DNA base flipping by a base pair-mimic nucleoside

Nucleic Acids Research

Volumn 33, Issue 22, 2005, Pages 7111-7119

  Nakano, Shu Ichi ^a   Uotani, Yuuki ^a   Uenishi, Kazuya ^b   Fujii, Masayuki ^b   Sugimoto, Naoki ^a  

^a KONAN UNIVERSITY   (Japan)

^b KINKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; AMIDE; AROMATIC HYDROCARBON; BENZENE DERIVATIVE; CYTOSINE; DEOXYADENOSINE DERIVATIVE; DNA BASE; DOUBLE STRANDED DNA; GUANINE; NAPHTHYL GROUP; NUCLEOSIDE; NUCLEOTIDE; PURINE; THYMINE;

ARTICLE; BASE PAIRING; BIOTECHNOLOGY; CHEMICAL BOND; CIRCULAR DICHROISM; CONFORMATION; DNA HELIX; FLUORESCENCE; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; PRIORITY JOURNAL; THERMODYNAMICS;

BASE PAIRING; CIRCULAR DICHROISM; DEOXYADENOSINES; DNA; NUCLEIC ACID CONFORMATION; SPECTROMETRY, FLUORESCENCE; THERMODYNAMICS;

EID: 31144440174     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki1018     Document Type: Article

References (41)

