The detection of intact double-stranded DNA by MALDI

The multifaceted roles of mass spectrometric analysis in nucleic acids drug discovery and development

The deceptively simple concepts of mass determination and fragment analysis are the basis for the application of mass spectrometry (MS) to a boundless range of analytes, including fundamental components and polymeric forms of nucleic acids (NAs). This platform affords the intrinsic ability to observe first-hand the effects of NA-active drugs on the chemical structure, composition, and conformation of their targets, which might affect their ability to interact with cognate NAs, proteins, and other biomolecules present in a natural environment. The possibility of interfacing with high-performance separation techniques represents a multiplying factor that extends these capabilities to cover complex sample mixtures obtained from organisms that were exposed to NA-active drugs. This report provides a brief overview of these capabilities in the context of the analysis of the products of NA-drug activity and NA therapeutics. The selected examples offer proof-of-principle of the applicability of this platform to all phases of the journey undertaken by any successful NA drug from laboratory to bedside, and provide the rationale for its rapid expansion outside traditional laboratory settings in support to ever growing manufacturing operations.

Imaging Mass Spectrometry: A New Tool to Assess Molecular Underpinnings of Neurodegeneration

Neurodegenerative diseases are prevalent and devastating. While extensive research has been done over the past decades, we are still far from comprehensively understanding what causes neurodegeneration and how we can prevent it or reverse it. Recently, systems biology approaches have led to a holistic examination of the interactions between genome, metabolome, and the environment, in order to shed new light on neurodegenerative pathogenesis. One of the new technologies that has emerged to facilitate such studies is imaging mass spectrometry (IMS). With its ability to map a wide range of small molecules with high spatial resolution, coupled with the ability to quantify them at once, without the need for a priori labeling, IMS has taken center stage in current research efforts in elucidating the role of the metabolome in driving neurodegeneration. IMS has already proven to be effective in investigating the lipidome and the proteome of various neurodegenerative diseases, such as Alzheimer's, Parkinson's, Huntington's, multiple sclerosis, and amyotrophic lateral sclerosis. Here, we review the IMS platform for capturing biological snapshots of the metabolic state to shed more light on the molecular mechanisms of the diseased brain.

Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions

Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

MS analysis of nucleic acids in the post-genomic era

Alternative approaches complementing the existing technologies for analysis of nucleic acids and their assemblies are necessary to take on the new challenges posed by the postgenomic era. The versatility of MS in biopolymer analysis and its ability to reach beyond sequence information are the basis of ever expanding applications aimed at the elucidation of nucleic acid structure-function relationships. This Feature summarizes the current state of MS-based approaches devised to overcome the limitations of traditional techniques and to advance different facets of nucleic acids research.

Ruthenium versus platinum: interactions of anticancer metallodrugs with duplex oligonucleotides characterised by electrospray ionisation mass spectrometry

The binding of the ruthenium-based anticancer drug candidates KP1019, NAMI-A and RAPTA-T towards different double-stranded oligonucleotides was probed by electrospray ionisation mass spectrometry and compared with that of the widely used platinum-based chemotherapeutics cisplatin, carboplatin and oxaliplatin. It was found that the extent of adduct formation decreased in the following order: cisplatin > oxaliplatin > NAMI-A > RAPTA-T > carboplatin > KP1019. In addition to the characterisation of the adducts formed with the DNA models, the binding sites of the metallodrugs on the oligonucleotides were elucidated employing top-down tandem mass spectrometry and were found to be similar for all the metallodrugs studied, irrespective of the sequence of the oligonucleotide. A strong preference for guanine residues was established.

Atmospheric pressure laser desorption/ionization of plant metabolites and plant tissue using colloidal graphite

Colloidal graphite is a promising matrix for atmospheric pressure laser desorption/ionization mass spectrometry. Intact [M+H](+) and [M-H](-) ions are readily produced from a wide range of small molecule plant metabolites, particularly anthocyanins, fatty acids, lipids, glycerides, and ceramides. Compared with a more traditional organic acid matrix, colloidal graphite provides more efficient ionization for small hydrophobic molecules and has a much cleaner background spectrum, especially in negative ion mode. Some important metabolites, e.g., fatty acids and glycosylated flavonoids, can be observed from Arabidopsis thaliana leaf and flower petal tissues in situ.

A role for the MS analysis of nucleic acids in the post-genomics age

The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age.

