메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages 7.20.1-7.20.18

NMR analysis of base-pair opening kinetics in DNA

Author keywords

Base pair opening; Exchange kinetics; High Q probes; Imino exchange; Longitudinal water relaxation NMR; Nucleic acids; Radiation damping; T1

Indexed keywords

DOUBLE STRANDED DNA; WATER; DNA;

EID: 84922599665     PISSN: 19349270     EISSN: 19349289     Source Type: Journal    
DOI: 10.1002/0471142700.nc0720s59     Document Type: Article
Times cited : (15)

References (46)
  • 1
    • 0042424322 scopus 로고
    • Spin-echo method for measuring relaxation times in two-line NMR spectra
    • Alexander, S. 1961. Spin-echo method for measuring relaxation times in two-line NMR spectra. Rev. Sci. Instrum. 32:1066-1067.
    • (1961) Rev. Sci. Instrum , vol.32 , pp. 1066-1067
    • Alexander, S.1
  • 3
    • 9744262003 scopus 로고
    • Nuclear magnetic resonance in liquids under high pressure
    • Benedek, G.B. and Purcell, E.M. 1954. Nuclear magnetic resonance in liquids under high pressure. J. Chem. Phys. 22:2003-2012.
    • (1954) J. Chem. Phys , vol.22 , pp. 2003-2012
    • Benedek, G.B.1    Purcell, E.M.2
  • 4
    • 36149018202 scopus 로고
    • Radiation damping in magnetic resonance experiments
    • Bloembergen, N. and Pound, R.V. 1954. Radiation damping in magnetic resonance experiments. Phys. Rev. 95:8-12.
    • (1954) Phys. Rev , vol.95 , pp. 8-12
    • Bloembergen, N.1    Pound, R.V.2
  • 5
    • 20144383176 scopus 로고    scopus 로고
    • Effect of 6-thioguanine on the stability of duplex DNA
    • Bohon, J. and Carlos, R. 2005. Effect of 6-thioguanine on the stability of duplex DNA. Nucleic Acids Res. 33:2880-2886.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2880-2886
    • Bohon, J.1    Carlos, R.2
  • 7
    • 33847534249 scopus 로고
    • Effects of diffusion on free precession in nuclear magnetic resonance experiments
    • Carr, H.Y. and Purcell, E.M. 1954. Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys. Rev. 94:630.
    • (1954) Phys. Rev , vol.94 , pp. 630
    • Carr, H.Y.1    Purcell, E.M.2
  • 8
    • 16644365966 scopus 로고    scopus 로고
    • Sequencedependence of the energetics of opening of AT basepairs in DNA
    • Chen, C. and Russu, I.M. 2004. Sequencedependence of the energetics of opening of AT basepairs in DNA. Biophys. J. 87:2545-2551.
    • (2004) Biophys. J , vol.87 , pp. 2545-2551
    • Chen, C.1    Russu, I.M.2
  • 9
    • 51249195542 scopus 로고
    • Proton relaxation in pure liquids and in liquids containing paramagnetic gases in solution
    • Chiarotti, G., Cristiani, G., and Giulotto, L. 1955. