Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins

Bioconjugation Techniques for Enhancing Stability and Targeting Efficiency of Protein and Peptide Therapeutics

Bioconjugation techniques have emerged as powerful tools for enhancing the stability and targeting efficiency of protein and peptide therapeutics. This review provides a comprehensive analysis of the various bioconjugation strategies employed in the field. The introduction highlights the significance of bioconjugation techniques in addressing stability and targeting challenges associated with protein and peptide-based drugs. Chemical and enzymatic bioconjugation methods are discussed, along with crosslinking strategies for covalent attachment and site-specific conjugation approaches. The role of bioconjugation in improving stability profiles is explored, showcasing case studies that demonstrate successful stability enhancement. Furthermore, bioconjugation techniques for ligand attachment and targeting are presented, accompanied by examples of targeted protein and peptide therapeutics. The review also covers bioconjugation approaches for prolonging circulation and controlled release, focusing on strategies to extend half-life, reduce clearance, and design-controlled release systems. Analytical characterization techniques for bioconjugates, including the evaluation of conjugation efficiency, stability, and assessment of biological activity and targeting efficiency, are thoroughly examined. In vivo considerations and clinical applications of bioconjugated protein and peptide therapeutics, including pharmacokinetic and pharmacodynamic considerations, as well as preclinical and clinical developments, are discussed. Finally, the review concludes with an overview of future perspectives, emphasizing the potential for novel conjugation methods and advanced targeting strategies to further enhance the stability and targeting efficiency of protein and peptide therapeutics.

Breaching the Fortress: Photochemistry of DNA-Caged Ag106

A DNA strand can encapsulate a silver molecule to create a nanoscale, aqueous stable chromophore. A protected cluster that strongly fluoresces can also be weakly photolabile, and we describe the laser-driven photochemistry of the green fluorophore C4AC4TC3GT4/Ag106+. The embedded cluster is selectively photoexcited at 490 nm and then bleached, and we describe how the efficiency, products, and route of this photochemical reaction are controlled by the DNA cage. With irradiation at 496.5 nm, the cluster absorption progressively drops to give a photodestruction quantum yield of 1.5 (±0.2) × 10-4, ∼103× less efficient than fluorescence. A new λabs = 335 nm chromophore develops because the precursor with 4 Ag0 is converted into a group of clusters with 2 Ag0 - Ag64+, Ag75+, Ag86+, and Ag97+. The 4-7 Ag+ in this series are chemically distinct from the 2 Ag0 because they are selectively etched by iodide. This halide precipitates silver to favor only the smallest Ag64+ cluster, but the larger clusters re-develop when the precipitated Ag+ ions are replenished. DNA-bound Ag106+ decomposes because it is electronically excited and then reacts with oxygen. This two-step process may be state-specific because O2 quenches the red luminescence from Ag106+. However, the rate constant of 2.3 (±0.2) × 106 M-1 s-1 is relatively small, which suggests that the surrounding DNA matrix hinders O2 diffusion. On the basis of analogous photoproducts with methylene blue, we propose that a reactive oxygen species is produced and then oxidizes Ag106+ to leave behind a loose Ag+-DNA skeleton. These findings underscore the ability of DNA scaffolds to not only tune the spectra but also guide the reactions of their molecular silver adducts.

Interrupted DNA and Slow Silver Cluster Luminescence

A DNA-silver cluster conjugate is a hierarchical chromophore with a partly reduced silver core embedded within the DNA nucleobases that are covalently linked by the phosphodiester backbone. Specific sites within a polymeric DNA can be targeted to spectrally tune the silver cluster. Here, the repeated (C₂A)₆ strand is interrupted with a thymine, and the resulting (C₂A)₂-T-(C₂A)₄ forms only Ag₁₀⁶⁺, a chromophore with both prompt (∼1 ns) green and sustained (∼10² μs) red luminescence. Thymine is an inert placeholder that can be removed, and the two fragments (C₂A)₂ and (C₂A)₄ also produce the same Ag₁₀⁶⁺ adduct. In relation to (C₂A)₂T(C₂A)₄, the (C₂A)₂ + (C₂A)₄ pair is distinguished because the red Ag₁₀⁶⁺ luminescence is ∼6× lower, relaxes ∼30% faster, and is quenched ∼2× faster with O₂. These differences suggest that a specific break in the phosphodiester backbone can regulate how a contiguous vs broken scaffold wraps and better protects its cluster adduct.

Chromatographic and mass spectrometric technologies for chemical analysis of Euodiae fructus: A review

INTRODUCTION

Euodiae fructus, also known as Evodiae fructus, is a popular Chinese herbal medicine derived from the dried, nearly ripe fruits of Tetradium ruticarpum (A. Juss.) T. G. Hartley. The main bioactive constituents of Euodiae fructus are alkaloids, limonoids, flavonoids, and anthraquinones. The contents of these compounds vary greatly between different plant species, geographic locations, and harvest times, which thus affect the therapeutic effects.

