Stability analysis for double-stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

Journal of Mass Spectrometry

Volumn 41, Issue 8, 2006, Pages 1086-1095

  Shi, Xiangguo ^a   Takamizawa, Atsushi ^b   Nishimura, Yoshifumi ^a   Hiraoka, Kenzo ^b   Akashi, Satoko ^a  

^a YOKOHAMA CITY UNIVERSITY   (Japan)

^b UNIVERSITY OF YAMANASHI   (Japan)

Author keywords

Binding affinity; Drug DNA complex; Laser spray; Noncovalent complex; Solution phase

Indexed keywords

BINDING ENERGY; COMPLEXATION; DNA; DRUG PRODUCTS; LASER APPLICATIONS; STABILITY; ULTRAVIOLET SPECTROSCOPY;

BINDING AFFINITY; DRUG-DNA COMPLEX; LASER SPRAY; NONCOVALENT COMPLEX; SOLUTION PHASE;

OLIGOMERS;

4',6 DIAMIDINO 2 PHENYLINDOLE; CONGOCIDINE; DAUNORUBICIN; DIMINAZENE ACETURATE; DOUBLE STRANDED DNA; HOE 33342; NOGALAMYCIN; OLIGOMER;

ARTICLE; BINDING AFFINITY; BINDING SITE; COVALENT BOND; DISSOCIATION CONSTANT; DNA BINDING; DNA DETERMINATION; DNA DRUG COMPLEX; DNA SEQUENCE; DRUG DNA BINDING; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; LASER; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN STABILITY; TEMPERATURE SENSITIVITY; THERMOSTABILITY; ULTRAVIOLET SPECTROSCOPY;

DNA; HYDROGEN BONDING; INDICATORS AND REAGENTS; INTERCALATING AGENTS; LASERS; PHARMACEUTICAL PREPARATIONS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 33748362863     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1069     Document Type: Article

References (40)

