Electrospray mass spectrometry of noncovalent complexes between small molecule ligands and nucleic acids

Gabelica, Valérie

No full text

Contribution to collective works (Parts of books)

Electrospray mass spectrometry of noncovalent complexes between small molecule ligands and nucleic acids

Gabelica, Valérie

2010 • In Joseph H., Banoub; Patrick A., Limbach (Eds.) Mass spectrometry of nucleosides and nucleic acids

Permalink
https://hdl.handle.net/2268/40772

Files (0)Send to Details Statistics Bibliography Similar publications

Files

Full Text

No document available.

Send to

RIS BibTex APA Chicago Permalink X Linkedin

Details

Keywords :

mass spectrometry; electrospray; dissociation; fragmentation; DNA; noncovalent; quadruplex; ligand; MS/MS

Abstract :

[en] CONTENTS 8.1 Introduction 8.1.1 ESI-MS of Noncovalent Complexes 8.1.2 Nucleic Acid Targeting by Small Molecules 8.2 Electrospray Mass Spectrometry of Nucleic Acid Noncovalent Complexes 8.2.1 Stoichiometries: Number of Strands and Detection of Nucleic Acid Higher-Order Structures 8.2.2 Stoichiometries: Number of Bound Ligands 8.2.3 Role of Cations in Nucleic Acid Structure and Ligand Binding 8.2.4 Determination of Equilibrium Binding Constants 8.2.5 Are the Relative Intensities Proportional to the Abundances in Solution? 8.3 Characterizing Noncovalent Ligand Binding by MS/MS of the Complexes 8.3.1 Overview of Dissociation Pathways 8.3.2 How Observed Pathways Depend on Instrumental Parameters 8.3.3 How Observed Pathways Depend on Ligand Binding 8.3.4 Probing the Energetics of Ligand-DNA Interactions 8.3.5 Determining the Ligand Binding Mode 8.3.6 Determining the Ligand Binding Site by MS/MS 8.4 Conclusion and Outlook References

Research Center/Unit :

Giga-Systems Biology and Chemical Biology - ULiège

Disciplines :

Biochemistry, biophysics & molecular biology
Chemistry

Author, co-author :

Gabelica, Valérie ; Université de Liège - ULiège > Département de chimie (sciences) > GIGA-R : Laboratoire de spectrométrie de masse (L.S.M.)

Language :

English

Title :

Electrospray mass spectrometry of noncovalent complexes between small molecule ligands and nucleic acids

Publication date :

2010

Main work title :

Mass spectrometry of nucleosides and nucleic acids

Editor :

Joseph H., Banoub

Patrick A., Limbach

Publisher :

CRC Press, Taylor and Francis Group, Boca Raton, FL, United States

ISBN/EAN :

978-1-4200-4402-7

Pages :

283-302

Funders :

F.R.S.-FNRS - Fonds de la Recherche Scientifique

Available on ORBi :

since 01 March 2010

Statistics

Number of views

201 (10 by ULiège)