Capillary gel electrophoresis of therapeutic oligonucleotides--analysis of single- and double-stranded forms

Recently, several therapeutic double-stranded (ds) oligonucleotides (ODNs) are in pharmaceutical development. During quality control, these therapeutic molecules have to be characterized with respect to their identity, their content and their impurity profile. It follows that the ds molecule as well as its process- and product-related impurities have to be quantified. The single strands are considered as process as well as product-related impurities in the ds drug substance. Applying well known, conventional, single-base resolution CE-CGE systems developed for the quality control of single-stranded antisense ODNs in the early 1990s, it turned out that the ds ODNs under investigation are migrating in broad, splitted peaks between the peaks reaction zones are observed. It follows that the quantification of the single strands in the drug substance as well as quantification of other product-related impurities, e.g. n-1; n-2 (loss of one and two bases (n), respectively) etc., are not possible without adaptation of the test system. The paper shows how the test system was adjusted in order to determine single-stranded strands as well as ds strands next to each other quantitatively in the ds drug substance under investigation.

Detection and relative quantification of siRNA double strands by MALDI mass spectrometry

While MALDI-MS is widely accepted for quality control of synthetic oligonucleotides, this method has been regarded as not applicable for a control of the purity and correct annealing of double strands. The results presented here show that the double-strand intensities measured by MALDI-MS maintain and reflect the solution conditions. Using a single-stranded RNA as internal standard, the double-strand intensity can be determined by measuring the intensity ratio of the single strands to the standard under "native" conditions and after denaturation with formic acid. For siRNAs with fully matched 20-21 base pairs, relative intensities of the double strands are between 94 and 97.2%. The stability determined by MALDI-MS for different RNA duplexes correlates well with calculated T m values and the content of G-C pairs. Furthermore, the quantification method enables one to determine an excess of one single strand and the contribution of duplex formation by truncated strands. The results show that MALDI-MS is a fast and reliable method for quality control of synthetic siRNA.

Charge state effect on the zwitterion influence on stability of non-covalent interaction of single-stranded DNA with peptides

Negative ion ESI mass spectrometry was used to study the gas-phase stability and dissociation pathways of peptide-DNA complexes. We show that bradykinin and three modified peptides containing the basic residue arginine or lysine form stable interactions with single-stranded oligonucleotides. ESI-MS/MS of complexes of T(8) with PPGFSPFRR resulted in a major dissociation pathway through cleavage of the peptide covalent bond. The stability of the complex is due to electrostatic interaction between the negatively charged phosphate group and the basic side chain of the arginine and lysine residues as demonstrated by Vertes et al. and Woods et al. In fact, the present work establishes the role played by zwitterions on complex stabilisation. The presence of protons in nucleobase and/or amino acid contributes in reinforcing the strength of the salt bridge (SB) interaction. The zwitterionic form of the most basic of amino acid residues, arginine, is assumed to form a strong SB interaction to the negatively charged phosphate groups of DNA. This non-covalent complex is stable enough to withstand disruption of the non-covalent interaction and to first break the covalent bond. Moreover, the dependence of fragmentation patterns upon the complex charge state is explained by the fact that the net number of negative charges modulates the number of zwitterionic sites, which stabilise the complexes. Finally, the weak influence of the nucleobase is assumed by the existence of competition for proton addition between the nucleobase and the R/K side chain leading to a decrease in the stabilisation of the SB interaction.

Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF

MALDI-MS was evaluated as a method for the study of noncovalent complexes involving DNA oligonucleotides and various polybasic compounds (basic polypeptides and polyamines). Complexes involving single-stranded DNA were successfully detected using DHAP matrix in the presence of an ammonium salt. Control experiments confirmed that the interactions involved basic sites of the polybasic compounds and that the complexes were not formed in the gas phase but were pre-existing in the matrix crystals. Moreover, the pre-existence in solution was probed by isothermal titration calorimetry at concentration and ionic strength similar to those used for mass spectrometry. Spectra showed no important difference between negative and positive ion modes. The influence of nature and size of DNA and polybasic compound on the relative intensities and stoichiometries of the complexes was investigated. Despite the fact that relative intensities can be affected by ionization yields and the gas-phase stabilities of the different species, numerous trends observed in the MALDI study were consistent with the expected in-solution behaviors. Experimental conditions related to sample preparation were investigated also. Complex abundance generally decreased when increasing the ammonium acetate concentration. It was dramatically decreased when using ATT instead of DHAP. Penta-L-arginine is an exception to these observations. Lastly, in the case of complexes involving DNA duplex, the ATT matrix was shown to favor the observation of specific DNA duplex but not that of its complex with polybasic compounds. Inversely, DHAP was appropriate for the conservation of DNA-polybasic compound interaction but not for the transfer of intact duplex.

