dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester and found that it is a potent microtubule depolymerizer. JG-03-14 caused a dose-dependent loss of cellular microtubules, formation of aberrant mitotic spindles, accumulation of cells in the G 2 /M phase of the cell cycle, and Bcl-2 phosphorylation. These events culminated in the initiation of apoptosis, as evidenced by the caspase 3-dependent cleavage of poly-(ADP-ribose) polymerase (PARP). JG-03-14 has antiproliferative activity against a wide range of cancer cell lines, with an average IC 50 value of 62 nM, and it is a poor substrate for transport by P-glycoprotein. JG-03-14 inhibited the polymerization of purified tubulin in vitro, consistent with a direct interaction between the compound and tubulin. JG-03-14 potently inhibited the binding of [ 3 H]colchicine to tubulin, suggesting that it bound to tubulin at a site overlapping the colchicine site. JG-03-14 had antitumor effects in the PC3 xenograft model, in which it caused greater than 50% reduction in tumor burden after 14 days of treatment. Molecular modeling studies indicated that the dimethoxyphenyl group of JG-03-14 occupies a space similar to that of the trimethoxyphenyl group of colchicine. However, the 2,3,5-trisubstituted pyrrole group, which is connected to the dimethoxyphenyl moiety, interacted with both ␣ and ␤ tubulin in space not shared with colchicine, suggesting significant differences compared with colchicine in the mechanism of binding to tubulin. Our results suggest that this tetrasubstituted pyrrole represents a new, biologically active chemotype for the colchicine site on tubulin.Microtubules are cellular structures that play a central role in metabolism, intracellular transport, and cell division. A wide range of chemicals have been identified that interrupt microtubule function. These compounds can be divided into microtubule stabilizers and microtubule depolymerizers. Microtubule stabilizers include paclitaxel, discodermolide, the epothilones, and the laulimalides. Microtubule stabilizers cause an increase in the density of cellular microtubules, and they stimulate the assembly of purified tubulin. In contrast, microtubule depolymerizers cause a loss of cellular microtubules, and they inhibit the assembly of purified tubulin. Microtubule depolymerizing compounds can be further subdivided into those that bind to tubulin within the colchicine site and those that bind within the vinca domain. Agents acting upon the colchicine site include 2ME2, combretastatin A-4, and podophyllotoxin. The phenotypic effects of microtubule stabilizing and depolymerizing agents are quite disparate when they are used at high concentrations in cells, but at their lowest antiproliferative concentrations, both classes of agents inhibit microtubule dynamics (Jordan and Wilson, 2004). In due course, inhibition of microtubule dynamics is believed to hinder the normal function of the mitotic spindle,

Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3=C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics. (J Am Soc Mass Spectrom 2010, 21, 144 -153)