Number of downloads

0 (0 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

Bibliography

Yamashita, M. and Fenn, J.B., Electrospray ion source. Another variation on the free-jet theme, J. Phys. Chem. 88, 4451, 1984.
Fenn, J.B. et al., Electrospray ionization for mass spectrometry, Science 246, 64, 1989.
Fenn, J.B. et al., Electrospray ionization—principles and practice, Mass Spectrom. Rev. 9, 37, 1990.
Ganem, B., Li, Y.-T., and Henion, J.D., Detection of non-covalent receptor-ligand complexes by mass spectrometry, J. Am. Chem. Soc. 113, 6294, 1991.
Schalley, C.A., Molecular recognition and supramolecular chemistry in the gas phase, Mass Spectrom. Rev. 20, 253, 2001.
Baytekin, B., Baytekin, H.T., and Schalley, C.A., Mass spectrometric studies of non-covalent compounds: Why supramolecular chemistry in the gas phase?, Org. Biomol. Chem. 4(15), 2825, 2006.
Smith, R.D. and Light-Wahl, K.J., The observation of non-covalent interactions in solution by electrospray ionization mass spectrometry: Promise, pitfalls and prognosis, Biol. Mass Spectrom. 22, 493, 1993.
Smith, R.D. et al., New mass spectrometric methods for the study of non-covalent associations of biopolymers, Chem. Soc. Rev. 26, 191, 1997.
Breuker, K., The study of protein-ligand interactions by mass spectrometry—a personal view, Int. J. Mass Spectrom. 239(1), 33, 2004.
Siegel, M.M., Early discovery drug screening using mass spectrometry, Curr. Top. Med. Chem. 2, 13, 2002.
Glish, G.L. and Vachet, R.W., The basis of mass spectrometry in the twenty-first century, Nat. Rev. Drug Discov. 2, 140, 2003.
Hofstadler, S.A. and Sannes-Lowery, K.A., Applications of ESI-MS in drug discovery: Interrogation of noncovalent complexes, Nat. Rev. Drug Discov. 5, 585, 2006.
Zehender, H. and Mayr, L.M., Application of mass spectrometry technologies for the discovery of lowmolecular weight modulators of enzymes and protein-protein interactions, Curr. Opin. Chem. Biol. 11(5), 511, 2007.
Annis, D.A. et al., Affinity selection-mass spectrometry screening techniques for small molecule drug discovery, Curr. Opin. Chem. Biol. 11(5), 518, 2007.
Hofstadler, S.A. and Griffey, R.H., Analysis of noncovalent complexes of DNA and RNA by mass spectrometry, Chem. Rev. 101, 377, 2001.
Beck, J. et al., Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins, Mass Spectrom. Rev. 20, 61, 2001.
Rosu, F., De Pauw, E., and Gabelica, V., Electrospray mass spectrometry to study drug-nucleic acid interactions, Biochimie 90(7), 1074, 2008.
Hofstadler, S.A., Sannes-Lowery, K.A., and Hannis, J.C., Analysis of nucleic acids by FTICR MS, Mass Spectrom. Rev. 24(2), 265, 2005.
Sannes-Lowery, K.A. et al., High throughput drug discovery with ESI-FTICR, Int. J. Mass Spectrom. 238(2), 197, 2004.
Banoub, J.H. et al., Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids, Chem. Rev. 105(5), 1869, 2005.
Kirpekar, F., Berkenkamp, S., and Hillenkamp, F., Detection of double-stranded DNA by IR- and UV-MALDI mass spectrometry, Anal. Chem. 71(13), 2334, 1999.
Yamaguchi, K., Cold-spray ionization mass spectrometry: Principle and applications, J. Mass Spectrom. 38, 473, 2003.
Sakamoto, S. and Yamaguchi, K., Hyperstranded DNA architectures observed by cold-spray ionization mass spectrometry, Angew. Chem. Int. Ed. 42, 905, 2003.
Shi, X. et al., Stability analysis for double-stranded DNA oligomers and their noncovalent complexes with drugs by laser spray, J. Mass Spectrom. 41(8), 1086, 2006.
Morgner, N. et al., Detecting specific ligand binding to nucleic acids: A test for ultrasoft laser mass spectrometry, Z. Phys. Chem. 221(5), 689, 2007.
Morgner, N., Barth, H.D., and Brutschy, B., A new way to detect noncovalently bonded complexes of biomolecules from liquid micro-droplets by laser mass spectrometry, Aus. J. Chem. 59(2), 109, 2006.
Morgner, N. et al., Binding sites of the viral RNA element TAR and of TAR mutants for various peptide ligands, probed with LILBID: A new laser mass spectrometry, J. Am. Soc. Mass Spectrom. 2008.