OBJECTIVES

We aimed to summarize the chromatographic and mass spectrometric technologies applied for chemical analysis and quality evaluation of Euodiae fructus. Moreover, we aimed to emphasize the diverse soft ionization techniques and mass analyzers of LC-MS methods for assessment of Euodiae fructus.

METHODOLOGY

A literature study was carried out by retrieving articles published between January 1988 and December 2021 from well-known databases, including PubMed, ASC, Elsevier, ScienceDirect, J·STAGE, Thieme, Taylor & Francis, Springer Link, Wiley Online Library, and CNKI. The chemical analysis methods were described in several categories in accordance with the used analytical techniques, including thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), high-performance liquid chromatography-mass spectrometry (HPLC-MS), gas chromatography-mass spectrometry (GC-MS), capillary electrophoresis (CE), and counter-current chromatography (CCC).

RESULTS

This review systematically summarizes the achievements in chemical analysis and quality evaluation of Euodiae fructus published in over three decades, covering the various chromatographic and mass spectrometric technologies applied for identification and quantification of phytochemical constituents.

CONCLUSION

The summary serves as an important basis for future phytochemical research and implementation of quality control methods in order to ensure the efficacy and safety of Euodiae fructus.

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag⁺-nucleobase base pairs, and Ag⁰ chromophores. The DNA host C₄-A₂-iC₄T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C₄-A₂-iC₄T)₂/Ag₁₁⁷⁺ with λ_abs/λ_em = 430/520 nm and (C₄-A₂-iC₄T)₂/Ag₁₄⁸⁺ with λ_abs/λ_em = 510/630 nm. The Ag⁺ and Ag⁰ constituents in these partially oxidized clusters are linked with structural elements in C₄-A₂-iC₄T. Ag⁺ alone binds sparsely but strongly to form C₄-A₂-iC₄T/3-4 Ag⁺ and (C₄-A₂-iC₄T)₂/7-8 Ag⁺ complexes, and these stoichiometries suggest that Ag⁺ cross-links pairs of cytosines to form a hairpin with a metallo-C₄/iC₄ duplex and an adenine loop. The Ag⁰ are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag⁺-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag⁺ disperses with the cytosines to create an adenine binding pocket for the Ag⁰ cluster chromophores.

Investigation of the binding site of ruthenium complexes to short single-stranded oligodeoxynucleotides using electrospray ionization tandem mass spectrometry

RATIONALE

In order to elucidate the nature of the interaction between metal complexes and DNA, use was made of short telomere single-stranded oligodeoxynucleotide (ODN) strand 5'-T₁ T₂ A₃ G₄ G₅ G₆ -3' (1) and strands 5'-T₁ C₂ A₃ G₄ G₅ G₆ -3' (2), 5'-T₁ T₂ A₃ C₄ G₅ G₆ -3' (3) and 5'-T₁ C₂ C₃ C₄ C₅ G₆ -3' (4) for the verification of the binding site with four different ruthenium complexes as possible anticancer drug candidates.

METHODS

The ability to form adducts between ruthenium complexes with short single-stranded 6-mers was investigated through the use of electrospray ionization mass spectrometry (ESI-MS). Full scan ESI mass spectra and collision-induced dissociation (CID) mass spectra were recorded on a high-resolution quadrupole time-of-flight mass spectrometer. The elemental compositions of the adducts and the most important product ions were calculated by exact mass measurements.

RESULTS

ESI-MS measurements showed that the mono-ruthenated ODNs were the main products produced under the conditions for the four ruthenium complexes and each of the ODNs. The CID results revealed that thymine and guanine are the preferred binding sites depending on the different compositions in the ODNs. However, for the ODN of the type: 5'-T₁ C₂ C₃ C₄ C₅ G₆ -3' the coordination site on cytosine was observed as well. The different ruthenium complexes interacted in the same way.

CONCLUSIONS

This study showed that the characterization of new ruthenium complexes with short single-stranded telomeric DNA (TTAGGG) and further different ODNs is possible with positive ESI-MS/MS measurement. The identification of thymine and cytosine besides guanine as possible binding sites suggests that the interaction site is highly affected by the ODN's structure.

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.

Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery

Guanine-rich sequences forming G-quadruplexes (GQs) are present in several genomes, ranging from viral to human. Given their peculiar localization, the induction of GQ formation or GQ stabilization with small molecules represents a strategy for interfering with crucial biological functions. Investigating the recognition event at the molecular level, with the aim of fully understanding the triggered pharmacological effects, is challenging. Native electrospray ionization mass spectrometry (ESI-MS) is being optimized to study these noncovalent assemblies. Quantitative parameters retrieved from ESI-MS studies, such as binding affinity, the equilibrium binding constant, and sequence selectivity, will be overviewed. Computational experiments supporting the ESI-MS investigation and boosting its efficiency in the search for GQ ligands will also be discussed with practical examples. The combination of ESI-MS and in silico techniques in a hybrid high-throughput-screening workflow represents a valuable tool for the medicinal chemist, providing data on the quantitative and structural aspects of ligand–GQ interactions.