Colloidal Graphite-Assisted Laser Desorption/Ionization MS and MSnof Small Molecules. 2. Direct Profiling and MS Imaging of Small Metabolites from Fruits

Due to a high background in the low-mass region, conventional MALDI is not as useful for detecting small molecules (molecular masses <500 Da) as it is for large ones. Also, spatial inhomogeneity that is inherent to crystalline matrixes can degrade resolution in imaging mass spectrometry (IMS). In this study, colloidal graphite was investigated as an alternative matrix for laser desorption/ionization (GALDI) in IMS. We demonstrate its advantages over conventional MALDI in the detection of small molecules such as organic acids, flavonoids, and oligosaccharides. GALDI provides good sensitivity for such small molecules. The detection limit of fatty acids and flavonoids in the negative-ion mode are in the low-femtomole range. Molecules were detected directly and identified by comparing the MS and MS/MS spectra with those of standards. Various fruits were chosen to evaluate the practical utility of GALDI since many types of small molecules are present in them. Distribution of these small molecules in the fruit was investigated by using IMS and IMS/MS.

Double cation adduction in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of electron deficient anthraquinone derivatives

Six anthraquinone derivatives were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). Clear (pseudo) molecular ions were observed for all the compounds. Interestingly, for some derivatives, strong ions with double cation adduction were also recorded in the positive mode. It is remarkable that all these ions are singly charged. In this work, possible mechanisms for the double cation adduction were investigated and discussed. It appears that the double cation adduction was due to the electron deficient nature of the derivatives, and formed by taking up two singly charged cations and one electron. Substituents on the anthraquinone ring were found to have a significant effect on the double cation adduction. In contrast, no considerable influence of the acidity of MALDI matrix/solution was observed, even on the double proton adduction. Furthermore, it was demonstrated that double cation adduction might occur in the MALDI gas-phase plume. In addition to the anthraquinones, three more electron deficient compounds of different types, i.e. a perylene bisimide derivative (PB), 3,7-decanoylamino-4,8-dihydrobenzo[1,2-b:4,5-b']dithiophene-4,8-dione (TQ) and 6,6-phenyl C61-butyric acid methyl ester (PCBM), were also analyzed with MALDI TOF MS. The results indicate that the 'abnormal' double cation adduction might be a 'normal' phenomenon in the MALDI TOF MS analysis of many electron deficient compounds.

Localization of noncovalent complexes in MALDI-preparations by CLSM

The unambiguous detection of noncovalent complexes (NCCs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still a far cry from being routine. For protein NCCs such as their quaternary structure it has been reported that signals of the intact complex are only obtained for the first or at most the first few laser exposures of a given sample area. This observation was called the first-shot phenomenon. In the present study, this first-shot phenomenon has been investigated for the hexameric protein complex allophycocyanine (APC) by two independent methods, MALDI-MS with a (nearly) pH-neutral matrix 6-aza-2-thiothymine (6-ATT) and by imaging the fluorescence of the complex in APC-6-ATT preparations by confocal laser scan microscopy (CLSM). The intact APC heterohexamer loses its visible fluorescence upon dissociation into its subunits. Both methods consistently show that intact APC complexes are precipitated at the matrix crystal surface, but dissociate upon incorporation into the matrix crystals.

Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.

The Mighty Arginine, the Stable Quaternary Amines, the Powerful Aromatics, and the Aggressive Phosphate: Their Role in the Noncovalent Minuet

In the age of proteomics, the role of certain amino acid residues and some post-translational modifications in noncovalent complex formation are gaining in importance, as the understanding of interactions between biological molecules, is at the heart of the structure function relationship puzzle. In this work, mass spectrometry is used to highlight ammonium- or guanidinium-aromatic interactions through Cation-pi bonds and ammonium- or guanidinium-phosphate interactions through salt bridge formation. Such interactions are crucial factors in certain ligand-receptor interactions and receptor-receptor interactions. In addition, the ability of phosphorylated residues and phosphorylated lipids to form noncovalent complexes with guanidinium and quaternary ammonium (mostly through Coulombic interactions) is demonstrated, and could explain the stability of certain membrane embedded protein, or a possible role for phosphorylation in protein-protein interactions. Dougherty's work demonstrates cation-pi interactions in intra-protein interactions and folding, the present work explores inter-peptide interactions, i.e., the formation of noncovalent complexes between peptides' epitopes containing adjacent aromatic residues and ones containing adjacent Arg as a model to better understand the role of cation-pi complexes in protein-protein interaction. Complexes of peptides containing aromatic residues with quaternary amines as well as the interaction of aromatic compounds, with the guanidinium group of Arg are also investigated. Considering that an inordinate number of therapeutic compounds contain aromatic rings and quaternary amines, the above-described interactions could possibly be of great importance in better understanding their mechanism of action.

Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to obtain spectra of peptide-DNA complexes formed by basic domain (BD15) of c-Fos protein and DNA AP-1 site (5'-TGAGTCA-3'). The noncovalent interaction between single stranded DNA and BD15 was observed and confirmed to be an ionic one between the negatively charged sugar-phosphate backbone of DNA and positively charged side chains of Arg- and lys-rich peptides as demonstrated by Vertes and coworkers and Woods and coworkers. But the specific noncovalent interaction between DNA AP-1 site and the dimer of BD15 was firstly detected in this paper. Various different sequence DNAs were studied and it was found that this interaction is a sequence-specific one, and AP-1 site was essential for this interaction. This specific interaction depends on the matrix. It was only observed in the ATT matrix and not in the other two matrixes (CHCA and DHBA).

Identification of Protein Ligands in Complex Biological Samples Using Intensity-Fading MALDI-TOF Mass Spectrometry

The easy detection of biomolecular interactions in complex mixtures using a minimum amount of material is of prime interest in molecular and cellular biology research. In this work, a mass spectrometry MALDI-TOF based approach, which we call intensity-fading (IF MALDI-TOFMS), and which was designed for just such a purpose, is reported. This methodology is based on the use of the MALDI ion intensities to detect quickly the formation of complexes between nonimmobilized biomolecules in which a protein is one of the partners (protein-protein, protein-peptide, protein-organic molecule, and protein-nucleic acid complexes). The complex is detected through the decrease (fading) of the molecular ion intensities of the partners as directly compared to the MALDI mass spectrum of the mixture (problem and control molecules) following the addition of the target molecule. The potential of the approach is examined in several examples of model interactions, mainly involving small nonprotein and protein inhibitors of proteases, at both the qualitative and semiquantitative levels. Using this method, different protein ligands of proteolytic enzymes in total extracts of invertebrate organisms have been identified in a simple way. The proposed procedure should be easily applied to the high-throughput screening of biomolecules, opening a new experimental strategy in functional proteomics.

Interaction of chlorisondamine with the neuronal nicotinic acetylcholine receptor

An epitope was found on the alpha2-nicotinic isoform of the neuronal nicotinic acetylcholine receptor that would likely form salt bridges with quaternary ammonium compounds and a cation-pi interaction with the pi-cloud of an aromatic ring. Chlorisondamine, a nicotinic antagonist, exerts a long-lasting, if not permanent, blockade of the ion channel gated by acetylcholine. Blocking of the ion channel prevents nicotine from exerting its rewarding effect on the CNS. Chlorisondamine contains two quaternary ammonium groups and a tetrachloroisoindoline ring. We propose that chlorisondamine interacts with an epitope on the alpha2 isoform of the rat neuronal nicotinic receptor (residues 388-402, GEREETEEEEEEEDE), where one or both of the quaternary ammonium groups of chlorisondamine form a salt bridge with dither a glutamic acid side chain or a phosphate group, whereas the tetrachlorobenzene portion of the tetrachloroisoindoline ring interacts with the guanidinium group of arginine in a cation-pi association: In this work, a new way of probing the interaction of a receptor epitope (alpha2) with organic molecules (chlorisondamine and hexachlorobenzene) was undertaken using matrix assisted laser desorption/ionization mass spectrometry.

Detection of immune complexes by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to detect an immune complex formed between beta-lactoglobulin and polyclonal anti-beta-lactoglobulin antibody in the gas phase. The most important experimental parameters to detect such a specific antibody-antigen complex by MALDI were the use of solutions at near-neutral pH and of sinapinic acid matrix prepared by the dried-droplet method. Under such conditions, predominantly one but also two molecules of antigen protein were complexed by the antibody. Specific formation of the antibody-antigen complex was confirmed by performing competitive reactions. Addition of antibody to a 1:1 mixture of beta-lactoglobulin and one control protein resulted not only in the appearance of the expected antibody-antigen complex, but also in a strong decrease in the free beta-lactoglobulin signal, while the abundance of the control protein was not influenced.

