Sequence effects of aminofluorene-modified DNA duplexes: Thermodynamic and circular dichroism properties

Nucleic Acids Research

Volumn 34, Issue 2, 2006, Pages 755-763

  Meneni, Srinivasa Rao ^a   D'Mello, Rhijuta ^a   Norigian, Gregory ^a   Baker, Gregory ^a   Gao, Lan ^b   Chiarelli, M Paul ^b   Cho, Bongsup P ^a  

^a UNIVERSITY OF RHODE ISLAND   (United States)

^b LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 FLUORENYLAMINE; CARCINOGEN; DOUBLE STRANDED DNA; OLIGODEOXYNUCLEOTIDE;

ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; DNA ADDUCT; DNA CONFORMATION; DNA SEQUENCE; EXCISION REPAIR; GENETIC HETEROGENEITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; THERMODYNAMICS; ULTRAVIOLET RADIATION;

BASE SEQUENCE; CIRCULAR DICHROISM; DNA ADDUCTS; EXONUCLEASES; FLUORENES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; THERMODYNAMICS;

EID: 32644440758     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkj480     Document Type: Article

References (52)

1. Heflich,R.H. and Neft,R.E. (1994) Genetic toxicity of 2-acetylaminofluorene, 2-aminofluorene and some of their metabolites and model metabolites. Mutat. Res., 318, 73-114.
2. Beland,F.A. and Kadlubar,F.F. (1990) Metabolic activation and DNA adducts of aromatic amines and nitroaromatic hydrocarbons. In Cooper,C.S. and Grover,P.L. (eds), Handbook of Experimental Pharmacology. Springer-Verlag and Heidelberg, pp. 267-325.
3. Gillet,L.C. and Scharer,O.D. (2006) Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem. Rev., DOI: 10.1021/ cr040483f, http://dx.doi.org/10.1021/cr040483f.
4. Gillet,L.C., Alzeer,J. and Scharer,O.D. (2005) Site-specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified 'ultra-mild' DNA synthesis. Nucleic Acids Res., 33, 1961-1969.
5. Cui,X.S., Eriksson,L.C. and Moller,L. (1999) Formation and persistence of DNA adducts during and after a long-term administration of 2-nitrofluorene. Mutat Res., 442, 9-18.
6. Pages,V. and Fuchs,R.P. (2002) How DNA lesions are turned into mutations within cells? Oncogene, 21, 8957-8966.
7. Hsu,G.W., Kiefer,J.R., Burnouf,D., Becherel,O.J., Fuchs,R.P. and Beese,L.S. (2004) Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase. J. Biol. Chem., 279, 50280-50285.
8. Dutta,S., Li,Y., Johnson,D., Dzantiev,L., Richardson,C.C., Romano,L.J. and Ellenberger,T. (2004) Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis. Proc. Natl Acad. Sci. USA, 101, 16186-16191.
9. Shibutani,S., Suzuki,N., Tan,X., Johnson,F. and Grollman,A.P. (2001) Influence of flanking sequence context on the mutagenicity of acetylaminofluorene-derived DNA adducts in mammalian cells. Biochemistry, 40, 3717-22.
10. Shibutani,S., Suzuki,N. and Grollman,A.P. (1998) Mutagenic specificity of (acetyl amino) fluorine-derived DNA adducts in mammalian cells. Biochemistry, 37, 12034-12041.
11. Zou,Y., Shell,S.M., Utzat,C.D., Luo,C., Yang,Z., Geacintov,N.E. and Basu,A.K. (2003) Effects of DNA adduct structure and sequence context on strand opening of repair intermediates and incision by UvrABC nuclease. Biochemistry, 42, 12654-12661.
12. Singer,B. and Hang,B. (2000) Nucleic acid sequence and repair: Role of adduct, neighbor bases and enzyme specificity. Carcinogenesis, 21, 1071-1078.
13. Seo,K.Y., Jelinsky,S.A. and Loechler,E.L. (2000) Factors that influence the mutagenic patterns of DNA adducts from chemical carcinogens. Mutat. Res., 463, 215-246.