Xavier, K.A., Eder, P.S., and Giordano, T., RNA as a drug target: Methods for biophysical characterization and screening, Trends Biotechnol. 18, 349, 2000.
Gallego, J. and Varani, G., Targeting RNA with small-molecule drugs: Therapeutic promise and chemical challenges, Acc. Chem. Res. 34, 836, 2001.
Wallis, M.G. and Schroeder, R., The binding of antibiotics to RNA, Prog. Biophys. Mol. Biol. 67(2-3), 141, 1997.
Schroeder, R., Waldsich, C., and Wank, H., Modulation of RNA function by aminoglycoside antibiotics, EMBO J. 19(1), 1, 2000.
Hermann, T. and Westhof, E., RNA as a drug target: Chemical, modeling, and evolutionary tools, Curr. Opin. Biotechnol. 9(1), 66, 1998.
Famulok, M., Mayer, G., and Blind, M., Nucleic acid aptamers—from selection in vitro to applications in vivo, Acc. Chem. Res. (33), 591, 2000.
Jiang, L.C. et al., Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer, Structure 7(7), 817, 1999.
Nelson, S.M., Ferguson, L.R., and Denny, W.A., DNA and the chromosome—varied targets for chemotherapy, Cell Chromosome 3(1), 2, 2004.
Chabner, B.A. and Roberts, T.G., Timeline—chemotherapy and the war on cancer, Nat. Rev. Cancer 5(1), 65, 2005.
Canals, A. et al., The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs, Acta Crystallogr. D Biol. Crystallogr. 61, 1009, 2005.
Waring, M.J., Drugs which affect the structure and function of DNA, Nature 219, 1320, 1968.
Wang, A.H.J., Intercalative drug binding to DNA, Curr. Opin. Struct. Biol. 2, 361, 1992.
Reha, D. et al., Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4’,6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study, J. Am. Chem. Soc. 124, 3366, 2002.
Ren, J., Jenkins, T.C., and Chaires, J.B., Energetics of DNA intercalation reactions, Biochemistry 39, 8439, 2000.
Wood, A.A. et al., Variability in DNA minor-groove width recognized by ligand-binding—the crystal structure of A bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2, Nucleic Acids Res. 23(18), 3678, 1995.
Pindur, J. and Fischer, G., DNA complexing minor groove-binding ligands: Perspective in antitumor and antimicrobial drug design, Curr. Med. Chem. 3, 379, 1996.
Geierstranger, B.H. and Wemmer, D.E., Complexes of the minor groove of DNA, Annu. Rev. Biomol. Struct. 24, 463, 1995.
Dervan, P.B., Design of sequence-specific DNA-binding molecules, Science 232, 64, 1986.
Dervan, P.B. and Bürli, R.W., Sequence-specific DNA recognition by polyamides, Curr. Opin. Chem. Biol. 3, 688, 1999.
Dervan, P.B., Molecular recognition of DNA by small molecules, Bioorg. Med. Chem. 9, 2215, 2002.
Belmont, P., Constant, J.-F., and Demeunynk, M., Nucleic acid conformation diversity: From structure to function and regulation, Chem. Soc. Rev. 30, 70, 2001.
Besch, R., Giovannangeli, C., and Degitz, K., Triplex-forming oligonucleotides—sequence-specific DNA ligands as tools for gene inhibition and for modulation of DNA-associated functions, Curr. Drug Targets 5(8), 691, 2004.
Chan, P.P. and Glazer, P.M., Triplex DNA: Fundamentals, advances, and potential applications for gene therapy. J. Mol. Med., 1997, pp. 267-282.
Gueron, M. and Leroy, J.L., The i-motif in nucleic acids, Curr. Opin. Struct. Biol. 10(3), 326, 2000.
Phan, A.-T., Kuryavyi, V., and Patel, D.J., DNA architecture: From G to Z, Curr. Opin. Struct. Biol. 16, 288, 2006.
Burge, S. et al., Quadruplex DNA: Sequence, topology and structure, Nucleic Acids Res. 34(19), 5402, 2006.
Han, H. and Hurley, L.H., G-quadruplex DNA: A potential target for anti-cancer drug design, Trends Pharm. Sci. 21, 136, 2000.
Jenkins, T.C., Targeting multi-stranded DNA structures, Curr. Med. Chem. 7, 99, 2000.
Ganem, B., Li, Y.-T., and Henion, J.D., Detection of oligonucleotide duplex forms by ionspray mass spectrometry, Tetrahedron Lett. 34, 1445, 1993.
Light-Wahl, K.J. et al., Observation of a small oligonucleotide duplex by electrospray ionization mass spectrometry, J. Am. Chem. Soc. 115, 803, 1993.
Goodlett, D.R. et al., Direct observation of a DNA quadruplex by electrospray ionization mass spectrometry, Biol. Mass Spectrom. 22, 181, 1993.