Investigation of sample preparation and instrumental parameters in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of noncovalent peptide/peptide complexes

The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to the direct detection and investigation of noncovalent solution-phase complexes is far from being routine and some principal problems and questions still exist. Therefore, this study systematically investigates several main problems, namely, the effect of sample preparation and some instrument-related parameters on the stability of the noncovalent complexes as well as the formation of nonspecific cluster ions in the case of the MALDI-MS analysis of specific peptide/peptide complexes. The complexes formed between biologically active fragments of human gastrin I, which contain the sequence motif EEEEE, and different peptides, which contain the interacting sequence motifs RR and RKR, were chosen as examples. A broad variety of MALDI matrices and sample preparation protocols were screened systematically and evaluated. The two 'less acidic' matrices 2,4,6-trihydroxyacetophenone and 6-aza-2-thiothymine, in combination with carefully selected solvents and additives, turned out to allow the reproducible detection of the solution-phase peptide/peptide complexes with good intensity, whereas the classical MALDI matrices could not be applied with the same success. Because both matrices also tend to induce the formation of nonspecific cluster ions, control experiments using nonbinding peptides were performed to definitely prove the specificity of the detected complexes. In contrast to the sensitivity of the peptide/peptide complexes to solution-phase conditions, the gas-phase stability during desorption/ionization was found to be extraordinary high. Neither the application of high laser fluence nor switching from continuous to delayed extraction mode as well as variation of the delay time up to 520 ns had considerable effect on the relative intensities of the specific peptide/peptide complexes.

Location of abasic sites in oligodeoxynucleotides by tandem mass spectrometry and by a chemical cleavage initiated by an unusual reaction of the ODN with MALDI matrix

We describe two approaches employing electrospray ionization (ESI) tandem mass spectrometry (MS/MS) and matrix assisted laser desorption/ionization (MALDI) post-source decay (PSD) for determining the location of an abasic site in modified oligodeoxynucleotides (ODNs). With MS/MS, we found both complementary fragment ions (a(n)' and w(n)') produced at the abasic site were predominant in the mass spectra and allowed the location to be determined. Under MALDI conditions, most ODNs carrying an abasic site are singly charged, and PSD gives predominately w(n)' ions at the abasic sites, revealing their location. We also describe another approach for identifying and locating abasic sites in model ODNs; namely, an "in situ" derivatization coupled with MALDI mass spectrometry (MS). In general, an ODN n-mer containing an abasic site at the m-th position from the 5-terminus can react with the matrix component, anthranilic acid, to form a Schiff base. The adduct upon MALDI breaks into 3' and 5' fragments (w(n-m), b(m), a(m), d(m-1)) at the abasic site, revealing its location. ESI MS methods are also applicable for detecting the hydrazone derivatives of abasic sites, and the fragmentation of hydrazones shows the location of the abasic site.

The use of MassARRAY technology for high throughput genotyping

This chapter will explore the role of mass spectrometry (MS) as a detection method for genotyping applications and will illustrate how MS evolved from an expert-user-technology to a routine laboratory method in biological sciences. The main focus will be time-of-flight (TOF) based devices and their use for analyzing single-nucleotide-polymorphisms (SNPs, pronounced snips). The first section will describe the evolution of the use of MS in the field of bioanalytical sciences and the protocols used during the early days of bioanalytical MALDI TOF mass spectrometry. The second section will provide an overview on intraspecies sequence diversity and the nature and importance of SNPs for the genomic sciences. This is followed by an exploration of the special and advantageous features of mass spectrometry as the key technology in modern bioanalytical sciences in the third chapter. Finally, the fourth section will describe the MassARRAY technology as an advanced system for automated high-throughput analysis of SNPs.

Additives for the stabilization of double-stranded DNA in UV-MALDI MS

Molecular complexes such as double-stranded oligonucleotides contain non-covalent bonds that are difficult to maintain in the MALDI experiment. Quantifiers are introduced in order to evaluate, summarize, and compare spectra from experiments in which additives are used to stabilize duplex oligonucleotides. Compounds known to complex with and stabilize duplex molecules can be useful as additives in MALDI. Spermine and methylene blue, present at concentrations similar to the matrix, are detected, bound to the duplex. When peptides are used as additives, the duplex is stabilized when the peptide is present at an amount less than that of the duplex.

Improvement of the MALDI-TOF analysis of DNA with thin-layer matrix preparation

A new method of sample preparation was developed for MALDI-TOF-MS analysis of oligonucleotides. First, aqueous DNA samples are dispensed and allowed to dry. Then 6-aza-2-thiothymine matrix dissolved in nonaqueous volatile solvents is applied on top of the DNA residue to form a thin homogeneous film. MALDI-TOF analysis shows such preparation generates much better shot-to-shot and sample-to-sample reproducibility and essentially eliminates the need to search for "hot" spots. The increased homogeneity of the matrix/analyte crystal distribution results in significant improvement for quantitative and high-throughput analyses of DNA. Using this method, isotopically resolved oligonucleotide spectra up to a 24-mer can also be easily obtained in a reflectron instrument. Due to the ease of preparation, this method could be widely useful for a number of applications such as for assays that are performed on surface in vitro, as the thin-layer matrix could be applied directly for MALDI analysis.

