Direct observation of a DNA quadruplex by electrospray ionization mass spectrometry

Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand

While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Mass Spectroscopic Study of G-Quadruplex

Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quadruplex. More specifically, electrospray ionization mass spectrometry (ESI-MS) has been successfully applied to probe various G-quadruplex formations and G-quadruplex-ligand interactions. The benefit of the ESI process is that the noncovalent interactions, which typically stabilize the multistranded motifs of G-quadruplex in solution, are preserved in the gas phase. Here we use ESI-MS to describe the structural characterization of G-quadruplex structures found in three G-rich sequences, as well as the ligand binding. Detailed structural information of G-quadruplexes and their ligand-bound complexes (such as the cation/ligand binding stoichiometry, and the number of strands and G-quartets) can be obtained from a single spectrum using this ESI-MS-based method.

The zinc form of carnosine dipeptidase 2 (CN2) has dipeptidase activity but its substrate specificity is different from that of the manganese form

Carnosine dipeptidase II (CN2), a metallopeptidase present in the cytosol of various vertebrate tissues, catalyzes the hydrolysis of carnosine and several other dipeptides in the presence of Mn²⁺. Although the metal-binding center of mouse CN2 is also able to associate with Zn²⁺in vitro, it was not known whether the zinc form of CN2 has any enzymatic activity. In the present study, we show that Zn²⁺ has a higher affinity for binding to CN2 than Mn²⁺, as evidenced by native mass spectrometry. The issue of whether the zinc form of CN2 has enzymatic activity was also examined using various dipeptides as substrates. The findings indicate that the zinc form of CN2 catalyzes the hydrolysis of several different dipeptides including Leu-His, Met-His and Ala-His at a reaction rate comparable to that for its manganese form. On the other hand, the zinc form of CN2 did not catalyze the hydrolysis of carnosine and several other dipeptides that are hydrolyzed by the manganese form of CN2. Substrate specificity was also examined in HEK293T cells expressing CN2, and the findings indicate that Leu-His, Met-His, but not carnosine, were hydrolyzed in the cell culture. These results suggest that the zinc form of CN2 is an active enzyme, but with a different substrate specificity from that of the manganese form.

Automated High Throughput Multiple Target Screening of Molecular Libraries by Microfluidic MALDI-TOF MS

Novel analytical techniques are demanded in parallel in the automated combinatorial library syntheses for accelerating the process of drug discovery. In this study, the integration of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and robotics for simultaneously identifying lead compounds with activity against multiple enzyme targets has been shown. MALDI-TOF MS monitors the interactions between multienzyme targets and a library of compounds and then identifies individual compounds from molecular libraries that affect the enzymatic activities of multiplexed target molecules to catalyze the conversion of substrates to products. The novel mass spectrometry screening in high-density format (~4,000 samples in a single 4.5 × 4.5 cm MALDI plate) provides much higher throughput over traditional screening approaches in terms of multiplex targets, attomole-level sensitivity, very low volume of samples required (10−9−10−121), and data acquisition for each sample within ten sec. The microfluidic multiple target screening approach mass spectrometry was shown for discovery of enzyme inhibitors as potential lead compounds.

Conformation types of ubiquitin [M+8H]8+ Ions from water:methanol solutions: evidence for the N and A States in aqueous solution

Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H](8+) ubiquitin ions formed upon electrospraying 20 different solutions from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena.

Charge and substituent effects on the stability of porphyrin/G-quadruplex adducts

The adduct ions of two tetramolecular G-quadruplexes formed from the d(TGGGGT) and d(TTGGGGGT) single strands with a group of cationic porphyrins, with different charges and substituents, and one neutral porphyrin, were investigated by ESI-MS and ESI-MS/MS in the negative ion mode. Formation of [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions (where Q = quadruplex, n = number of quartets minus 1, P = porphyrin and p(+) = 0,1,2,3,4) indicates that the porphyrins are bound outside the quadruplexes providing an additional stabilization to those structures. The fragmentation pathways of the [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions depend on the number of positive charges (p(+)) of the porphyrins and on the overall complex charge (z(-)), but do not show a significant dependence on the type of the substituent groups in the porphyrins. Formation of the 'unfilled' ions [Q + P(p+)-(z + p)H(+)](z-) predominates for porphyrins with a higher number of positive charges. Strand separation with the formation of [T + P(p+)-(z-2 + p)H(+)]((z-2)-) and (SS-2H(+))(2-) ions, where T = [d(TG(4)T)](3) and [d(T(2)G(5)T)](3) and SS = d(TG(4)T) and d(T(2)G(5)T) is only observed for the complexes with a higher overall negative charge. Porphyrin loss with the formation of [Q + nNH(4)(+)-(z + n)H(+)](z-) ions occurs predominantly for the neutral and monocharged porphyrins. The predominant formation of the 'unfilled' ions, [Q + P(p+)-(z + n)H(+)](z-), for porphyrins with a higher number of charges shows that these porphyrins can prevent strand separation and preserve, at least partially, the quadruplex structure.

Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation

G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.

Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes

Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.

Frontiers of mass spectrometry in nucleic acids analysis

Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.

A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder

A new method for the determination of the relative affinity of a ligand against various dsDNA sequences is presented by using electrospray ionization time-of-flight mass spectrometry (ESI-QTOF) mass spectrometry. The principle is described here through the complexation of double-stranded DNA by a polyamide ligand including twelve N-methylpyrrole rings. However this method could be applied to other ligands especially when dissociation constants (Kd) are in nanomolar range. This method does not require knowing the ligand concentration accurately. It allows determination of the relative affinity of a ligand against various dsDNA sequences for 1 : 1 complex stoichiometries in a quick manner without labeling.

Hybridization of short complementary PNAs to G-quadruplex forming oligonucleotides: An electrospray mass spectrometry study

We investigated the interaction of the short peptide nucleic acid (PNA) strand [acccca]-PNA with oligodeoxynucleotides containing one, two, or four tracts of TGGGGT units. Electrospray ionization mass spectrometry allowed exploring the wide variety of complex stoichiometries that were found to coexist in solution. In water, the PNA strand forms short heteroduplexes with the complementary DNA sequences, but higher-order structures are also found, with PNA(2n).DNA(n) triplex units, culminating in precipitation at very low ionic strength. In the presence of ammonium acetate, there is a competition between PNA.DNA heteroduplex formation and DNA G-quadruplex formation. Heteroduplex formation is favored when the PNA + DNA mixture in ammonium acetate is heated and cooled at room temperature, but not if the PNA is added at room temperature to the preformed G-quadruplex. We also found that the short [acccca]-PNA strand binds to G-quadruplexes.

Chloro acridone derivatives as cytotoxic agents active on multidrug-resistant cell lines and their duplex DNA complex studies by electrospray ionization mass spectrometry

We report herein in vitro anti-proliferative activity and duplex DNA complex studies of a series of N10-substituted acridone derivatives. All the molecules have been designed on the basis of the presence of specific recognition patterns consisting of hydrogen bond acceptors (or electron donors), carbonyl, chloro groups with precise spatial separation and structural features (lipophilicity, positive charge at neutral pH and presence of aromatic rings). The in vitro cytotoxic effects have been demonstrated against human promyelocytic leukemia sensitive cell line (HL-60), including its multidrug cross-resistance of two main (P-gp and MRP) phenotype sublines vincristine-resistant (HL-60/VINC) and doxorubicin-resistant (HL-60/DX) cancer cell lines. Compound 4 showed very good activity against sensitive and resistant cell lines. The noncovalent complexes of these molecules with DNA duplex has been investigated in gas phase by using a fast, robust and sensitive electrospray ionization mass spectrometry (ESI-MS) technique. Equilibrium association constants (K1) and percentage of intact complexes were determined. The combined results show that these acridone derivatives interact with DNA duplex by intercalation between the base pairs, possess higher affinity to GC than AT base pairs of the DNA and they could not interact noncovalently with the minor grooves of the DNA in solution-free gas phase. Examination of the relationship between lipophilicity and cytotoxic properties of acridone derivatives showed a poor correlation. The in vitro cytotoxic studies in resistant cancer cell lines of compound 4 showed that it might be a promising new hit for further development of anti-MDR agent.

Analysis of oligonucleotides by electrospray ionization mass spectrometry

Because of the high molecular weights and thermal lability of biomolecules such as nucleic acids and protein, they can be difficult to analyze by mass spectrometry. Such analyses require a "soft" ionization method that is capable of generating intact molecular ions. In addition, most mass analyzers have a limited upper mass range that is not sufficient for studying these large molecules. ESI-MS can be used to analyze molecules with a molecular weight that is larger than the mass-to-charge ratio limit of the analyzer. This unit describes how ESI allows for analysis of high-molecular-weight compounds through the generation of multiply charged ions in the gas phase. It discusses analyzer configurations, solvent selection, and gives protocols for sample preparation. For applications of ESI-MS, the unit discusses molecular weight determination and gives protocols for sequencing and for analyzing oligonucleotide modifications.

Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: the role of central cations and small planar ligands

A promising approach for anticancer strategies is the stabilization of telomeric DNA into a G-quadruplex structure. To explore the intrinsic stabilization of folded G-quadruplexes, we combined electrospray ionization mass spectrometry, ion mobility spectrometry, and molecular modeling studies to study different DNA sequences known to form quadruplexes. Two telomeric DNA sequences of different lengths and two DNA sequences derived from the NHE III1 region of the c-myc oncogene (Pu22 and Pu27) were studied. NH4+ and the ligands PIPER, TMPyP4, and the three quinacridines MMQ1, MMQ3, and BOQ1 were complexed with the DNA sequences to determine their effect on the stability of the G-quadruplexes. Our results demonstrate that G-quadruplex intramolecular folds are stabilized by NH4+ cations and the ligands listed. Furthermore, the ligands can be classified according to their ability to stabilize the quadruplexes and end stacking is shown to be the dominant mode for ligand attachment. In all cases our solvent-free experimental observations and theoretical modeling reveal structures that are highly relevant to the solution-phase structures.

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS

The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Infrared multiphoton dissociation of duplex DNA/drug complexes in a quadrupole ion trap

Noncovalent duplex DNA/drug complexes formed between one of three 14-base pair non-self-complementary duplexes with variable GC content and one of eight different DNA-interactive drugs are characterized by infrared multiphoton dissociation (IRMPD), and the resulting spectra are compared to conventional collisionally activated dissociation (CAD) mass spectra in a quadrupole ion trap mass spectrometer. IRMPD yielded comparable information to previously reported CAD results in which strand separation pathways dominate for complexes containing the more AT-rich sequences and/or minor groove binding drugs, whereas drug ejection pathways are prominent for complexes containing intercalating drugs and/or duplexes with higher GC base content. The large photoabsorptive cross section of the phosphate backbone at 10.6 mum promotes highly efficient dissociation within short irradiation times (<2 ms at 50 W) or using lower laser powers and longer irradiation times (<15 W at 15 ms), activation times on par with or shorter than standard CAD experiments. This large photoabsorptivity leads to a controllable ion activation method which can be used to produce qualitatively similar spectra to CAD while minimizing uninformative base loss dissociation pathways or instead be tuned to yield a high degree of secondary fragmentation. Additionally, the low-mass cutoff associated with conventional CAD plays no role in IRMPD, resulting in richer MS/MS information in the low m/z region. IRMPD is also used for multiadduct dissociation in order to increase MS/MS sensitivity, and a two-stage IRMPD/IRMPD method is demonstrated as a means to give specific DNA sequence information that would be useful when screening drug binding by mixtures of duplexes.

Theoretical and gas-phase studies of specific cationized purine base quartet

Guanine tetraplexes are biological non-covalent systems stabilized by alkali cations. Thus, self-clustering of guanine, xanthine and hypoxanthine with alkali cations (Na(+), K(+) and Li(+)) is investigated by electrospray ionization mass spectrometry (ESI-MS) in order to provide new insights into G-quartets, hydrogen-bonded complexes. ESI assays displayed magic numbers of tetramer adducts with Na(+), Li(+) and K(+), not only for guanine, but also for xanthine bases. The optimized structures of guanine and xanthine quartets have been determined by B3LYP hybrid density functional theory calculations. Complexes of metal ions with quartets are classified into different structure types. The optimized structures obtained for each quartet explain the gas-phase results. The gas-phase binding sequence between the monovalent cations and the xanthine quartet follows the order Li(+) > Na(+) > K(+), which is consistent with that obtained for the guanine quartet in the literature. The smallest stabilization energy of K(+) and its position versus the other alkali metal ions in guanine and xanthine quartets is consistent with the fact that the potassium cation can be located between two guanine or xanthine quartets, for providing a [gua(or (xan))(8)+K](+) octamer adduct. Even if an abundant octamer adduct with K(+) for xanthine was detected by ESI-MS, it was not the case for guanine.

