Comparison of different amines for the one-lane sequence determination of 5′-end-labeled oligodeoxyribonucleotides by chemical cleavage

Analytical Biochemistry

Volumn 369, Issue 1, 2007, Pages 112-119

  González Jasso, Eva ^a   Arredondo Vázquez, Guadalupe ^a   Martínez, Pedro ^a   Pless, Reynaldo C ^a  

^a INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

Author keywords

Aminolysis; Chemical cleavage; Oligodeoxyribonucleotides; Sequencing

Indexed keywords

IONIC STRENGTH; OLIGONUCLEOTIDES; POSITIVE IONS;

ALIPHATIC AMINES; AMINOLYSIS; CHEMICAL CLEAVAGE; ELECTROPHORETIC RESOLUTION; HETEROCYCLIC BASIS; OLIGODEOXYRIBONUCLEOTIDES; RADIOACTIVITY PATTERNS; SEQUENCING;

AMINES;

AMINE; GUANINE; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHORUS 32;

AMINOLYSIS; ARTICLE; ELECTROPHORESIS; IONIC STRENGTH; ISOTOPE LABELING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

EID: 34548169922     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2007.06.009     Document Type: Article

References (38)

1. Sanger F., Nicklen S., and Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74 (1977) 5463-5468
2. Maxam A.M., and Gilbert W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74 (1977) 560-564
3. Maxam A.M., and Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65 (1980) 499-560
4. Friedman T., and Brown D.M. Base-specific reactions useful for DNA sequencing: methylene blue-sensitized photooxidation of guanine and osmium tetroxide modification of thymine. Nucleic Acids Res. 5 (1978) 615-622
5. Rubin C.M., and Schmid C.W. Pyrimidine-specific chemical reactions useful in DNA sequencing. Nucleic Acids Res. 8 (1980) 4613-4619
6. Krayev A.S. The use of diethylpyrocarbonate for sequencing adenines and guanines in DNA. FEBS Lett. 130 (1981) 19-22
7. Simoncsits A., and Török I. A photoinduced cleavage of DNA useful for determining T residues. Nucleic Acids Res. 10 (1982) 7959-7964
8. Sverdlov E.D., and Kalinina N.F. Interaction of DNA and hydrogen peroxide. A method of localizing pyrimidine bases in DNA. Bioorg. Khim. 9 (1983) 1696-1698
9. Iverson B.L., and Dervan P.B. Adenine specific DNA chemical sequencing reaction. Nucleic Acids Res. 15 (1987) 7823-7830
10. Ambrose B.J.B., and Pless R.C. Analysis of DNA sequences using a single chemical cleavage procedure. Biochemistry 24 (1985) 6194-6200
11. Ambrose B.J.B., and Pless R.C. DNA sequencing: chemical methods. Methods Enzymol. 152 (1987) 522-538
12. Ambrose B.J.B., Pless R.C., and Ayers M.E. Sequence analysis of end-labeled DNA fragments by solvolysis in hot aqueous piperidine solutions. Anal. Biochem. 169 (1988) 151-158
13. Testoff M.A., and Pless R.C. Sequence analysis of end-labeled DNA fragments by solvolysis in aqueous solutions of different amines. Anal. Biochem. 197 (1991) 316-320
14. Negri R., Costanzo G., and Di Mauro E. A single-reaction method for DNA sequence determination. Anal. Biochem. 197 (1991) 389-395
15. Ferraboli S., Negri R., Di Mauro E., and Barlati S. One-lane chemical sequencing of 3′-fluorescent-labeled DNA. Anal. Biochem. 214 (1993) 566-570
16. Negri R., Ferraboli S., Barlati S., and Di Mauro E. Chemical method for DNA sequence determination from the 5′-extremity on PCR amplified fragments. Nucleic Acids Res. 22 (1994) 111-112
17. Di Mauro E., Costanzo G., and Negri R. One-lane chemical sequencing of PCR amplified DNA: the use of terminal transferase and of the base analogue inosine. Nucleic Acids Res. 22 (1994) 3811-3812