Sodium-tolerant matrix for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay of oligonucleotides

A mixture of 2',4',6'-trihydroxyacetophenone in acetonitrile and aqueous triammonium citrate solution in a 1:1 molar proportion (0.2 M concentration) was found to be a good matrix for the detection of synthetic oligodeoxynucleotide samples. A high proportion of volatile solvent as well as the high salt content ensure fast co-crystallization of the matrix, co-matrix and analyte molecules. Matrix-assisted laser desorption/ionization (MALDI) mass spectra obtained in negative ion reflectron mode from samples prepared with this protocol show deprotonated molecules [M - H](-), rather than sodium adducts, as the most abundant ions even when up to 50 mM of sodium chloride is present in the sample. The matrix is shown to be effective for low mass modified single nucleotides as well as for longer oligodeoxynucleotides (up to 18mer). Post-source decay (PSD) mass spectra can also be obtained by increasing the laser fluence. Simple sequence information such as the identity and localization of a deleted base or the 5'/3' orientation can then easily be obtained. The calibration method and mass accuracy required are discussed depending on the type of information required.

A study of peptide--peptide interaction by matrix-assisted laser desorption/ionization

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to study peptide-peptide interaction. The interaction was seen when 6-aza-2-thiothymine was used as a matrix (pH 5.4), but was disrupted with a more acidic matrix, alpha-cyano-4-hydroxycinnamic acid (pH 2.0). In the present study, we show that dynorphin, an opioid peptide, and five of its fragments that contain two adjacent basic residues (Arg6-Arg7), all interact noncovalently with peptides that contain two to five adjacent acidic residues (Asp or Glu). Two other nonrelated peptides containing two (Arg6-Arg7) or three (Arg1-Lys2-Arg3) adjacent basic amino acid residues were studied and exhibited the same behavior. However, peptides containing adjacent Lys or His did not form noncovalent complexes with acidic peptides. The noncovalent bonding was sufficiently stable that digestion with trypsin only cleaved Arg and Lys residues that were not involved in hydrogen bonding with the acidic residues. In an equimolar mixture of dynorphin, dynorphin fragments (containing the motif RR), and an acidic peptide (minigastrin), the acidic peptide preferentially complexed with dynorphin. If the concentration of minigastrin was increased 10 fold, noncovalent interaction was seen with dynorphin and all its fragments containing the motif RR. In the absence of dynorphin, minigastrin formed noncovalent complexes with all dynorphin fragments. These findings suggest that conformation, equilibrium, and concentration do play a role in the occurrence of peptide-peptide interaction. Observations from this study include: (1) ionic bonds were not disrupted by enzymatic digests, (2) conformation and concentration influenced complex formation, and (3) the complex did not form with fragments of dynorphin or unrelated peptides that did not contain the motifs RR or RKR, nor with a fragment of dynorphin where Arg7 was mutated to a phenylalanine residue. These findings strongly suggest that peptide-peptide interaction does occur, and can be studied by MALDI if near physiologic pH is maintained.

Matrix-assisted laser desorption/ionization mass spectrometry methods for oligodeoxynucleotides: improvements in matrix, detection limits, quantification, and sequencing

A comatrix of anthranilic acid and nicotinic acid is optimum for the matrix-assisted laser desorption/ionization time of flight determination of oligodeoxynucleotides that are comprised of up to 21 nucleotides. A detection limit of approximately 200 amol was obtained for an oligonucleotide 21mer. The comatrix system is also suitable for quantification of oligodeoxynucleotides provided an internal standard having one more or less nucleotide than the number in the analyte is used. Furthermore, the matrix, when used in combination with the ladder method of sequencing, allows the complete sequence of tens of picomoles of model oligodeoxynucleotides to be determined.

Characterizing DNA photo-oxidation reactions by high-resolution mass measurements with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

High-resolution mass measurements by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were employed to characterize laser-induced oxidation of guanine in a small synthetic deoxyoligonucleotide. The oligonucleotide was exposed to high-intensity UV radiation at 266 nm to produce modifications on the guanine base. The primary product showed a +16 Da mass shift relative to the original strand, whereas secondary products showed mass shifts of +32 and +34 Da. The mass shift of the primary product is consistent with an 8-oxoguanine modification. However, the reactivity of the primary product with hot piperidine and other secondary oxidizing agents was different from that of a synthetic oligonucleotide containing 7,8-dihydro-8-oxo-2'-deoxyguanine (8-oxoG). Based upon the results, a new reaction scheme involving the formation of an epoxide ring across the C-4 and C-5 positions by UV laser-induced oxidation is suggested. The results also illustrate the ability of MALDI to characterize chemical reactivity rapidly at the a low picomolar level.