Cation Exchange in Lipophilic G-Quadruplexes: Not All Ion Binding Sites Are Equal

Lipophilic guanosine derivatives that form G-quadruplexes are promising building blocks for ionophores and ion channels. Herein, cation exchange between solvated cations (K+ and NH4+) and bound cations in the G-quadruplex [G1]16.4Na+.4DNP- was studied by electrospray ionization mass spectrometry and solution 1H, 15N NMR spectroscopy. The ESI-MS and 1H NMR data provided evidence for the formation of mixed-cationic Na+, K+ G-quadruplexes. The use of 15NH4+ cations in NMR titrations, along with 15N-filtered 1H NMR and selective NOE experiments, identified two mixed-cationic intermediates in the cation exchange pathway from [G1]16.4Na+.4DNP- to [G1]16.4NH4+.4DNP-. The central Na+, bound between the two symmetry-related G8-Na+ octamers, exchanges with either K+ or NH4+ before the two outer Na+ ions situated within the C4 symmetric G8 octamers. A structural rationale, based on differences in the cations' octahedral coordination geometries, is proposed to explain the differences in site exchange for these lipophilic G-quadruplexes. Large cations such as Cs+ can be exchanged into the central cation binding site that holds the two symmetry-related C4 symmetric G8 octamer units together. The potential relevance of these findings to both supramolecular chemistry and DNA G-quadruplex structure are discussed.

Electron Photodetachment Dissociation of DNA Polyanions in a Quadrupole Ion Trap Mass Spectrometer

We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer single strands and 12-base pair double strands. In all cases, laser irradiation causes electron detachment from the multiply charged DNA anions. Electron photodetachment efficiency directly depends on the number of guanines in the strand, and maximum efficiency is observed between 260 and 275 nm. Subsequent collision-induced dissociation (CID) of the radical anions produced by electron photodetachment results in extensive fragmentation. In addition to neutral losses, a large number of fragments from the w, d, a*, and z* ion series are obtained, contrasting with the w and (a-base) ion series observed in regular CID. The major advantage of this technique, coined electron photodetachment dissociation (EPD) is the absence of internal fragments, combined with good sequence coverage. EPD is therefore a highly promising approach for de novo sequencing of oligonucleotides. EPD of nucleic acids is also expected to give specific radical-induced strand cleavages, with conservation of other fragile bonds, including noncovalent bonds. In effect, preliminary results on a DNA hairpin and on double strands suggest that EPD could also be used to probe intra- and intermolecular interactions in nucleic acids.

Applications of mass spectrometry in early stages of target based drug discovery

Mass spectrometry (MS) has been applied to drug discovery for many years. With the advent of new ionization techniques, MS has emerged as an important analytical tool in identification and characterization of protein targets, structure elucidation of synthetic compounds, and early drug metabolism and pharmacokinetics studies. Two MS-based strategies, function-based and affinity-based, have been employed in recent years for screening and evaluation of compounds. In the function-based approach, the effects of compounds on the biological activity of a target molecule are measured. In the affinity-based approach, compounds are screened based on their binding affinities to target molecules. The interaction between targets and compounds can be directly evaluated by monitoring the formation of non-covalent target-ligand complexes (direct detection) or indirectly evaluated by detecting the compounds after separating bound compounds from unbound (indirect detection). Various techniques including high performance liquid chromatography (HPLC)-MS, size exclusion chromatography (SEC)-MS, frontal affinity chromatography (FAC)-MS and desorption/ionization on silicon (DIOS)-MS can be applied. The recent advances, relative advantages, and limitations of each MS-based method as a tool in compound screening and compound evaluation in the early stages of drug discovery are discussed in this review.

Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes

The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.

Structural characterization of G-quadruplexes in deoxyguanosine clusters using ion mobility mass spectrometry