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.

Photodissociative Cross-Linking of Diazirine-Tagged Peptides with DNA Dinucleotides in the Gas Phase

Non-covalent complexes of DNA dinucleotides dAA, dAT, dGG, dGC, and dCG with diazirine-tagged Cys-Ala-Gln-Lys peptides were generated as singly charged ions in the gas phase. Laser photodissociation at 355 nm of the diazirine ring in the gas-phase complexes created carbene intermediates that underwent covalent cross-linking to the dinucleotides. The dinucleotides differed in the cross-linking yields, ranging from 27 to 36% for dAA and dAT up to 90-98% for dGG, dGC, and dCG. Collision-induced dissociation tandem mass spectrometry (CID-MS³) of the cross-linked conjugates revealed that fragmentation occurred chiefly in the dinucleotide moieties, resulting in a loss of a nucleobase and backbone cleavages. The CID-MS³ spectra further revealed that cross-links were primarily formed in the 3'-nucleotides for the dAT, dGC, and dCG combinations. Gas-phase and solution structures of dGG complexes with S-tagged CAQK were investigated by Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations. The low free-energy complexes had zwitterionic structures in which the peptide was protonated at the N-terminus and in the Lys residue whereas the carboxyl or dGG phosphate were deprotonated, corresponding to the respective (Cys⁺, Lys⁺, COO^-)⁺ and (Cys⁺, Lys⁺, phosphate^-)⁺ protomeric types. Both types preferred structures in which the peptide N-terminal cysteine carrying the S-photo-tag was aligned with the 3'-guanine moiety. BOMD trajectories at 310 K were analyzed for close contacts of the incipient peptide carbene with the positions in dGG that pointed to frequent contacts with the N-1, NH₂, and N-7 atoms of 3'-guanine, in agreement with the cross-linking results. Carbene insertion to the guanine N-1-H and NH₂ bonds was calculated by density functional and Møller-Plesset perturbational theory to be 350-380 kJ mol^-1 exothermic. Based on calculations, we proposed a mechanism for the carbene reaction with guanine starting with an exothermic attack at N-7 to form a dipolar intermediate that can close an aziridine ring in another exothermic reaction, forming a stable covalent cross link. Graphical Abstract.

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

Abstract

Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that are formed alter the DNA structure, contributing to inhibition of function and ultimately cancer cell death. Despite its success as an anticancer drug, cisPt has a number of drawbacks that reduce its efficacy, including repair of adducts and drug resistance. Some approaches to overcome this problem involve development of compounds that coordinate to other purine nucleobases, including those found in RNA. In this work, amino acid-linked platinum(II) (AAPt) compounds of alanine and ornithine (AlaPt and OrnPt, respectively) were studied. Their reactivity preferences for DNA and RNA purine nucleosides (i.e., 2′-deoxyadenosine (dAdo), adenosine (Ado), dGuo, and guanosine (Guo)) were determined. The chosen compounds form predominantly monofunctional adducts by reacting at the N1, N3, or N7 positions of purine nucleobases. In addition, features of AAPt compounds that impact the glycosidic bond stability of Ado residues were explored. The glycosidic bond cleavage is activated differentially for AlaPt-Ado and OrnPt-Ado isomers. Formation of unique adducts at non-canonical residues and subsequent destabilization of the glycosidic bonds are important features that could circumvent platinum-based drug resistance.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-019-01693-y) contains supplementary material, which is available to authorized users.

Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry

The clinically widely-used anticancer drug, cisplatin, binds strongly to DNA as a DNA-damaging agent. Herein, we investigated the interaction of cisplatin with a 15-mer single-stranded C,T-rich oligodeoxynucleotide, 5′-CCTT₄CTT₇G₈C₉T₁₀TCTCC-3′ (ODN15), using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with tandem mass spectrometry (top-down MS). Top-down MS analysis with collision-induced dissociation (CID) fragmentation of the mono-platinated and di-platinated ODN15 provided abundant and informative Pt-containing or Pt-free a/[a − B], w and internal fragments, allowing the unambiguous identification of T₄, T₇, C₉, and T₁₀ as the platination sites on the cisplatin-ODN15 adducts. These results revealed that, in addition to the well-established guanine site, the unexpected thermodynamic binding of cisplatin to cytosine and thymine bases was also evident at the oligonucleotide level. Furthermore, the binding models of cisplatin with cytosine and thymine bases were built as the Pt coordinated to cytosine-N(3) and thymine-N(3) with displacement of the proton or tautomerization of thymine. These findings contribute to a better understanding of the mechanism of action of cisplatin and its preference for gene loci when the drug binds to cellular DNA, and also demonstrate the great potential and superiority of FT-ICR MS in studying the interactions of metallodrugs with large biomolecules.