1. Turner,D.H., Sugimoto,N., Kierzek,R. and Dreiker,S.D. (1987) Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc., 109, 3783-3784.
2. Bommarito,S.V., Peyret,N. and SantaLucia,J.Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
3. Moody,E.M. and Bevilacqua,P.C. (2003) Folding of a stable DNA motif involves a highly cooperative network of interactions. J. Am. Chem. Soc., 125, 16285-16293.
4. Morales,J.C. and Kool,E.T. (2000) Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry, 39, 12979-12988.
5. Kool,E.T., Morales,J.C. and Guckian,K.M. (2000) Mimicking the structure and function of DNA: Insights into DNA stability and replication. Angew. Chem. Int. Ed. Engl., 39, 990-1099.
6. Hendrickson,C.L., Devine,K.G. and Benner,S.A. (2004) Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2′-deoxyadenosine. Nucleic Acids Res., 32, 2241-2250.
7. Berger,M., Luzzi,A., Henry,A.A. and Romesberg,F.E. (2002) Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues. J. Am. Chem. Soc., 124, 1222-1226.
8. Liu,H., Gao,J., Maynard,L., Saito,D. and Kool,E,T. (2004) Toward a new genetic system with expanded dimensions: Size-expanded analogues of deoxyadenosine and thymidine. J. Am. Chem. Soc., 126, 1102-1009.
9. Arkin,M.R., Stemp,E.D., Pulver,S.C. and Barton,J.K. (1997) Long-range oxidation of guanine by Ru(III) in duplex DNA. Chem. Biol., 4, 389-400.
10. Kuzuya,A., Mizoguchi,R., Morisawa,F., Machida,K. and Komiyama,M. (2002) Metal ion-induced site-selective RNA hydrolysis by use of acridine-bearing oligonucleotide as cofactor. J. Am. Chem. Soc., 124, 6887-6894.
11. Lermer,L., Roupioz,Y., Ting,R. and Perrin,D.M. (2002) Toward an RNaseA mimic: A DNAzyme with imidazoles and cationic amines. J. Am. Chem. Soc., 124, 9960-9961.
12. Lewis,F.D., Liu,J., Weigel,W., Rettig,W., Kumikov,I.V. and Beratan.D.N. (2002) Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA. Proc. Natl Acad. Sci. USA, 99, 12536-12541.
13. Tanaka,K., Tengeiji,A., Kato,T., Toyama,N. and Shionoya,M. (2003) A discrete self-assembled metal array in artificial DNA. Science, 299, 1212-1213.
14. Liu,H., Gao,J., Lynch,S.R., Saito,Y.D., Maynard,L. and Kool,E.T. (2003) A four-base paired genetic helix with expanded size. Science, 302, 868-871.
15. Amann,N., Huber,R. and Wagenknecht,H.A. (2004) Phenanthridinium as an artificial base and charge donor in DNA. Angew. Chem. Int. Ed. Engl., 43, 1845-1847.
16. Okamoto,A., Ichiba,T. and Saito,I. (2004) Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J. Am. Chem. Soc., 126, 8364-8365.
17. Nakano,S., Uotani,Y., Nakashima,S., Anno,Y., Fujii,M. and Sugimoto,N. (2003) Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group. J. Am. Chem. Soc., 125, 8086-8087.
18. Kierzek,R., Caruthers,M.H., Longfellow,C.E., Swinton,D., Turner,D.H. and Freier,S.M. (1986) Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry, 25, 7840-7846.
19. Sugimoto,N., Nakano,S., Yoneyama,M. and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
20. Nakano,S., Kanzaki,T. and Sugimoto,N. (2004) Influences of ribonucleotide on a duplex conformation and its thermal stability: Study with the chimeric RNA-DNA strands. J. Am. Chem. Soc., 126, 1088-1095.
21. Richards,E.G. (1975) Use of tables in calculation of absorption, optical rotatory dispersion and circular dichroism of polyribonucleotides. In Fasman,G.D. (ed.), Handbook of Biochemistry and Molecular Biology, 3rd edn. CRC Press, Cleveland, OH, Vol. 1, pp. 596-603.
22. Marky,L.A. and Breslauer,K.J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
23. Puglisi,J.D. and Tinoco,I.,Jr (1989) Absorbance melting curves of RNA. Methods Enzymol., 180, 304-325.
24. 2. Biochemistry, 32, 3583-3595.
25. Allawi,H.T. and SantaLucia,J.,Jr (1998) Nearest neighbor thermodynairtic parameters for internal G.A. mismatches in DNA. Biochemistry, 37, 2170-2179.
26. Allawi,H.T. and SantaLucia,J.,Jr (1998) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: Sequence dependence and pH effects. Biochemistry, 37, 9435-9444.
27. Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J.,Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry, 38, 3468-3477.
28. Barsky,D., Foloppe,N., Ahmadia,S., Wilson,D.M.III. and MacKerell,A.D.,Jr (2000) New insights into the structure of abasic DNA from molecular dynamics simulations. Nucleic Acids Res., 28, 2613-2626.
29. Sugimoto,N., Nakano,M. and Nakano,S. (2000) Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry, 39, 11270-11281.
30. 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.
31. Sági,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.
32. Pompizi,I., Häberli,A. and Leumann,C.J. (2000) Oligodeoxynucleotides containing conformationally constrained abasic sites: A UV and fluorescence spectroscopic investigation on duplex stability and structure. Nucleic Acids Res., 28, 2702-2708.
33. Nakano,S., Uotani,Y., Uenishi,K., Fujii,M. and Sugimoto,N. (2005) Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside. J. Am. Chem. Soc., 127, 518-519.
34. Lipscomb,L.A., Zhou,F.X., Presnell,S.R., Woo,R.J., Peek,M.E., Plaskon,R.P. and Williams,L.D. (1996) Structure of DNA-porphyrin complex. Biochemistry, 35, 2818-2823.
35. Tuma,J., Connors,W.H., Stitelman,D.H. and Richert,C. (2002) On the effect of covalently appended quinolones on termini of DNA duplexes. J. Am. Chem. Soc., 124, 4236-4246.
36. David,A., Bleimling,N., Beuck,C., Lehn,J.-M., Weinhold,E. and Teulade-Fichou,M.-P. (2003) DNA mismatch-specific base flipping by a bisacridine macrocycle. Chembiochem., 4, 1326-1331.
37. Singh,I., Hecker,W., Prasad,A.K., Parmar,V.S. and Seitz,O. (2002) Local disruption of DNA-base stacking by bulky base surrogates. Chem. Commun., 7, 500-501.
38. Beuck,C., Singh,I., Bhattacharya,A., Hecker,W., Parmar,V.S., Seitz,O. and Weinhold,E. (2003) Polycyclic aromatic DNA-base surrogates: high-affinity binding to an adenine-specific base-flipping DNA methyltransferase. Angew. Chem. Int. Ed. Engl., 42, 3958-3960.
39. Jiang,Y.L., Kwon,K. and Stivers,J.T. (2001) Turning On uracil-DNA glycosylase using a pyrene nucleotide switch. J. Biol. Chem., 276, 42347-42354.
40. Jiang,Y.L., Stivers,J.T. and Song,F. (2002) Base-flipping mutations of uracil DNA glycosylase: Substrate rescue using a pyrene nucleotide wedge. Biochemistry, 41, 11248-11254.
41. Kwon,K., Jiang,Y.L. and Stivers,J.T. (2003) Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pYrene base pair. Chem. Biol., 10, 351-359.