Detection of double-stranded DNA by IR- and UV-MALDI mass spectrometry

Double-stranded DNA ranging from 9 kDa to over 500 kDa were desorbed and analyzed by MALDI TOF mass spectrometry. IR-MALDI with glycerol as matrix yielded excellent results for larger double-stranded DNA by adjustment of the ionic strength through the addition of salts. Very little fragmentation and a routine sensitivity in the subpicomole range were observed in IR-MALDI when double-stranded analytes harboring 70 base pairs or more were probed. In the lower mass range (up to approximately 70 base pairs), UV-MALDI with 6-aza-2-thiothymine as matrix was the ionization method of choice because it allowed specific double-stranded complexes containing relatively few base pairs to be desorbed intactly. In this mode, an essentially quantitative detection of the double-stranded form was observed for a 70-mer. The UV-MALDI was accompanied by a significant fragmentation and a resulting reduced sensitivity and mass resolution. The methods described open MALDI-MS for the analysis of large DNA-DNA and DNA-protein complexes.

Identification of single stranded regions of DNA by enzymatic digestion with matrix-assisted laser desorption/ionization analysis

Elucidating structure function relationships of DNA in cellular processes requires fast, reliable methods that can be applied to picomole amounts of sample. Higher order structure can be inferred by distinguishing paired and unpaired regions. It is shown here that enzymatic digestion coupled with product analysis by matrix-assisted laser desorption ionization (MALDI) is able to identify unpaired bases within structured DNA regions. The method is demonstrated with DNA duplexes having a five nucleotide mismatch as a 5' overhang, a 3' overhang, and an internal loop. Exo- and endonuclease digestions are performed under solution conditions (temperature, annealing, and enzyme buffers) which promote base pairing and specific enzyme activity. For each type of mismatch, the length and sequence of the single stranded region can be inferred from MALDI spectra taken as a function of digestion time.

Matrix-assisted laser desorption/ionization mass spectra reflect solution-phase zinc finger peptide complexation

The complexation between an 18-residue zinc finger peptide of CCHC type (CCHC = Cys-X2-Cys-X4-His-X4-Cys, X = variable amino acid) from the gag protein p55 of human immunodeficiency virus type 1 (HIV-1) and various transition metal ions was studied by means of circular dichroism spectroscopy and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). A correlation between the complexation behavior in solution and in MALDI-MS could be established. It was shown that MALDI-MS is a fast method suitable for studying metal binding properties of zinc finger complexes.

MALDI mass spectrometry of dye-peptide and dye-protein complexes

Immobilized sulfonate dyes are widely used for protein separation and purification, but the mode of interaction between the dye molecules and the proteins is largely unknown. Here we show that specific noncovalent dye-protein and dye-peptide complexes can be observed using MALDI mass spectrometry. We prove that the interaction is prodominantly electrostatic and that it involves protonated sites of the peptides and proteins, including the NH2 terminus, and deprotonated SO3 groups of the dyes. Furthermore, we show that MALDI-MS of such complexes with a nonacidic matrix, p-nitro-aniline, can be used to determine the number of accessible basic sites of a protein or peptide in its folded structure. Our results are in good agreement with measurements of the same property done with electrospray ionization.

Detection of noncovalent tRNA.aminoacyl-tRNA synthetase complexes by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) was used for the study of complexes formed by yeast seryl-tRNA synthetase (SerRS) and tyrosyl-tRNA synthetase (TyrRS) with tRNASer and tRNATyr. Cognate and noncognate complexes were easily distinguished due to a large mass difference between the two tRNAs. Both homodimeric synthetases gave MS spectra indicating intact desorption of dimers. The spectra of synthetase-cognate tRNA mixtures showed peaks of free components and peaks assigned to complexes. Noncognate complexes were also detected. In competition experiments, where both tRNA species were mixed with each enzyme only cognate alpha2.tRNA complexes were observed. Only cognate alpha2.tRNA2 complexes were detected with each enzyme. These results demonstrate that MALDI-MS can be used successfully for accurate mass and, thus, stoichiometry determination of specific high molecular weight noncovalent protein-nucleic acid complexes.

HIV-1 Tat peptide binding to TAR RNA by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent complexes formed from the interaction between HIV-1 Tat peptide and Tat protein with TAR RNA. Both positive ion and negative ion ESI mass spectra showed a maximum stoichiometry of 3:1 between Tat peptide and TAR RNA. However, the higher order complexes only occurred at high relative concentrations of Tat peptide. The 1:1 Tat peptide-TAR RNA complex is believed to involve only specific interactions, whereas the higher order complexes involve nonspecific interactions. Relative binding affinities between Tat peptide and TAR RNA and its various mutants (TAR missing the three-nucleotide bulge, TAR with a poly(ethylene glycol) linker in the bulge region, and TAR with a poly(ethylene glycol) linker in the loop region) can be differentiated by competitive binding experiments and ESI-MS measurements. The gas phase mass spectrometry experiments are consistent with solution phase studies, as they show that mutations in the bulge region reduce TAR RNA affinity to Tat peptide.