Ion Mobility-Mass Spectrometry Reveals Details of Formation and Structure for GAA·TCC DNA and RNA Triplexes

DNA and RNA triplexes are thought to play key roles in a range of cellular processes such as gene regulation and epigenetic remodeling and have been implicated in human disease such as Friedreich's ataxia. In this work, ion mobility-mass spectrometry (IM-MS) is used with supporting UV-visible spectroscopy to investigate DNA triplex assembly, considering stability and specificity, for GAA·TTC oligonucleotide sequences of relevance to Friedreich's ataxia. We demonstrate that, contrary to other examples, parallel triplex structures are favored for these sequences and that stability is enhanced by increasing oligonucleotide length and decreasing pH. We also provide evidence for the self-association of these triplexes, consistent with a proposed model of higher order DNA structures formed in Friedreich's ataxia. By comparing triplex assembly using DNA- and RNA-based triplex-forming oligonucleotides, we demonstrate more favorable formation of RNA triplexes, suggesting a role for their formation in vivo. Finally, we interrogate the binding properties of netropsin, a known polyamide triplex destabilizer, with RNA-DNA hybrid triplexes, where preference for duplex binding is evident. We show that IM-MS is able to report on relevant solution-phase populations of triplex DNA structures, thereby further highlighting the utility of this technology in structural biology. Our data therefore provides new insights into the possible DNA and RNA assemblies that may form as a result of GAA triplet repeats. Graphical Abstract ᅟ.

Controlling with light the interaction between trans-tetrapyridyl ruthenium complexes and an oligonucleotide

Three new trans-ruthenium(ii) complexes coordinated to tetrapyridyl ligands, namely [Ru(bapbpy)(dmso)Cl]Cl ([2]Cl), [Ru(bapbpy)(Hmte)₂](PF₆)₂ ([3](PF₆)₂), and [Ru(biqbpy)(Hmte)₂](PF₆)₂ ([4](PF₆)₂), were prepared as analogues of [Ru(biqbpy)(dmso)Cl]Cl ([1]Cl), a recently described photoactivated chemotherapy agent. The new complexes were characterized, and their crystal structures showed the distorted coordination octahedron typical of this family of complexes. Their photoreactivity in solution was analyzed by spectrophotometry and mass spectrometry, which showed that the sulfur ligand was substituted upon blue light irradiation. The binding of the ruthenium complexes to a reference single-stranded oligonucleotide (s(^5'CTACGGTTTCAC^3')) was explored both in the dark and under light irradiation by gel electrophoresis and high-resolution mass spectrometry. While adduct formation in the dark was negligible for the four complexes, light irradiation led to the formation of adducts with one or two ruthenium centers per oligonucleotide. The absence of interactions in the dark and the presence of complex-oligonucleotide adducts demonstrate that visible light controls the interaction of these ruthenium complexes with nucleic acids.

ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)₂ Cl₂ , 3 and Cu(1-MsC-N3)₂ Cl₂ and 4 with biologically important cations: Na⁺ , K⁺ , Ca²⁺ , Mg²⁺ and Zn²⁺ . The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1-4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.

A Ligand That Targets CUG Trinucleotide Repeats

The development of small molecules that can recognize specific RNA secondary and tertiary structures is currently an important research topic for developing tools to modulate gene expression and therapeutic drugs. Expanded CUG trinucleotide repeats, known as toxic RNA, capture the splicing factor MBNL1 and are causative of neurological disorder myotonic dystrophy type 1 (DM1). Herein, the rational molecular design, synthesis, and binding analysis of 2,9-diaminoalkyl-substituted 1,10-phenanthroline (DAP), which bound to CUG trinucleotide repeats, is described. The results of melting temperature (T_m ) analyses, surface plasmon resonance (SPR) assay, and electrospray spray ionization time-of-flight (ESI-TOF) mass spectrometry showed that DAP bound to r(CUG)₉ but not to r(CAG)₉ and r(CGG)₉ . The dual luciferase assay clearly indicated DAP bound to the r(CUG)_n repeat by affecting the translation in vitro.

Mass Spectrometry Uncovers Molecular Reactivities of Coordination and Organometallic Gold(III) Drug Candidates in Competitive Experiments That Correlate with Their Biological Effects

The reactivity of three cytotoxic organometallic gold(III) complexes with cyclometalated C,N,N and C,N ligands (either six- or five-membered metallacycles), as well as that of two representative gold(III) complexes with N-donor ligands, with biological nucleophiles has been studied by ESI-MS on ion trap and time-of-flight instruments. Specifically, the gold compounds were reacted with mixtures of nucleophiles containing l-histidine (imine), l-methionine (thioether), l-cysteine (thiol), l-glutamic acid (carboxylic acid), methylseleno-l-cysteine (selenoether), and in situ generated seleno-l-cysteine (selenol) to judge the preference of the gold compounds for binding to selenium-containing amino acid residues. Moreover, the gold compounds' reactivity was studied with proteins and nucleic acid building blocks. These experiments revealed profound differences between the coordination and organometallic families and even within the family of organometallics, which allowed insights to be gained into the compounds mechanisms of action. In particular, interactions with seleno-l-cysteine appear to reflect well the compounds' inhibition properties of the seleno-enzyme thioredoxin reductase and to a certain extent their antiproliferative effects in vitro. Therefore, mass spectrometry is successfully applied for linking the molecular reactivity and target preferences of metal-based drug candidates to their biological effects. Finally, this experimental setup is applicable to any other metallodrug that undergoes ligand substitution reactions and/or redox changes as part of its mechanism of action.

G-Quadruplex DNA-binding quaternary alkaloids from Tylophora atrofolliculata

Quaternary alkaloids from T. atrofolliculata with human telomeric DNA G-quadruplex binding capacity.

Plug-and-playable fluorescent cell imaging modular toolkits using the bacterial superglue, SpyTag/SpyCatcher

Simple plug-and-playable fluorescent cell imaging modular toolkits are established and target cells are visualized with selective colors on demand.

Identification and discrimination of binding sites of an organoruthenium anticancer complex to single-stranded oligonucleotides by mass spectrometry

We here report the identification of the binding sites of an organometallic ruthenium anticancer complex [(η(6)-biphenyl)Ru(en)Cl](+) (1) to single-stranded oligodeoxynucleotides (ODNs) 5'-CCCA4G5C6CC-3' (I) and 5'-CCC3G4A5CCC-3' (II) by mass spectrometry. The MS analysis of exonuclease ladders demonstrated that the 5'-exonuclease bovine spleen phosphodiesterase digestion of I and II mono-ruthenated by complex 1 was arrested solely at A4 and partially at C3 and G4, respectively, and that the 3'-exonuclease snake venom phosphodiesterase digestion of the ruthenated ODNs was arrested solely at G5 and G4, respectively, due to the ruthenation. These results did not allow unambiguous identification of ruthenation sites on the metallated ODNs. In contrast, tandem mass spectrometry analysis with CID fragmentation of the mono-ruthenated ODNs provided sequential and complementary [a(i) - B]/wi fragments, leading to unambiguous identification of G5 in I and G4 in II as the ruthenation sites on the ODN adducts, which is in line with the high selectivity of the complex towards guanine base as reported previously. These findings suggest that caution should be raised with regard to the identification of the binding sites of metal complexes, in particular complexes with bulky ligands, like biphenyl in complex 1, to DNA by MS analysis of exonuclease ladders of the metallated adducts, because the bulky ligands may adopt such an orientation that they block the exonuclease cleavage of the 5'- or 3'-side phosphodiester bonds adjacent to the binding sites, leading to digestion stalling at the nucleotides before the binding sites.

Ten-atom silver cluster signaling and tempering DNA hybridization

Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near-infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ(max) = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ(max) = 490 nm) and strong green emission (λ(max) = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag(+), high concentrations of the oxidizing agent O2, and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes.

Excited state proton transfer of natural flavonoids and their chromophores in duplex and tetraplex DNAs

Fisetin (3,7,3',4'-tetrahydroxyflavone) and quercetin (3,5,7,3',4'-pentahydroxyflavone) are the bioactive plant flavonoids that are potentially useful therapeutic drugs for the treatment of a broad spectrum of diseases, including atherosclerosis, cardiovascular disease, obesity, hypertension, and cancer. 3-Hydroxyflavone (3HF) and 7-hydroxyflavone (7HF) are the synthetic chromophores of fisetin and quercetin. We have exploited dual luminescence properties of fisetin and quercetin along with 3-HF and 7HF to examine their efficacy of binding and compare their interactions with DNA, which is one of the macromolecular targets of flavonoids in physiological systems. Following the sequence of the human telomeric DNA 5'-d (CCCTAA-)n/(-TTAGGG)n-5', two single-stranded DNA oligonucleotides, 5'-d(C3TA2)3C3-3' and 5'-d(T2AG3)4-3', and their duplex were used as receptors to study binding by the ligands quercetin, fisetin, and their chromophores. Circular dichroism, differential absorption, UV thermal melting, and size exclusion chromatographic studies indicated the formation of unusual DNA structures (such as C4 and G4 tetraplexes) for both the C- and G-rich single-stranded DNAs. Upon binding to DNA, dramatic changes were observed in the intrinsic fluorescence behavior of the flavonoids. Molecular docking studies were performed to describe the likely binding sites for the ligands. The spectroscopic studies on flavonoid-DNA interactions described herein demonstrate a powerful approach for examining their DNA binding through exploiting the highly sensitive intrinsic fluorescence properties of the flavonoids as their own "reporter" for their interactions with macromolecular targets.

