Studies of the intermolecular DNA triplexes of C+·GC and T·AT triplets by electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry

Journal of Mass Spectrometry

Volumn 43, Issue 2, 2008, Pages 164-172

  Wan, Cuihong ^a   Guo, Xinhua ^a   Liu, Zhiqiang ^a   Liu, Shuying ^a  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

Author keywords

CD spectrum; Correlation of DNA triplex in gas phase and solution; DNA triplex stability; ESI MS; SORI CID

Indexed keywords

CYCLOTRON RESONANCE; DISSOCIATION; ELECTROSPRAY IONIZATION; MASS SPECTROMETRY; MOLECULAR STRUCTURE; PHASE INTERFACES;

ACIDIC CONDITIONS; GAS PHASE; TRIPLEX STABILITY;

DNA;

ARTICLE; CHROMATOGRAPHY; CIRCULAR DICHROISM; CORRELATION ANALYSIS; DISSOCIATION; DNA DETERMINATION; ELECTROSPRAY; GAS DIFFUSION; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; MELTING POINT; PRIORITY JOURNAL;

BASE SEQUENCE; DNA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TANDEM MASS SPECTROMETRY;

EID: 39749132877     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1277     Document Type: Article

References (37)

1. Felsenfeld G, Davies DR, Rich A. Formation of a three-stranded polynucleotide molecule. Journal of the American Chemical Society 1957; 79: 2023.
2. Postel EH, Flint SJ, Kessler DJ, Hogan ME. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proceedings of the National Academy of Sciences of the United States of America 1991; 88: 8227, DOI: 10.1073/pnas.88.18.8227.
3. Dudand RH, Kessler DJ, Gumell S, Duvics M, Pettitt BM, Hogan ME. Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry 1991; 30: 9246.
4. Goni JR, Cruz X, Orozco M. Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Research 2004; 32: 354, DOI: 10.1093/nar/gkh188.
5. Morgan AR, Wells RD. Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. Journal of Molecular Biology 1968; 37: 63, DOI: 10.1016/0022-2836(68)90073-9.
6. Knauert MP, Glazer PM. Triplex forming oligonucleotides: sequence-specific tool for gene targeting. Human Molecular Genetics 2001; 10: 2243.
7. Chan PP, Glazer PM. Triplex DNA: fundamentals, advances, and potential applications for gene therapy. Journal of Molecular Medicine 1997; 75: 267, DOI: 10.1007/s001090050112.
8. Sun JS, Garestier T, Hélène C. Oligonucleotide directed triple helix formation. Current Opinion in Structural Biology 1996; 6: 327, DOI: 10.1016/S0959-440X(96)80051-0.
9. Frank-Kamenetskii MD, Mirkin SM. Triplex DNA structure. Annual Review of Biochemistry 1995; 64: 65, DOI: 10.1146/annurev.bi.64.070195. 000433.
10. Wu P, Kawamoto Y, Hara H, Sugimoto N. Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helices. Journal of Inorganic Biochemistry 2002; 91: 277, DOI: 10.1016/S0162-0134(02)00444-0.
11. Sugimoto N, Wu P, Hara H, Kawamoto Y. pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes. Biochemistry 2001; 40: 9396, DOI: 10.1021/bi0106661.
12. Asensio JL, Lane AN, Dhesi J, Bergqvist S, Brown T. The contribution of cytosine protonation to the stability of parallel DNA triple helices. Journal of Molecular Biology 1998; 275: 811, DOI: 10.1006/jmbi.1997.1520.
13. Koshlap KM, Schultze P, Brunar H, Dervan PB, Feigon J. Solution structure of an intramolecular DNA triplex containing an N-7-glycosylated guanine which mimics a protonated cytosine. Biochemistry 1997; 36: 2659, DOI: 10.1021/bi962438a.
14. Leitner D, Schroder W, Weisz K. Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability. Biochemistry 2000; 39: 5886, DOI: 10.1021/bi992630n.
15. Roberts RW, Crothers DM. Prediction of the stability of DNA triplexes. Proceedings of the National Academy of Sciences of the United States of America 1996; 93: 4320, DOI: 10.1073/pnas.93.9.4320.
16. +·GC and T·AT triplets. Nucleic Acids Research 2003; 31: 5598, DOI: 10.1093/nar/gkg782.
17. Kiessling LL, Griffin LC, Dervan PB. Flanking sequence effect within the pyrimidine triple-helix motif characterized by affinity cleaving. Biochemistry 1992; 31: 2829.
18. Daniel JM, Friess SD, Rajagopalan S, Wendt S, ZenobiR. Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry. International Journal of Mass Spectrometry 2002; 216: 1, DOI: 10.1016/S1387-3806(02)00585-7.
19. Beck JL, Colgrave ML, Ralph SF, Sheil MM. Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Mass Spectrometry Reviews 2001; 20: 61, DOI: 10.1002/mas.1003.
20. Hofstadler SA, Sannes-Lowery KA, Hannis JC. Analysis of nucleic acids by FTICR MS. Mass Spectrometry Reviews 2005; 24: 256, DOI: 10.1002/mas.20016.
21. Guo X, Liu Z, Liu S, Bentzley CM, Bruist MF. Structural features of L-argininamide-binding DNA aptamer studied with ESI-FTMS. Analytical Chemistry 2006; 78: 7259, DOI: 10.1021/ac060606r.
22. Rosu F, Gabelica V, Houssier C, De Pauw E. Triplex and quadruplex DNA structures studied by electrospray mass spectrometry. Rapid Communications in Mass Spectrometry 2002; 16: 1792, DOI: 10.1002/rcm.778.
23. Gidden J, Baker ES, Ferzoco A, Bowers MT. Structural motifs of DNA complexes in the gas phase. International Journal of Mass Spectrometry 2005; 240: 183, DOI: 10.1016/j.ijms.2004.09.011.
24. 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. Journal of the American Society for Mass Spectrometry 2000; 11: 450, DOI: 10.1016/S1044-0305(00)00095-7.
25. Guittat L, Alberti P, Rosu F, Van Miert S, Thetiot E, Pieters L, Gabelica V, De Pauw E. Interactions of cryptolepine and neocryptolepine with unusual DNA structures. Biochimie 2003; 85: 535, DOI: 10.1016/S0300-9084(03) 00035-X.
26. Santhana Mariappan SV, Cheng X, van Breemen RB, Silks LA, Gupta G. Analysis of GAA/TTC DNA triplexes using nuclear magnetic resonance and electrospray ionization mass spectrometry. Analytical Biochemistry 2004; 334: 216, DOI: 10.1016/j.ab.2004.07.036.
27. Pan S, Sun X, Lee JK. DNA stability in the gas versus solution phases: a systematic study of thirty-one duplexes with varying length, sequence, and charge level. Journal of the American Society for Mass Spectrometry 2006; 17: 1383, DOI: 10.1016/j.jasms.2006.07.016.
28. Yang M, Thompson R, Hall G. Comparative stability determination of oligonucleotide duplexes in gas and solution phase. Journal of the American Society for Mass Spectrometry 2004; 15: 1354, DOI: 10.1016/j.jam.2004.06.008.
29. 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. Journal of the American Chemical Society 1998; 120: 9605, DOI: 10.1021/ja973534h.
30. Gabelica V, De Pauw E. Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes. Journal of Mass Spectrometry 2001; 36: 397, DOI: 10.1002/jms.141.
31. Gabelica V, De Pauw E. Comparison of the collision-induced dissociation of duplex DNA at different collision regimes: evidence for a multistep dissociation mechanism. Journal of the American Society for Mass Spectrometry 2002; 13: 91, DOI: 10.1016/S1044-0305(01)00335-X.
32. Wan KX, Shibue T, Gross ML. Non-covalent complexes between DNA-dinding drugs and double-stranded oligodeoxynucleotides: A study by ESI ion-trap mass spectrometry. Journal of the American Chemical Society 2000; 122: 300, DOI: 10.1021/ja990684e.
33. + base triplet stacks. Journal of the American Chemical Society 2002; 124: 14355, DOI: 10.1021/ja026952h.
34. LeProust EM, Pearso CE, Sinden RR, Gao X. Unexpected formation of parallel duplex in GAA and TTC trinucleotide repeats of Friedreich's Ataxia. Journal of Molecular Biology 2000; 302: 1063, DOI: 10.1006/jmbi.2000.4073.
35. Volker J, Klump HH. Electrostatic effects in DNA triple helices. Biochemistry 1994; 33: 13502.
36. Kebarle P. A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. Journal of Mass Spectrometry 2000; 35: 804, DOI: 10.1002/1096-9888(200007)35:7<804::AID-JMS22>3.0.CO;2- Q.
37. Cole RB. Some tenets pertaining to electrospray ionization mass spectrometry. Journal of Mass Spectrometry 2000; 35: 763, DOI: 10.1002/1096-9888(200007)35:7<763::AID-JMS16>3.0.CO;2-#.