Ding, J. and Anderegg, R.J., Specific and non-specific dimer formation in the electrospray ionization mass spectrometry of oligonucleotides, J. Am. Soc. Mass Spectrom. 6, 159, 1995.
Schnier, P.D. et al., Activation energies for dissociation of double strand oligonucleotide anions: Evidence for Watson-Crick base pairing in vacuo, J. Am. Chem. Soc. 120, 9605, 1998.
Gabelica, V. and De Pauw, E., Collision-induced dissociation of 16-mer DNA duplexes with various sequences: Evidence for conservation of the double helix conformation in the gas phase, Int. J. Mass Spectrom. 219, 151, 2002.
Gabelica, V. and De Pauw, E., Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes, J. Mass Spectrom. 36, 397, 2001.
Gidden, J. et al., Structural motifs of DNA complexes in the gas phase, Int. J. Mass Spectrom. 240, 183, 2004.
Gidden, J. et al., Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment, J. Am. Chem. Soc. 126, 15132, 2004.
Baker, E.S. and Bowers, M.T., B-DNA helix stability in a solvent-free environment, J. Am. Soc. Mass Spectrom. 18(7), 1188, 2007.
Perez, A. et al., Exploring the essential dynamics of B-DNA, J. Chem. Theor. Comput. 1(5), 790, 2005.
Rueda, M. et al., The structure and dynamics of DNA in the gas phase, J. Am. Chem. Soc. 125, 8007, 2003.
Muddiman, D.C., Null, A.P., and Hannis, J.C., Precise mass measurement of a double-stranded 500 basepair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, Rapid Commun. Mass Spectrom. 13, 1201, 1999.
Rosu, F. et al., Triplex and quadruplex DNA structures studied by electrospray mass spectrometry, Rapid Commun. Mass Spectrom. 16, 1729, 2002.
Mariappan, S.V.S. et al., Analysis of GAA/TTC DNA triplexes using nuclear magnetic resonance and electrospray ionization mass spectrometry, Anal. Biochem. 334(2), 216, 2004.
Baker, E.S. et al., PNA/dsDNA complexes: Site specific binding and dsDNA biosensor applications, J. Am. Chem. Soc. 128(26), 8484, 2006.
Delvolve, A. et al., Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase, J. Mass Spectrom. 41(11), 1498, 2006.
Davis, J.T., G-quartets 40 years later: From 5′-GMP to molecular biology and supramolecular chemistry, Angew. Chem. Int. Ed. 43(6), 668, 2004.
Fukushima, K. and Iwahashi, H., 1:1 complex of guanine quartet with alkali metal cations detected by electrospray ionization mass spectrometry, Chem. Commun. 895, 2000.
Manet, I. et al., An ESI-MS and NMR study of the self-assembly of guanosine derivates, Helv. Chim. Acta 84, 2096, 2001.
Koch, K.J. et al., Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: Implications for mechanisms of multistrand DNA stabilization, J. Mass Spectrom. 37, 676, 2002.
Aggerholm, T. et al., Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine, deoxyguanosine and uridine observed by ESI-MS/MS, J. Mass Spectrom. 38(1), 87, 2003.
Sakamoto, S. et al., Formation and destruction of the guanine quartet in solution observed by cold-spray ionization mass spectrometry, Chem. Commun. 788, 2003.
Shi, X. et al., Lipophilic G-quadruplexes are self-assembled ion pair receptors, and the bound anion modulates the kinetic stability of these complexes, J. Am. Chem. Soc. 125, 10830, 2003.
Baker, E.S., Bernstein, S.L., and Bowers, M.T., Structural characterisation of G-quadruplexes in deoxyguanosine clusters using ion mobility mass spectrometry, J. Am. Soc. Mass Spectrom. 16, 989, 2005.
Krishnan-Ghosh, Y., Liu, D.S., and Balasubramanian, S., Formation of an interlocked quadruplex dimer by d(GGGT), J. Am. Chem. Soc. 126(35), 11009, 2004.
Krishnan-Ghosh, Y., Whitney, A.M., and Balasubramanian, S., Dynamic covalent chemistry on self- templating PNA oligomers: Formation of a bimolecular PNA quadruplex, Chem. Commun. 3068, 2005.
Datta, B. et al., Quadruplex formation by a guanine-rich PNA oligomer, J. Am. Chem. Soc. 127(12), 4199, 2005.
Baker, E.S. et al., G-quadruplexes in telomeric repeats are conserved in a solvent-free environment, Int. J. Mass Spectrom. 253(3), 225, 2006.
Gros, J. et al., Guanines are a quartet’s best friend: Impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes, Nucleic Acids Res. 35(9), 3064, 2007.
Gabelica, V. et al., Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: The role of central cations and small planar ligands, J. Am. Chem. Soc. 129, 895, 2007.
Carrasco, C. et al., Tight binding of the antitumor drug ditercalinium to quadruplex DNA, ChemBioChem 3, 100, 2002.
David, W.M. et al., Investigation of quadruplex oligonucleotide-drug interactions by electrospray ionization mass spectrometry, Anal. Chem. 74, 2029, 2002.
Rosu, F. et al., Selective interaction of ethidium derivatives with quadruplexes. An equilibrium dialysis and electrospray ionization mass spectrometry analysis., Biochemistry 42, 10361, 2003.
Li, W. et al., Interactions of daidzin with intramolecular G-quadruplex, FEBS Lett. 580(20), 4905, 2006.
Mazzitelli, C.L. et al., Evaluation of binding of perylene diimide and benzannulated perylene diimide ligands to DNA by electrospray ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 17(4), 593, 2006.
Li, H., Yuan, G. and Du, D., Investigation of formation, recognition, stabilization, and conversion of dimeric G-quadruplexes of HIV-1 integrase inhibitors by electrospray ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 19(4), 550, 2008.
Smargiasso, N. et al., G-quadruplex DNA assemblies: Loop length, cation identity, and multimer formation, J. Am. Chem. Soc. 130(31), 10208, 2008.
Hsieh, Y.L. et al., Studies of non-covalent interactions of actinomycin D with single stranded oligodeoxynucleotides by ion spray mass spectrometry and tandem mass spectrometry, Biol. Mass Spectrom. 23, 272, 1994.
Gale, D.C. et al., Observation of duplex DNA-drug non-covalent complexes by electrospray ionization mass spectrometry, J. Am. Chem. Soc. 116, 6027, 1994.
Fagan, P. and Wemmer, D.E., Cooperative binding of distamycin A to DNA in the 2:1 mode, J. Am. Chem. Soc. 114, 1080, 1992.
Gabelica, V., De Pauw, E., and Rosu, F., Interaction between antitumor drugs and double-stranded DNA studied by electrospray ionization mass spectrometry, J. Mass Spectrom. 34, 1328, 1999.
Gale, D.C. and Smith, R.D., Characterization of non-covalent complexes formed between minor groove binding molecules and duplex DNA by electrospray ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 6, 1154, 1995.
Kapur, A., Beck, J.L., and Sheil, M.M., Observation of daunomycin and nogalamycin complexes with duplex DNA using electrospray ionization mass spectrometry, Rapid Commun. Mass Spectrom. 13, 2489, 1999.
Rosu, F. et al., Positive and negative ion mode ESI-MS and MS/MS for studying drug-DNA complexes, Int. J. Mass Spectrom. 253, 156, 2006.
Guo, X.H. et al., Structural features of the l-argininamide-binding DNA aptamer studied with ESIFTMS, Anal. Chem. 78(20), 7259, 2006.
Zhou, J., Yuan, G., and Tang, F.L., Estimation of binding constants for complexes of polyamides and human telomeric DNA sequences by electrospray ionization mass spectrometry, Rapid Commun. Mass Spectrom. 20(15), 2365, 2006.
Ravikumar, M., Prabhakar, S., and Vairamani, M., Chiral discrimination of alpha-amino acids by the DNA triplet GCA, Chem. Commun. 392, 2007.
Smith, S.I. et al., Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry, J. Mass Spectrom. 42(5), 681, 2007.
Mazzitelli, C.L., Rodriguez, M., Kerwin, S.M., and Brodbelt, J.S., Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 19, 209-218, 2007.
Evans, S.E. et al., End-stacking of copper cationic porphyrins on parallel-stranded guanine quadruplexes, J. Biol. Inorg. Chem. 12(8), 1235, 2007.
Monchaud, D. et al., Ligands playing musical chairs with G-quadruplex DNA: A rapid and simple displacement assay for identifying selective G-quadruplex binders, Biochimie 90(8), 1207, 2008.
Rosu, F. et al., Cooperative 2:1 binding of a bisphenothiazine to duplex DNA, ChemBioChem, accepted, 2008.
Talib, J. et al., A comparison of the binding of metal complexes to duplex and quadruplex DNA, Dalton Trans. (8), 1018, 2008.
Bahr, M. et al., Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators, Nucleic Acids Res. 36(15), 5000, 2008.
Wang, Z. et al., Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 19(7), 914, 2008.
Ambrus, A. et al., Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution, Nucleic Acids Res. 34(9), 2723, 2006.
Xu, Y., Noguchi, Y., and Sugiyama, H., The new models of the human telomere d[AGGG(TTAGGG)3] in K+ solution, Bioorg. Med. Chem. 14(16), 5584, 2006.
Keller, K.M. et al., Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity, J. Mass Spectrom. 40(10), 1327, 2005.
Reyzer, M. et al., Evaluation of complexation of metal-mediated DNA-binding drugs to oligonucleotides via electrospray ionization mass spectrometry, Nucleic Acids Res. 29(21), e103, 2001.
Greig, M.J. and Robinson, J.M., Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening, J. Biomol. Screening 5(6), 441, 2000.
Wilhelmsson, L.M., Lincoln, P., and Norden, B., Slow DNA binding, in Sequence-Specific DNA Binding Agents, M.J. Waring, ed., RSC Publishing, Cambridge, Chapter 4, p. 69, 2006.
Griffey, R.H. et al., Characterization of low-affinity complexes between RNA and small molecules using electrospray ionization mass spectrometry, J. Am. Chem. Soc. 122, 9933, 2000.
Teulade-Fichou, M.-P. et al., Selective recogniton of G-quadruplex telomeric DNA by a bis(quinacridine) macrocycle, J. Am. Chem. Soc. 125, 4732, 2003.
Schmidt, A., Bahr, U., and Karas, M., Influence of pressure in the first pumping stage on analyte desolvation and fragmentation in nano-ESI MS, Anal. Chem. 73, 6040, 2001.
Gabelica, V., De Pauw, E., and Karas, M., Influence of the capillary temperature and the source pressure on the internal energy distribution of electrosprayed ions, Int. J. Mass Spectrom. 231, 189, 2004.
Gabelica, V. and De Pauw, E., Internal energy and fragmentation of ions produced in electrospray sources, Mass Spectrom. Rev. 24, 566, 2005.
Enke, C.G., A predictive model for matrix and analyte effects in electrospray ionization of singly-charged ionic analytes, Anal. Chem. 69, 4885, 1997.
Cech, N.B. and Enke, C.G., Effect of affinity for droplet surfaces on the fraction of analyte molecules charged during electrospray droplet fission, Anal. Chem. 73(19), 4632, 2001.
Cech, N.B. and Enke, C.G., Relating electrospray ionization response to nonpolar character of small peptides, Anal. Chem. 72, 2717, 2000.
Schmidt, A., Karas, M., and Dulcks, T., Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: When does ESI turn into nano-ESI?, J. Am. Soc. Mass Spectrom. 14(5), 492, 2003.
Kuprowski, M.C. and Konermann, L., Signal response of coexisting protein conformers in electrospray mass spectrometry, Anal. Chem. 79(6), 2499, 2007.
Rosu, F. et al., Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry, Nucleic Acids Res. 30(16), e82, 2002.
Gabelica, V. et al., Influence of response factors on determining equilibrium association constants of noncovalent complexes by electrospray ionization mass spectrometry, J. Mass Spectrom. 38, 491, 2003.
Guittat, L. et al., Interactions of cryptolepine and neocryptolepine with unusual DNA structures, Biochimie 85, 535, 2003.
Guittat, L. et al., Ascididemin and meridine stabilise G-quadruplexes and inhibit telomerase in vitro, Biochim. Biophys. Acta 1724(3), 375, 2005.
Wu, J. and McLuckey, S.A., Gas-phase fragmentation of oligonucleotide ions, Int. J. Mass Spectrom. 237(2-3), 197, 2004.
Gabelica, V. and De Pauw, E., Comparison of the collision-induced dissociation of duplex DNA at different collision regimes: Evidence for a multistep dissociation mechanism, J. Am. Soc. Mass Spectrom. 13, 91, 2002.
Klassen, J.S., Schnier, P.D., and Williams, E.R., Blackbody infrared radiative dissociation of oligonucleotide anions, J. Am. Soc. Mass Spectrom. 9, 1117, 1998.
Wan, K.X., Shibue, T., and Gross, M.L., Gas-phase stability of double-stranded oligodeoxynucleotide and their noncovalent complexes with DNA-binding drugs is revealed by collisional activation in an ion trap, J. Am. Soc. Mass Spectrom. 11, 450, 2000.
Keller, K.M. et al., Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes, J. Mass Spectrom. 40(10), 1362, 2005.
Alves, S., Woods, A., and Tabet, J.C., Charge state effect on the zwitterion influence on stability of non-covalent interaction of single-stranded DNA with peptides, J. Mass Spectrom. 42(12), 1613, 2007.
Alves, S. et al., Influence of salt bridge interactions on the gas-phase stability of DNA/peptide complexes, Int. J. Mass Spectrom. 278, 122-128, 2008.
Rosu, F. et al., Ligand binding mode to duplex and triplex DNA assessed by combining electrospray tandem mass spectrometry and molecular modeling, J. Am. Soc. Mass Spectrom. 18(6), 1052, 2007.
Gabelica, V. et al., Gas phase thermal denaturation of an oligonucleotide duplex and its complexes with minor groove binders, Rapid Commun. Mass Spectrom. 14, 464, 2000.
Ramos, C.I.V. et al., Interactions of cationic porphyrins with double-stranded oligodeoxynucleotides: A study by electrospray ionisation mass spectrometry, J. Mass Spectrom. 40(11), 1439, 2005.
Pothukuchy, A. et al., Duplex and quadruplex DNA binding and photocleavage by trioxatriangulenium lone, Biochemistry 44(6), 2163, 2005.
David-Cordonnier, M.H. et al., Covalent binding of antitumor benzoacronycines to double-stranded DNA induces helix opening and the formation of single-stranded DNA: Unique consequences of a novel DNA-bonding mechanism, Mol. Cancer Ther. 4(1), 71, 2005.
Turner, K.B. et al., Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry, J. Am. Soc. Mass Spectrom. 17, 1401, 2006.
Wilson, J.J. and Brodbelt, J.S., Infrared multiphoton dissociation of duplex DNA/drug complexes in a quadrupole ion trap, Anal. Chem. 79(5), 2067, 2007.
Griffey, R.H. et al., Targeting site-specific gas-phase cleavage of oligoribonucleotides. Application in mass spetrometry-based identification of ligand binding sites, J. Am. Chem. Soc. 121, 474, 1999.
Mazzitelli, C.L. and Brodbelt, J.S., Probing ligand binding to duplex DNA using KMnO4 reactions and electrospray ionization tandem mass spectrometry, Anal. Chem. 79(12), 4636, 2007.
Yu, E. and Fabris, D., Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization Fourier transform mass spectrometry, J. Mol. Biol. 330(2), 211, 2003.
Yu, E. and Fabris, D., Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform mass spectrometry, Anal. Biochem. 334(2), 356, 2004.
Yu, E.T., Zhang, Q.G., and Fabris, D., Untying the FIV frameshifting pseudoknot structure by MS3D, J. Mol. Biol. 345(1), 69, 2005.
Kellersberger, K.A. et al., Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation, Anal. Chem. 76(9), 2438, 2004.
Baker, E.S. et al., Cyclo[n]pyrroles: Size and site-specific binding to G-quadruplexes, J. Am. Chem. Soc. 128(8), 2641, 2006.
Mo, J.J. and Hakansson, K., Characterization of nucleic acid higher order structure by high-resolution tandem mass spectrometry, Anal. Bioanal. Chem. 386(3), 675, 2006.
Gabelica, V. et al., Electron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer, Anal. Chem. 78(18), 6564, 2006.
Oh, H.B. et al., Infrared photodissociation spectroscopy of electrosprayed ions in a Fourier transform mass spectrometer, J. Am. Chem. Soc. 127(11), 4076, 2005.
Oomens, J. et al., Charge-state resolved mid-infrared spectroscopy of a gas-phase protein, Phys. Chem. Chem. Phys. 7(7), 1345, 2005.
Polfer, N.C. et al., Differentiation of isomers by wavelength-tunable infrared multiple-photon dissociation- mass spectrometry: Application to glucose-containing disaccharides, Anal. Chem. 78(3), 670, 2006.
Bush, M.F. et al., Infrared spectroscopy of cationized arginine in the gas phase: Direct evidence for the transition from nonzwitterionic to zwitterionic structure, J. Am. Chem. Soc. 129(6), 1612, 2007.
Gabelica, V. et al., Infrared signature of DNA G-quadruplexes in the gas phase, J. Am. Chem. Soc. 130, 1810, 2008.
Andersen, L.H. et al., Absorption of Schiff-base retinal chromophores in vacuo, J. Am. Chem. Soc. 127(35), 12347, 2005.
Gabelica, V. et al., Base-dependent electron photodetachment from negatively charged DNA strands upon 260-nm laser irradiation, J. Am. Chem. Soc. 129, 4706, 2007.
Gabelica, V. et al., Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores, J. Am. Soc. Mass Spectrom. 18(11), 1990, 2007.