The synthesis, characterisation and cytotoxicity of bisintercalating (2,2′:6′,2′′-terpyridine)platinum(ii) complexes

Dinuclear (2,2′:6′,2′′-terpyridine)platinum(ii) complexes were synthesised by tethering either thiol or pyridine based linkers. The cytotoxicity of the complexes was determined against human ovarian carcinoma cells (A2780) and its cisplatin-resistant sub-line A2780cis, as well as L1210 murine leukemia cells.

Recognition of chelerythrine to human telomeric DNA and RNA G-quadruplexes

A study on binding of antitumor chelerythrine to human telomeric DNA/RNA G-quadruplexes was performed by using DNA polymerase stop assay, UV-melting, ESI-TOF-MS, UV-Vis absorption spectrophotometry and fluorescent triazole orange displacement assay. Chelerythrine selectively binds to and stabilizes the K(+)-form hybrid-type human telomeric DNA G-quadruplex of biological significance, compared with the Na(+)-form antiparallel-type DNA G-quadruplex. ESI-TOF-MS study showed that chelerythrine possesses a binding strength for DNA G-quadruplex comparable to that of TMPyP4 tetrachloride. Both 1:1 and 2:1 stoichiometries were observed for chelerythrine's binding with DNA and RNA G-quadruplexes. The binding strength of chelerythrine with RNA G-quadruplex is stronger than that with DNA G-quadruplex. Fluorescent triazole orange displacement assay revealed that chelerythrine interacts with human telomeric RNA/DNA G-quadruplexes by the mode of end- stacking. The relative binding strength of chelerythrine for human telomeric RNA and DNA G-quadruplexes obtained from ESI-TOF-MS experiments are respectively 6.0- and 2.5-fold tighter than that with human telomeric double-stranded hairpin DNA. The binding selectivity of chelerythrine for the biologically significant K(+)-form human telomeric DNA G-quadruplex over the Na(+)-form analogue, and binding specificity for human telomeric RNA G-quadruplex established it as a promising candidate in the structure-based design and development of G-quadruplex specific ligands.

Strong ionic interactions in noncovalent complexes between poly(ethylene imine), a cationic electrolyte, and Cibacron Blue, a nucleotide mimic--implications for oligonucleotide vectors

Cationic polymers can bind DNA to form polyplexes, which are noncovalent complexes used for gene delivery into the targeted cells. For more insight on such biologically relevant systems, the noncovalent complexes between the cationic polymer poly(ethylene imine) (PEI) and the nucleotide mimicking dye Cibacron Blue F3G-A (CB) were investigated using mass spectrometry methods. Two PEIs of low molecular weight were utilized (Mn  ≈ 423 and 600 Da). The different types of CB anions produced by Na(+)/H(+) exchanges on the three sulfonic acid groups of CB and their dehydrated counterparts were responsible for complex formation with PEI. The CB anions underwent noncovalent complex formation with protonated, but not with sodiated PEI. A higher proportion of cyclic oligomers were detected in PEI423 than PEI600, but both architectures formed association products with CB. Tandem mass spectrometry studies revealed a significantly stronger noncovalent interaction between PEI and dehydrated CB than between PEI and intact CB.

Differentiation and distributions of DNA/cisplatin crosslinks by liquid chromatography-electrospray ionization-infrared multiphoton dissociation mass spectrometry

Liquid chromatography-electrospray ionization-infrared multiphoton dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), which have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared with the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink.

Ion mobility spectrometry reveals duplex DNA dissociation intermediates

Electrospray ionization (ESI) soft desolvation is widely used to investigate fragile species such as nucleic acids. Tandem mass spectrometry (MS/MS) gives access to the gas phase energetics of the intermolecular interactions in the absence of solvent, by following the dissociation of mass-selected ions. Ion mobility mass spectrometry (IMS) provides indications on the tridimensional oligonucleotide structure by attributing a collision cross section (CCS) to the studied ion. Electrosprayed duplexes longer than eight bases pairs retain their helical structure in a solvent-free environment. However, the question of conformational changes under activation in MS/MS studies remains open. The objective of this study is to probe binding energetics and characterize the unfolding steps occurring prior to oligonucleotide duplex dissociation. Comparing the evolution of CCS with collision energy and breakdown curves, we characterize dissociation pathways involved in CID-activated DNA duplex separation into single strands, and we demonstrate here the existence of stable dissociation intermediates. At fixed duplex length, dissociation pathways were found to depend on the percentage of GC base pairs and on their position in the duplex. Our results show that pure GC sequences undergo a gradual compaction until reaching the dissociation intermediate: A-helix. Mixed AT-GC sequences were found to present at least two conformers: a classic B-helix and an extended structure where the GC tract is a B-helix and the AT tract(s) fray. The dissociation in single strands takes place from both conformers when the AT base pairs are enclosed between two GC tracts or only from the extended conformer when the AT tract is situated at the end(s) of the sequence.