Studying noncovalent protein complexes by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry has been used to study protein interactions driven by noncovalent forces. The gentleness of the electrospray ionization process allows intact protein complexes to be directly detected by mass spectrometry. Evidence from the growing body of literature suggests that the ESI-MS observations for these weakly bound systems reflect, to some extent, the nature of the interaction found in the condensed phase. Stoichiometry of the complex can be easily obtained from the resulting mass spectrum because the molecular weight of the complex is directly measured. For the study of protein interactions, ESI-MS is complementary to other biophysical methods, such as NMR and analytical ultracentrifugation. However, mass spectrometry offers advantages in speed and sensitivity. The experimental variables that play a role in the outcome of ESI-MS studies of noncovalently bound complexes are reviewed. Several applications of ESI-MS are discussed, including protein interactions with metal ions and nucleic acids and subunit protein structures (quaternary structure).

Peptide nucleic acid characterization by MALDI-TOF mass spectrometry

Peptide nucleic acids (PNAs) are a new class of DNA mimics in which the regular nucleobases of adenine, thymine, cytosine, and guanine are connected via a peptide-like backbone. PNA molecules retain the same Watson-Crick base pairing as regular oligonucleotides, with the added benefits of greater specificity and resistance to enzymatic digestion. While the use of PNAs has grown rapidly because of their potential applications in biotechnology, little work has been done on developing analytical procedures for characterizing them. We have found matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to be an effective tool for PNA analysis. PNA molecules survive the MALDI process intact and are easily ionized with almost no multiply-charged species. These features allow mixtures to be easily characterized. Traditional protein matrices (e.g., sinapinic acid,2,5-dihydroxybenzoic acid, alpha-cyano-4-hydroxycinnamic acid) were found to be superior to DNA matrices (e.g., trihydroxy-acetophenone, 3-hydroxypicolinic acid, picolinic acid). In addition, the new DNA matrix 6-aza-2-thiothymine worked well. The ability of MALDI-TOF-MS to ascertain PNA purity and sequence information at low picomole levels will be important as greater quality control of PNA synthesis is needed (e.g., when PNAs are used as antisense or antigene drugs).

Oligonucleotide sequence and composition determined by matrix-assisted laser desorption/ionization

Molecular weight measurements of several oligonucleotides ranging in size from 12 to 60 bases were performed by matrix-assisted laser desorption/ionization with a time-of-flight mass spectrometer (MALDI-TOF). In each case, the mass accuracy was better than 0.1%. Sequences for two 12-base oligonucleotides and a 24-base oligonucleotide were determined using calf spleen phosphodiesterase to sequentially cleave from the 5' end. A MALDI-TOF spectrum of the digest mixture shortly after the addition of the enzyme produced a characteristic oligonucleotide ladder. Molecular ions in the mass spectrum corresponded to the products of enzymatic cleavage, and the mass differences between these peaks identified the individual nucleotides. The resolution and mass accuracy of MALDI-TOF were sufficient to unambiguously identify the individual nucleotides in the 12- and 24-base strands.

Mass spectrometry of nucleic acids

The present article is a survey of ESI and MALDI mass spectrometric analysis of nucleic acid oligomers and polymers. In order to limit the extent of the review, mass spectrometry of mononucleotides is generally not considered, except where such data are important for an understanding of the analysis of larger nucleic acids. The first part of the review is a condensed description of the structure and the acid-base properties of nucleic acids. The remaining part is divided into three main sections, dealing with the practical aspects of the two ionization techniques, fragmentation, and applications, respectively. The first section includes an extensive discussion of experimental parameters and problems, which are important for the analysis of different types of nucleic acid samples, including noncovalent complexes and mixtures. At the end of this section, as well as the following one, a comparison between MALDI and ESI as ionization techniques for nucleic acid is given. In addition to a detailed discussion of ion fragmentation, the fragmentation section includes an overview of the direct mass spectrometric sequencing of nucleic acids performed with either technique. The fragmentation reactions occurring upon MALDI and ESI are compared. The last section describes the life science applications of ESI-MS and MALDI-MS of nucleic acids; an account of experiments demonstrating the potential of a method, and of the bona fide solving of problems by ESI and MALDI is given. © 1997 John Wiley & Sons, Inc.