14. 2-dG benzo[a]pyrene adducts in the identical 5′-CGC sequence used in NMR studies: G→T mutations dominate in each case. Mutagenesis, 20, 441-448.
15. Cho,B.P. (2004) Dynamic conformational heterogeneities of carcinogen-DNA adducts and their mutagenic relevance. J. Environ. Sci. Health C Environ. Carcinog. Ecotoxicol. Rev., 22, 57-90.
16. Patel,D.J., Mao,B., Gu,Z., Hingerty,B.E., Gorin,A., Basu,A.K. and Broyde,S. (1998) Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. Chem. Res. Toxicol., 11, 391-407.
17. Isaacs,R.J. and Spielmann,H.P. (2004) A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility. DNA Repair, 4, 455-464.
18. Geacintov,N.E., Broyde,S., Buterin,T., Naegeli,H., Wu,M., Yan,S. and Patel,D.J. (2002) Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery. Biopolymers, 65, 202-210.
19. 19F NMR Evidence. J. Am. Chem. Soc., 119, 5384-5389.
20. 19F NMR spectroscopy. Biochemistry, 38, 7572-7583.
21. Lee,M.S. and King,C.M. (1981) New syntheses of N-(guanosin-8-yl)-4-aminobiphenyl and its 5′-monophosphate. Chem. Biol. Interact., 34, 239-248.
22. Marques,M.M. and Beland,F.A. (1990) Synthesis, characterization and solution properties of ras sequences modified by arylamine carcinogens at the first base of codon 61. Chem. Res. Toxicol., 3, 559-565.
23. Cho,B.P., Beland,F.A. and Marques,M.M. (1992) NMRstructural studies of a 15-mer DNA duplex from a ras proto-oncogene modified with the carcinogen 2-aminofluorene: Conformational heterogeneity. Biochemistry, 31, 9587-9602.
24. Cho,B.P., Beland,F.A. and Marques,M.M. (1994) NMR structural studies of a 15-mer DNA duplex from a ras protooncogene modified with the carcinogen 2-aminofluorene: Conformational heterogeneity. Biochemistry, 33, 1373-1384.
25. Arghavani,M.B., SantaLucia,J. and Romano,L.J. (1998) Effect of mismatched complementary strands and 5′-change in sequence context on the thermodynamics and structure of benzo[a]pyrene-modified oligonucleotides. Biochemistry, 37, 8575-8583.
26. Marky,L.A. and Breslauer,K.J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
27. Tanaka,F., Kameda,A., Yamamoto,M. and Ohuchi,A. (2004) Thermodynamic parameters based on a nearest-Neighbor model for DNA sequences with a single-bulge loop. Biochemistry, 43, 7143-7150.
28. Allawi,H.T. and SantaLucia,J. (1998) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acid Res., 26, 2694-2701.
29. Brown,K., Harvey,C.A., Turteltaub,K.W. and Shields,S.J. (2003) Structural characterization of carcinogen-modified oligodeoxynucleotide adducts using matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom., 38, 68-79.
30. McLuckey,S.A. and Habibigoudarzi,S. (1993) Decompositions of multiply charged oligonucleotide anions. J. Am. Chem. Soc., 115, 12085-12095.
31. Wu,H. and Aboleneen,H. (2000) Sequencing oligonucleotides with blocked termini using exonuclease digestion and electrospray mass spectrometry. Anal. Biochem., 287, 126-135.
32. Mikulecky,P.J. and Feig,A.L. (2004) Heat capacity changes in RNA folding: Application of perturbation theory to hammerhead ribozyme cold denaturation. Nucleic Acids. Res., 32, 3967-3976.
33. Fasman,G.D. (1996) Circular Dichroism and the Conformational Analysis of Biomolecules. Plenum Press, NY.
34. Nakanishi,K., Berova,N. and Woody,R. (1994) Circular Dichroism: Principle and Applications. VCH, New York, NY.