Large mixed complexes involving uracil, cytosine, thymine and/or 1-methyl uracil around Ca2+ ions: an electrospray ionization/MS study

We investigated the possible formation of mixed B(n)B'(n')Ca(2+) complexes where B and B' are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1-methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers.

Competitive binding sites of a ruthenium arene anticancer complex on oligonucleotides studied by mass spectrometry: ladder-sequencing versus top-down

We report identification of the binding sites for an organometallic ruthenium anticancer complex [(η (6)-biphenyl)Ru(en)Cl][PF6] (1; en = ethylenediamine) on the 15-mer single-stranded oligodeoxynucleotides (ODNs), 5'-CTCTCTX7G8Y9CTTCTC-3' [X = Y = T (I); X = C and Y = A (II); X = A and Y = T (III); X = T and Y = A (IV)] by electrospray ionization mass spectrometry (ESI-MS) in conjunction with enzymatic digestion or tandem mass spectrometry (top-down MS). ESI-MS combined with enzymatic digestion (termed MS-based ladder-sequencing), is effective for identification of the thermodynamically-favored G-binding sites, but not applicable to determine the thermodynamically unstable T-binding sites because the T-bound adducts dissociate during enzymatic digestion. In contrast, top-down MS is efficient for localization of the T binding sites, but not suitable for mapping ruthenated G bases, due to the facile fragmentation of G bases from ODN backbones prior to the dissociation of the phosphodiester bonds. The combination of the two MS approaches reveals that G8 in each ODN is the preferred binding site for 1, and that the T binding sites of 1 are either T7 or T11 on I and IV, and either T6 or T11 on II and III, respectively. These findings not only demonstrate for the first time that T-bases in single-stranded oligonucleotides are kinetically competitive with guanine for such organoruthenium complexes, but also illustrate the relative merits of the combination of ladder-sequencing and top-down MS approaches to elucidate the interactions of metal anticancer complexes with DNA.

Comparison of MS/MS methods for characterization of DNA/cisplatin adducts

The development of activation/dissociation techniques such as ultraviolet photodissociation (UVPD), infrared multiphoton dissociation (IRMPD), and electron transfer dissociation (ETD) as alternatives to collision induced dissociation (CID) has extended the range of strategies for characterizing biologically relevant molecules. Here, we describe a comprehensive comparison of CID, IRMPD, UVPD, ETD, and hybrid processes termed ETcaD and ET-IRMPD (and analogous hybrid methods in the negative mode NETcaD and NET-IRMPD) for generating sequence-specific fragment ions and allowing adduction sites to be pinpointed for DNA/cisplatin adducts. Among the six MS/MS methods, the numerous products generated by the IRMPD and UVPD techniques resulted in the most specific and extensive backbone cleavages. We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra.

Sensitive Marker of the Cisplatin-DNA Interaction: X-Ray Photoelectron Spectroscopy of CL

The development of cisplatin and Pt-based analogues anticancer agents requires knowledge concerning the molecular mechanisms of interaction between such drugs with DNA. However, the binding dynamics and kinetics of cisplatin reactions with DNA determined by traditional approaches are far from satisfactory. In this study, a typical 20-base oligonucleotide (CGTGACAGTTATTGCAGGCG), as a simplified model representing DNA, was mixed with cisplatin in different molar ratios and incubation time. High-resolution XPS spectra of the core elements C, N, O, P, and Cl were recorded to explore the interaction between cisplatin and DNA. From deconvoluted Cl spectra we could readily differentiate the covalently bound chlorine from ionic chloride species in the cisplatin-oligo complexes, which displayed distinct features at various reaction times and ratios. Monitoring the magnitude and energy of the photoelectron Cl 2p signal by XPS could act as a sensitive marker to probe the interaction dynamics of chemical bonds in the reaction of cisplatin with DNA. At 37°C, the optimum incubation time to obtain a stable cisplatin-oligo complex lies around 20 hrs. This novel analysis technique could have valuable implications to understand the fundamental mechanism of cisplatin cytotoxicity and determine the efficiency of the bonds in treated cancer cells.