1. Baraldi PG, Bovero A, Fruttarolo F, Preti D, Tabrizi MA, Pavani MG, Romagnoli R. DNA minor groove binders as potential antitumor and antimicrobial agents. Med. Res. Rev. 2004; 32: 475.
2. Chaires JB. Drug-DNA interactions. Curr. Opin. Struct. Biol. 1998; 8: 314.
3. Zewail-Foote M, Hurley LH. Molecular approaches to achieving control of gene expression by drug intervention at the transcriptional level. Anti-Cancer Drug Des. 1999; 14: 1.
4. Geierstanger BH, Wemmer DE. Complexes of the minor groove of DNA. Annu. Rev. Biophys. Biomol. Struct. 1995; 24: 463.
5. Wiederholt K, Rajur SB, Giuliano J, O'Donnell M, McLaughlin L. DNA-tethered Hoechst groove-binding agents: duplex stabilization and fluorescence characteristics. J. Am. Chem. Soc. 1996; 118: 7055.
6. Chaires JB, Satyanarayana S, Suh D, Fokt I, Przewloka T, Priebe W. Parsing the free energy of anthracycline antibiotic binding to DNA. Biochemistry 1996; 35: 2047.
7. Light-Wahl KJ, Springer DL, Winger BE, Edmonds CG, Camp DG, Thrall BD, Smith RD. Observation of a small oligonucleotide duplex by electrospray ionization mass spectrometry. J. Am. Chem. Soc. 1993; 115: 803.
8. Ganem B, Li YT, Henion JD. Detection of oligonucleotide duplex forms by ion-spray mass spectrometry. Tetrahedron Lett. 1993; 34: 1445.
9. Ding J, Anderegg RJ. Specific and nonspecific dimer formation in the electrospray ionization mass spectrometry of oligonucleotides. J. Am. Soc. Mass Spectrom. 1995; 6: 159.
10. Sannes-Lowery KA, Mack DP, Hu PF, Mei HY, Loo JA. Positive ion electrospray ionization mass spectrometry of oligonucleotides. J. Am. Soc. Mass Spectrom. 1997; 8: 90.
11. Schnier PD, Klassen JS, Strittmatter EF, Williams ER. Activation energies for dissociation of double strand oligonucleotide anions: evidence for Watson-Crick base pairing in vacuo. J. Am. Chem. Soc. 1998; 119: 9605.
12. Kapur A, Beck JL, Shell MM. Observation of daunomycin and nogalamycin complexes with duplex DNA using electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom. 1999; 13: 2489.
13. Gabelica V, De Pauw E, Rosu F. Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry. J. Mass Spectrom. 1999; 34: 1328.
14. Greig MJ, Robinson JM. Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening. J. Biomol. Screen. 2000; 5: 441.
15. Gabelica V, Rosu F, Houssier C, De Pauw E. Gas phase thermal denaturation of an oligonucleotide duplex and its complexes with minor groove binders. Rapid Commun. Mass Spectrom. 2000; 14: 464.
16. Wan KX, Shibue T, Gross ML. Non-covalent complexes between DNA-binding drugs and double-stranded oligodeoxynu-cleotides: a study by ESI ion-trap mass spectrometry. J. Am. Chem. Soc. 2000; 122: 300.
17. Wan KX, Gross ML, Shibue T. Gas-phase stability of double-stranded oligodeoxynucleotides and their noncovalent complexes with DNA-binding drugs as revealed by collisional activation in an ion trap. J. Am. Soc. Mass Spectrom. 2000; 11: 450.
18. Gupta R, Kapur A, Beck JL, Sheil MM. Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes. Rapid Commun. Mass Spectrom. 2001; 15: 2472.
19. Gabelica V, De Pauw E. Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes. J. Mass Spectrom. 2001; 36: 397.
20. Rosu F, Gabelica V, Houssier C, De Pauw E. Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. Nucleic Acids Res. 2002; 30: e82.
21. Gupta R, Beck JL, Ralph SF, Sheil MM, Aldrich-Wright JR. Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 2004; 15: 1382.
22. Gabelica V, 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. 2002; 13: 91.
23. Keller KM, Zhang J, Oehlers L, Brodbelt JS. Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes. J. Mess Spectrom. 2005; 40: 1362.
24. Ramos CI, Barros CM, Fernandes AM, Santana-Marques MG, Correia AJ, Tome JP, Carrilho Mdo C, Faustino MA, Tome AC, Neves MG, Cavaleiro JA. Interactions of cationic porphyrins with double-stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry. J. Mass Spectrom. 2005; 40: 1439.
25. Beck JL, Colgrave ML, Ralph SF, Sheil MM. Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Mess Spectrom. Rev. 2001; 20: 61.
26. Gabelica V, De Pauw E. Internal energy and fragmentation of ions produced in electrospray sources. Mass Spectrom. Rev. 2005; 24: 566.
27. Akashi S. Investigation of molecular interaction within biological macromolecular complexes by mass spectrometry. Med. Res. Rev. 2006; 26: 339.
28. Kojima T, Kudaka I, Sato T, Asakawa T, Akiyama R, Kawashima Y, Hiraoka K. Observation of triply charged metal ion clusters by electrospray and laser spray. Rapid Commun. Mass Spectrom. 1999; 13: 2090.
29. Kudaka I, Kojima T, Saito S, Hiraoka K. A comparative study of laser spray and electrospray. Rapid Commun. Mass Spectrom. 2000; 14: 1558.
30. Hiraoka K, Asakawa Y, Yamamoto Y, Nakamura M, Ueda K. High-sensitivity negative-ion laser spray for liquid chromatography/mass spectrometry. Rapid Commun. Mass Spectrom. 2001; 15: 2020.
31. Hiraoka K, Asakawa Y, Ueda K, Hori A, Sakai T, Okazaki S, Nakamura M. Does thermal degradation occur in laser spray ionization? Rapid Commun. Mass Spectrom. 2002; 16: 1100.
32. Hiraoka K. Laser spray: electric field-assisted matrix-assisted laser desorption/ionization. J. Mass Spectrom. 2004; 39: 341.
33. Hiraoka K, Asakawa Y, Kawashima Y, Okazaki S, Nakamura M, Yamamoto Y, Takamizawa A. The effect of the presence of foreign salts on the formation of gaseous ions for electrospray and laser spray. Rapid Commun. Mass Spectrom. 2004; 18: 2437.
34. Takamizawa A, Itoh Y, Osawa R, Iwasaki N, Nishimura Y, Akashi S, Hiraoka K. Selective dissociation of non-covalent bonds in biological molecules by laser spray. J. Mass Spectrom. 2004; 39: 1053.
35. Takamizawa A, Fujimaki S, Sunner J, Hiraoka K. Denaturation of lysozyme and myoglobin in laser spray. J. Am. Soc. Mass Spectrom. 2005; 16: 860.
36. Sunner J, Beech IB, Hiraoka K. On the distributions of ion/neutral molecule clusters in electrospray and laser spray-a cluster division model for the electrospray process. J. Am. Soc. Mass Spectrom. 2006; 17: 151.
37. Shi XG, Takamizawa A, Nishimura Y, Hiraoka K, Akashi S. Evaluation of binding affinity of protein-mutant DNA complexes in solution by laser spray mass spectrometry. J. Am. Soc. Mass Spectrom. 2006; 17: 611.
38. Fox KR, Brassett C, Waring MJ. Kinetics of dissociation of nogalamycin from DNA: comparison with other anthracycline antibiotics. Biochim. Biophys. Acta. 1985; 840: 383.
39. Sakamoto S, Yamaguchi K. Hyperstranded DNA architectures observed by cold-spray ionization mass spectrometry. Angew. Chem., Int. Ed. Engl. 2003; 42: 905.
40. Nakatani K, Hagihara S, Sando S, Sakamoto S, Yamaguchi K, Maesawa C, Saito I. Induction of a remarkable conformational change in a human telomeric sequence by the binding of naphthyridine dimer: inhibition of the elongation of a telomeric repeat by telomerase. J. Am. Chem. Soc. 2003; 125: 662.