35. Sagi,J., Hang,B. and Singer,B. (1999) Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: Role of thermodynamic stability imposed by neighbor bases. Chem. Res. Toxicol., 12, 917-923.
36. Sagi,J., Guliaev,A.B. and Singer,B. (2001) 15-mer DNA duplexes containing an abasic site are thermodynamically more stable with adjacent purines than with pyrimidines. Biochemistry, 40, 3859-3868.
37. Baase,W.A. and Johnson,W.C. (1979) Circular dichroism and DNA secondary structure. Nucleic Acids Res., 6, 797-814.
38. Spodheim-Maurizot,M., Saint-Ruf,G. and Leng,M. (1979) Conformational changes induced in DNA by in vitro reaction with N-hydroxy-N-2-aminofluorene. Nucleic Acids Res., 6, 1683-1694.
39. Van Houte,L.P., Westra,J.G., Retel,J. and Van Grondelle,R. (1988) A spectroscopic study of the conformation of poly d(G-C).poly d(G-C) modified with the carcinogenic 2-aminofluorene. Carcinogenesis, 9, 1017-10127.
40. Van Houte,L.P.A., Bokma,J.T., Lutgerink,J.T., Westra,J.G., Retel,J., Van Grondelle,R. and Blok,J. (1987) Anoptical study of the conformation of the aminofluorene-DNA complex. Carcinogenesis, 8, 759-766.
41. Van Houte,L.P.A., Westra,J.G., Retel,J. and Van Grondelle,R. (1991) A circular dichroism study on the conformation of d(CGT) modified with N-acetyl-2-aminofluorene or 2-aminofluorene. J. Biomol. Struct. Dyn., 9, 45-59.
42. Marky,L.A., Rentzeperis,D., Luneva,N.P., Cosman,M., Geacintov,N.E. and Kupke,D.W. (1996) Differential hydration thermodynamics of stereo isomeric DNA-benzo[a]pyrene adducts derived from diol epoxide enantiomers with different tumorigenic potentials. J. Am. Chem. Soc., 118, 3804-3810.
43. Sagi,J., Chenna,A., Hang,B. and Singer,B. (1998) A single cyclic p-benzoquinone adduct can destabilize a DNA oligonucleotide duplex. Chem. Res. Toxicol., 11, 329-334.
44. Gelfand,C.A., Plum,G.E., Grollman,A.P., Johnson,F. and Breslauer,K.J. (1998) The impact of an exocyclic cytosine adduct on DNA duplex properties: Significant thermodynamic consequences despite modest lesion-induced structural alterations. Biochemistry, 37, 12507-12512.
45. 6-ethenoadenine. J. Biol. Chem., 273, 33406-33413.
46. 4-ethenocytosine adduct incorporated into the same sequence contexts. Chem. Res. Toxicol., 13, 839-845.
47. Gelfand,C.A., Plum,G.E., Grollman,A.P., Johnson,F. and Breslauer,K.J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry, 37, 7321-7327.
48. Venkatarangan,L., Sivaprasad,A. and Johnson,F. (2001) Site-specifically located 8-amino-2′-deoxyguanosine: Thermodynamic stability and mutagenic properties in Escherichia coli. Nucleic Acids Res., 29, 1458-1463.
49. Pradhan,P., Jernstrom,B., Seidel,A., Norden,B. and Graslund,A. (1998) Induced circular dichroism of benzo[a]pyrene-7,8-dihydrodiol 9,10-epoxide stereoisomers covalently bound to deoxyribooligonucleotides used to probe equilibrium distribution between groove binding and intercalative adduct conformations. Biochemistry, 37, 4664-4673.
50. Pradhan,P., Tirumala,S., Liu,X., Sayer,J.M., Jerina,D.M. and Yeh,H.J. (2001) Solution structure of a trans-opened (10S)-dA adduct of
51. Mekhovich,O., Tang,M. and Romano,L.J. (1998) Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: Comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. Biochemistry, 37, 571-579.
52. Buterin,T., Meyer,C., Giese,B. and Naegeli,H. (2005) DNA quality control by conformational readout on the undamaged strand of the double helix. Chem. Biol., 12, 913-922.