Development and validation of LC-MS/MS method for the detection and quantification of CpG oligonucleotides 107 (CpG ODN107) and its metabolites in mice plasma

CpG oligodeoxynucleotide 107 (CpG ODN107) could be used as a novel radiosensitizer for glioma. Herein, a novel and sensitive reversed-phase HPLC coupled with electrospray triple quadrupole mass spectrometry (LC-MS/MS) following a one-step C18 solid-phase extraction (SPE) for biological matrix removal was developed and fully validated for the determination of CpG ODN107 and its metabolites such as 5'N-1, 3'N-1, 3'N-2, and 3'N-3 in mouse plasma. The analytes were separated on an Extend-C18 analytical column (150 mm × 2.1 mm, 3.5 μm) using an eluent of acetonitrile-0.05% aqueous NH(3) (20:80, v/v) and detected by electrospray ionization (ESI) mass spectrometry in the negative multiple reaction monitoring mode (MRM). The assay was specific, and it showed a good linearity with a determination coefficient (r(2)) that was greater than or equal to 0.998 for CpG ODN107 and its metabolites in the biological matrices. The precision, accuracy, and relative recovery values were found to be <15%, ±15%, and 95-105%, respectively. This method was successfully applied to measure the concentrations of CpG ODN107 and its metabolites in the plasma following the intravenous administration of 15.0 mg/kg of CpG ODN107 in mice; therefore, the method was suitable for preclinical pharmacokinetic studies on CpG ODN107 and its metabolites.

Cationic β-vinyl substitutedmeso-tetraphenylporphyrins: synthesis and non-covalent interactions with a short poly(dGdC) duplex

Several cationic beta-vinyl-pyridinium and beta-vinyl-quinolinium-meso-tetraphenylporphyrin derivatives were synthesized starting from 2-formyl-meso-tetraphenylporphyrin, and the corresponding Zn(II) complex, and different N-alkyl derivatives of 2- and 4-methylpyridine and 2- and 4-methylquinoline. The new compounds were obtained in a one-step process via base catalyzed aldol-type condensation reactions. Electrospray ionization mass spectrometry (ESI-MS) and ultraviolet-visible (UV-vis) spectroscopy were used to investigate the binding mode of the synthesized cationic beta-vinyl-pyridinium and beta-vinyl-quinolinium-meso-tetraphenylporphyrin derivatives with a short GC duplex oligonucleotide. Analysis of the obtained mass spectrometry results indicates the probable occurrence of outside binding. UV-vis spectroscopy data also points to non-intercalation. The potential photosensitizing capacity of these compounds was also ascertained from preliminary photophysical studies.

Electrospray mass spectrometry for the study of the non-covalent interactions of porphyrins and duplex desoxyribonucleotides

An overview of the use of electrospray mass spectrometry for the study of non-covalent interactions of cationic porphyrins and small DNA duplexes, highlighting the work developed in the Mass Spectrometry Laboratory of the University of Aveiro, is presented here.

Applications of mass spectrometry to the study of siRNA

RNA interference (RNAi) has quickly become a well-established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double-stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field.

Bioanalytical LC-MS of therapeutic oligonucleotides

Therapeutic oligonucleotides (OGNTs) are important biopharmaceutical drugs for the future, due to their ability to selectively reduce or knockout the expression of target genes. For the development of OGNTs, reliable and relatively high-throughput bioanalytical methods are required to perform the quantitative bioanalysis of OGNTs and their metabolites in biological fluids (e.g., plasma, urine and tissue). Although immunoaffinity methods, especially ELISA, are currently widely applied for this purpose, the potential of LC-MS in OGNT analysis is under investigation. Owing to its inherent ability to monitor the individual target OGNTs as well as their metabolites, LC-MS is now evolving into the method-of-choice for the bioanalysis of OGNTs. In this paper, the state-of-the-art of bioanalytical LC-MS of OGNTs and their metabolites in biological fluids is critically reviewed and its advantages and limitations highlighted. Finally, the future perspective of bioanalytical LC-MS, that is, lower detection levels and potential generic LC-MS methodology, is discussed.

Infrared multiphoton dissociation tandem charge detection-mass spectrometry of single megadalton electrosprayed ions

This work presents the implementation of tandem mass spectrometry for experiments on single electrosprayed ions from compounds of megadalton (MDa) molecular weight, using two charge detection devices. The first mass spectrometry stage (first charge detection device) combined with an ion gate allows both mass-to-charge ratio and charge selections of the megadalton ion of interest. The second stage is based on an electrostatic ion trap and consists of an image charge detection tube mounted between two ion mirrors. Single MDa ions can be stored for several dozen milliseconds. During the trapping time, single ions can be irradiated by a continuous wavelength CO(2) laser. We observe stepwise changes in the charge of a single trapped ion owing to multiphoton activation. Illustration of infrared multiphoton dissociation tandem mass spectrometry are given for single megadalton ions of poly(ethylene oxide)s and DNAs.

Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.

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.

Bioanalysis of siRNA and oligonucleotide therapeutics in biological fluids and tissues

This article summarizes bioanalytical avenues for the determination of siRNA and oligonucleotide therapeutics, with an emphasis on hybridization methods. Aspects of the chemistry and delivery of investigational oligonucleotide therapeutics are considered. The nature of the oligonucleotide under investigation will dictate the best analytical course of action; each method has its advantages and disadvantages, depending upon the oligonucleotide test article and the anticipated toxicokinetic and pharmacokinetic study parameters. Stringent method development and specific validation criteria are essential to attain the best quality results in support of a regulatory filing.

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.