The aggregation and conformation of deoxyguanosine (dG) in an ammonium acetate buffer solution were examined using mass spectrometry, ion mobility, and molecular mechanics/dynamics calculations. The nano-ESI mass spectrum indicated that 4 and 6 dGs cluster with 1 NH4+; 11 dGs with 2 NH4+; 14, 16, and 17 dGs with 3 NH4+; and 23 dGs with 4 NH4+. The collision cross sections with helium were measured and compared with calculated cross sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct arrival time distribution (ATD) peaks were observed for (4dG + NH4)+. One peak was assigned to the quadruplex structure of (4dG + NH4)+, while the other two peaks corresponded to the quadruplex structures of (8dG + 2NH4)2+ and (12dG + 3NH4)3+, all with the same m/z. Four ATD peaks were observed for (6dG + NH4)+ and assigned to the globular structure of (6dG + NH4)+, and the quadruplex structures of (12dG + 2NH4)2+, (18dG + 3NH4)3+, and (24dG + 4NH4)4+. Two ATD peaks were observed for (11dG + 2NH4)2+ and assigned to the quadruplex structures of (11dG + 2NH4)2+ and (22dG + 4NH4)4+. All of the other clusters in the mass spectrum (14, 16, and 17 dGs with 3 NH4+ and 23 dGs with 4 NH4+) only had one peak in their ATDs and in all cases the theoretical structures in a quadruplex arrangement agreed with the experimental cross sections. These results provide compelling evidence that quadruplexes are present in solution and retain their structure during the spray process, dehydration, and detection.

Dynamic covalent chemistry on self-templating PNA oligomers: formation of a bimolecular PNA quadruplex

The tetramolecular PNA quadruplex motif has been probed using a dynamic covalent chemistry (DCC) approach to create and characterize a bimolecular PNA quadruplex.

Fast gas-phase hydrogen/deuterium exchange observed for a DNA G-quadruplex

The gas-phase hydrogen/deuterium (H/D) exchange kinetics of DNA G-quadruplexes has been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The quadruplex [(TGGGGT)4 . 3NH4+] undergoes very fast H/D exchange, in both the positive and in the negative ion modes, compared to DNA duplexes and other quadruplexes tested, and compared to the corresponding single-stranded TGGGGT. Substitution of NH4+ for K+ did not alter this fast H/D exchange, indicating that the hydrogens of the ammonium ions are not those exchanged. However, stripping of the interior cations of the quadruplex by source collision-induced dissociation (CID) in the positive ion mode showed that the presence of the inner cations is essential for the fast exchange to be possible. Molecular dynamics simulations show that the G-quadruplex is very rigid in the gas phase with NH4+ ions inside the tetrads. We suggest that the fast H/D exchange is favored by this rigid quadruplex conformation. This example illustrates that the concept that compact DNA structures exchange H for D slower than unfolded ones is a misconception.

Formation of an interlocked quadruplex dimer by d(GGGT)

A tetranucleotide sequence d(GGGT) has been shown to self-assemble into an interlocking quadruplex dimer. UV-melting studies indicated the existence of two species that each showed distinct quadruplex melting transitions, a low-T(m) species, Q(l), and a high-T(m) species, Q(h). Conditions were controlled to favor the formation of either Q(l) or Q(h). Q(l) and Q(h) each showed circular dichroism spectra characteristic of parallel quadruplexes. Negative ion nano-electrospray ionization mass spectrometry confirmed that Q(l) was a tetrameric complex, d(GGGT)(4), and Q(h) was an octameric complex, d(GGGT)(8). High-resolution (1)H NMR spectroscopy evidenced that d(GGGT)(4) was a C(4)-symmetric parallel tetramolecular quadruplex. The (1)H NMR spectrum of d(GGGT)(8) was consistent with a structure formed by the dimerization of a parallel, "slipped" tetramolecular quadruplex that has its diagonal strands staggered by one base. This "slippage" results in two guanine bases at the 5' end of the quadruplex being presented diagonally that are not involved in tetrads. Two such "slipped" quadruplexes dimerize via these free G-bases at the 5' ends by forming an extra G-tetrad. Each "slipped" quadruplex contributes two guanine bases to this extra G-tetrad. The formation of a novel GTGT tetrad is also observed at both the 3' ends of the interlocked quadruplex dimer.

How a modification (8-aza-3-deaza-2'-deoxyguanosine) influences the quadruplex structure of Hotoda's 6-mer TGGGAG with 5'- and 3'-end modifications

We have synthesized a modified 6-mer using Hotoda's 6-mer TGGGAG with 5'- and 3'-end modifications as a template. We have replaced from one to all four 2'-deoxyguanosines by 8-aza-3-deaza-2'-deoxyguanosine (c3z8dG, 1) in order to investigate the anti-HIV structure activity relationship (SAR). ODN 4 (TGGG*AG) is the only one that exhibits a moderate anti-HIV-1 activity.