18. Negri R., Costanzo G., Saladino R., and Di Mauro E. One-step, one-lane chemical DNA sequencing by N-methylformamide in the presence of metal ions. BioTechniques 21 (1996) 910-917
19. Rosenthal A., Sproat B., Voss H., Stegemann J., Schwager C., Erfle H., Zimmermann J., Coutelle C., and Ansorge W. Automated sequencing of fluorescently labeled DNA by chemical degradation. DNA Seq. 1 (1990) 63-71
20. Saladino R., Crestini C., Mincione E., Costanzo G., Di Mauro E., and Negri R. Mechanism of degradation of 2′-deoxycytidine by formamide: implications for chemical DNA sequencing procedures. Bioorg. Med. Chem. 5 (1997) 2041-2048
21. Albert A., and Brown D.J. Purine studies: I. Stability to acid and alkali. Solubility. Ionization. Comparison with pteridines. J. Chem. Soc. (1954) 2060-2071
22. Jones A.S., Mian A.M., and Walker R.Y. The action of alkali on some purines and their derivatives. J. Chem. Soc. C (1966) 692-694
23. Saladino R., Mincione E., Crestini C., Negri R., Di Mauro E., and Costanzo G. Mechanism of degradation of purine nucleosides by formamide: Implications for chemical DNA sequencing procedures. J. Am. Chem. Soc. 118 (1996) 5615-5619
24. Clauwaert J., and Stockx J. Interactions of polynucleotides and their components: I. Dissociation constants of the bases and their derivatives. Z. Naturforsch. B 23 (1968) 25-30
25. Okawa N., Suyama Y., and Kaji A. Reduced cleavage by sodium hydroxide of methyladenine in DNA sequencing. Nucleic Acids Res. 13 (1985) 7639-7645
26. 2]. J. Am. Chem. Soc. 90 (1968) 319-326
27. Shi Y., and Tyler B.M. Pyrrolidine, a non-controlled substance, can replace piperidine for the chemical sequencing of DNA. Nucleic Acids Res. 17 (1989) 3317
28. Southern E.M. Measurement of DNA length by gel electrophoresis. Anal. Biochem. 100 (1979) 319-323
29. Hetzer H.B., Bates R.G., and Robinson R.A. Dissociation constant of morpholinium ion and related thermodynamic quantities from 0 to 50 °C. J. Phys. Chem. 70 (1966) 2869-2872
30. Emelin E.A., and Raner D. Issledovaniye osnovnykh svoistv tretichnikh aminov. Zh. Fiz. Khim. 50 (1976) 917-919
31. Everett D.H., and Landsman D.A. A redetermination of the dissociation constant of the ammonium ion and the base strength of ammonia in water. Trans. Faraday Soc. 50 (1954) 1221-1229
32. Powell H.K., and Curtis N.F. The free energy, enthalpy, and entropy changes for the neutralization of some C-1-substituted 1,2-diaminoethanes. J. Chem. Soc. B (1966) 1205-1211
33. Everett D.H., and Pinsent B.R.W. The dissociation constants of ethylene diammonium and hexamethylene diammonium ions from 0 degrees to 60 degrees. Proc. Roy. Soc. A 215 (1952) 416-429
34. Fyfe W.S. Complex-ion formations: III. The entropies of reaction of the silver and hydrogen ions with some aliphatic amines. J. Chem. Soc. (1955) 1347-1350
35. Cox M.C., Everett D.H., Landsman D.A., and Munn R.J. The thermodynamics of the acid dissociation of some alkylammonium ions in water. J. Chem. Soc. B (1968) 1373-1379
36. Grob C.A., Kaiser A., and Renk E. Electrostatic effects in the ground and excited states of mesomeric molecules. Chem. Ind. (London) (1957) 598-599
37. Rosenblatt D.H., Hull L.A., De Luca D.C., Davis G.T., Weglein R.C., and Williams H.K.R. Oxidation of amines: II. Substituent effects in chlorine dioxide oxidations. J. Am. Chem. Soc. 89 (1967) 1158-1163
38. Hetzer H.B., Bates R.G., and Robinson R.A. Dissociation constant of pyrrolidinium ion and related thermodynamic quantities from 0 to 50 °C. J. Phys. Chem. 67 (1963) 1124-1127