A PNA4 quadruplex

A tetrameric PNA, TGGG, has been shown to form an intermolecular G-quadruplex. Nanoelectrospray mass spectrometry, combined with solution-phase H/D exchange, established formation of a specific tetramolecular complex. UV melting studies show that this complex undergoes a quadruplex melting transition. This is a novel four-stranded structure that offers the gross structural features of a DNA quadruplex, but without the negatively charged backbone.

G-quadruplex formation of thrombin-binding aptamer detected by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry detected the formation of the G-quadruplex structure of the thrombin-binding aptamer, d(GGTTGGTGTGGTTGG), and established its specific interaction with metal ions. One piece of evidence that the bonding in the gas phase is via the G-quadruplex form is the enhanced binding, with respect to other metal ions, of the aptamer with Sr2+, Pb2+, Ba2+, and K+, which are of similar size. Another is the lack of specific binding with controls in which the G's are replaced with A's. The most convincing evidence is the extent of H/D exchange of the gas-phase aptamer as compared to that bound to K+ and Sr2+. The latter two complexes exchange six and nine fewer H's, indicating a significant increase in protection upon binding to the metals. Mass spectrometry will be an important tool in understanding G-quadruplexes, which are particularly important in DNA telomers.

Investigation of quadruplex oligonucleotide-drug interactions by electrospray ionization mass spectrometry

Selectivity, binding stoichiometry, and mode of binding of Tel01, distamycin A, and diethylthiocarbocyanine iodide (DTC) to the parallel stranded G4-quadruplex [d(T2G5T)]4 were investigated by ESI-MS. The first drug/quadruplex complexes observed by ESI-MS are described. Tel01, distamycin A, and DTC all form complexes with quadruplex DNA, but only Tel01 is completely selective for quadruplex versus duplex oligonucleotide under the conditions employed. Previous solution determinations of the binding mode of Tel01 and distamycin A to quadruplex oligonucleotides indicate that Tel01 interacts through end-stacking with guanine tetrads of quadruplex DNA, while distamycin A interacts by binding to quadruplex grooves. When these two different drug/quadruplex complexes are subjected to collisionally activated dissociation in a mass spectrometer, the observed fragmentation patterns are distinct. Tel01/quadruplex complexes undergo facile loss of drug and dissociation to single-strand oligonucleotide ions, while distamycin/quadruplex complexes fragment into single-strand oligonucleotide ions in which the drug molecule is retained. Dissociation patterns for DTC/quadruplex complexes are similar to those of distamycin; therefore, it is concluded that DTC interacts with [d(T2G5T)]4 through groove-binding. These ESI-MS results are applicable to both the identification and characterization of G-quadruplex interactive agents and may also be useful in probing unusual DNA structures.

Triplex and quadruplex DNA structures studied by electrospray mass spectrometry

DNA triplex and quadruplex structures have been successfully detected by electrospray ionization mass spectrometry (ESI-MS). Circular dichroism and UV-melting experiments show that these structures are stable in 150 mM ammonium acetate at pH 7 for the quadruplexes and pH 5.5 for the triplexes. The studied quadruplexes were the tetramer [d(TGGGGT)](4), the dimer [d(GGGGTTTTGGGG)](2), and the intramolecular folded strand dGGG(TTAGGG)(3), which is an analog of the human telomeric sequence. The absence of sodium contamination allowed demonstration of the specific inclusion of n - 1 ammonium cations in the quadruplex structures, where n is the number of consecutive G-tetrads. We also detected the complexes between the quadruplexes and the quadruplex-specific drug mesoporphyrin IX. MS/MS spectra of [d(TGGGGT)](4) and the complex with the drug are also reported. As the drug does not displace the ammonium cations, one can conclude that the drug binds at the exterior of the tetrads, and not between them. For the triplex structure the ESI-MS spectra show the detection of the specific triplex, at m/z values typically higher than those typically observed for duplex species. Upon MS/MS the antigene strand, which is bound into the major groove of the duplex, separates from the triplex. This is the same dissociation pathway as in solution. To our knowledge this is the first report of a triplex DNA structure by electrospray mass spectrometry.

Using solution phase hydrogen/deuterium (H/D) exchange to determine the origin of non-covalent complexes observed by electrospray ionization mass spectrometry: in solution or in vacuo?

Electrospray ionization (ESI) is a soft ionization technique that is able to transfer intact ions, as well as solution phase non-covalent complexes into the gas phase. With small molecules that have a high tendency to form hydrogen bonds, the observation of non-covalent complexes by ESI-MS can be the result of a non-specific interaction, due to the nature of the electrospray process. Special precautions and additional steps should be performed to identify the origin of the complexes observed with ESI-MS, and we have utilized solution phase hydrogen/deuterium (H/D) exchange as a method to determine the specificity of the complexes. By comparing the average number of exchanges for the monomer subunits to the average number of exchanges for the complex, one can distinguish if a specific complex is formed in solution. In this paper we have investigated non-covalent complexes of some common chemotherapy agents: paclitaxel, doxorubicin, and etoposide by ESI-MS. By using the solution phase H/D exchange, we were able to identify several specific drug-drug complexes. Thus, solution phase H/D exchange combined with ESI-MS provides for a convenient method in ascertaining the specificity of non-covalent complexes as being formed in solution or in vacuo.

Interaction of fusarium mycotoxins, fusaproliferin and fumonisin B1, with DNA studied by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) in negative ion mode was used to monitor the possible noncovalent adduct formations between DNA analogue oligonucleotides and two Fusarium mycotoxins, fumonisin B1 and fusaproliferin. Using mild experimental ESI conditions specific noncovalent interactions were detected between both single- and double-stranded model oligonucleotides and fusaproliferin with 1:1 stoichiometry. Similar association complexes were observed for the deacetyl derivative of fusaproliferin. There were no peaks due to adduct formation present in the mass spectra of fumonisin B1, incubated with oligonucleotides in a wide concentration range, suggesting no specific interaction for this molecule. In a competitive complexation reaction, another mycotoxin, the beauvericin, forms more stable association complex with DNA than fusaproliferin. These findings can be of use in the understanding of molecular mechanisms of action during apoptosis and can be correlated with the teratogenic effect of fusaproliferin.

Gas-phase stability of double-stranded oligodeoxynucleotides and their noncovalent complexes with DNA-binding drugs as revealed by collisional activation in an ion trap

The intrinsic (gas-phase) stabilities of duplex, self-complementary oligonucleotides were measured in a relative way by subjecting the duplex precursor ions to increasing amounts of collision energy during the collisional-activated decomposition (CAD) events in an ion-trap mass spectrometer. The results are displayed as a dissociation profile, an s-shaped curve that shows the dependence of the relative abundance of the duplex on the applied collision energy. The total number of charges, the total number of base pairs, and the location of the high proton-affinity bases (i.e., G and C) are the main factors that affect the intrinsic stability of the duplex oligonucleotides. If the charge state is the same, the stability, as measured as a half-wave collision energy, E1/2, correlates well with the total number of H bonds for the duplex. The intrinsic stabilities of noncovalent complexes between duplex oligonucleotide and some DNA-binding drugs were also measured by using the newly developed method. Although duplexes are stabilized in the gas phase when they bind to drug molecules, correlations between gas-phase stabilities and the solution-binding affinities have not yet been obtained. Complexes in which the drug is bound in the minor groove must be joined tightly because they tend to dissociate in the gas phase by breaking covalent bonds of the oligonucleotide to give base loss and small sequence-ion formation. Complexes in which the drug is known to favor intercalation dissociate by breaking weak, noncovalent bonds to form single-stranded oligonucleotides although cleavage of covalent bonds of the oligonucleotide also occurs.

Analysis of transcription complexes and effects of ligands by microelectrospray ionization mass spectrometry

The human vitamin D receptor (VDR) and retinoid X receptor-alpha (RXRalpha) modulate gene activity by forming homodimeric or heterodimeric complexes with specific DNA sequences and interaction with other elements of the transcriptional apparatus in the presence of their known endogenous ligands 1alpha,25-dihydroxyvitamin D3 (1, 25-[OH]2D3) and 9-cis-retinoic acid (9-c-RA). We used rapid buffer exchange gel filtration in conjunction with microelectrospray ionization mass spectrometry (microESI-MS) to study the binding of these receptors to the osteopontin vitamin D response element (OP VDRE). In the absence of DNA, both VDR and RXRalpha existed primarily as monomers, but in the presence of OP VDRE, homodimeric RXRalpha and heterodimeric RXRalpha-VDR complexes were shown to bind OP VDRE. Addition of 9-c-RA increased RXRalpha homodimer-OP VDRE complexes, and addition of 1,25-(OH) 2D3 resulted in formation of 1, 25-(OH)2D 3-VDR-RXRalpha-OP VDRE complexes. Addition of low-affinity binding ligands had no detectable effect on the VDR-RXRalpha-OP VDRE transcription complex. These results demonstrate the utility of microESI-MS in analyzing multimeric, high-molecular-weight protein-protein and protein-DNA complexes, and the effects of ligands on these transcriptional complexes.

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.

Probing RegA/RNA interactions using electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry

The interactions of bacteriophage T4 regA protein, a unique translational regulator, with RNAs of various size and sequence were studied using electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry. Using very gentle interface conditions, regA/RNA complexes with a 1:1 binding stoichiometry were observed for all four target RNAs studied, consistent with solution binding studies. Competitive binding of target RNAs and their degradation products with regA demonstrated that the loss of a single nucleotide resulted in a dramatic change in binding affinity in some cases. Competitive binding of regA with four target RNAs revealed similar relative binding affinity order to that suggested by previous in vitro repression experiments. The use of sustained off-resonance irradiation for collisionally induced dissociation of a regA/RNA complex suggested the potential for directly obtaining information regarding the regA binding domain.

Low temperature aqueous electrospray ionization mass spectrometry of noncovalent complexes

In the present study we describe conditions that permit the characterization of noncovalent protein-substrate complexes in aqueous solution by microspray electrospray ionization-mass spectrometry (ESI-MS), using a heated transfer capillary at low temperature (45 degrees C). Specifically, we examined the binding of calmodulin to two polypeptides; the calmodulin-binding domain of calmodulin-dependent protein kinase II (CamK-II) and melittin. Calmodulin, a well known calcium-binding protein, binds to a number of small amphipathic peptides in a calcium-dependent manner. Our results directly show that both peptides form equimolar complexes with calmodulin only in the presence of calcium. The stoichiometry necessary for the formation of each complex was 1:1:4 for calmodulin:peptide (melittin or CamK-II):Ca2+, respectively. Furthermore, it is demonstrated that the detection of the complex in ESI-MS is source temperature dependent.

The observation of chaperone-ligand noncovalent complexes with electrospray ionization mass spectrometry

Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was applied for the study of noncovalent chaperone SecB-ligand complexes produced in solution and examined in the gas phase with the aid of electrospray ionization (ESI). Since chaperone proteins are believed to recognize and bind only with ligands with nonnative tertiary structure, this work required careful unfolding of the ligand and subsequent reaction with the intact chaperone (the noncovalent tetrameric protein, SecB). A high denaturant concentration was employed to produce nonnative structures of the OppA, and microdialysis of the resulting solutions containing the chaperone-ligand complexes was carried out to rapidly remove the denaturant prior to analysis. Multistage mass spectrometry was essential to the successful study of these complexes since the initial mass spectra indicated extensive adduction that precluded mass measurements, even after microdialysis. However, low energy collisional activation of the ions in the FTICR trap proved useful for adduct removal, and careful control of excitation level preserved the intact complexes of interest, revealing a 1:1 SecB:OppA stoichiometry. To our knowledge, these results present the first direct observation of chaperone-ligand noncovalent complexes and the highest molecular weight heterogeneous noncovalent complex observed to date by mass spectrometry. Furthermore, these results highlight the capabilities of FTICR for the study of such complex systems, and the development of a greater understanding of chaperone interactions in protein export.

Metal mediated sterol receptor-DNA complex association and dissociation determined by electrospray ionization mass spectrometry

The vitamin D receptor (VDR) binds to specific DNA sequences termed vitamin D response elements (VDREs) thereby enhancing or repressing transcription. We have used electrospray ionization mass spectrometry to examine the interaction between the DNA-binding domain of the vitamin D receptor (VDR DBD) with a double-stranded DNA (dsDNA) sequence containing the VDRE from the mouse osteopontin gene. The VDR DBD was shown to bind to the appropriate DNA sequence only when bound to 2 moles of zinc (Zn2+) or cadmium (Cd2+) per mole of protein. Additional binding of Zn2+ or Cd2+ by the protein caused the protein to dissociate from the dsDNA. These results show that the VDR DBD/DNA metal-dependent association occurs when the receptor is occupied by 2 moles of Zn2+ per mole of protein and that further binding of Zn2+ to the protein causes dissociation of the complex.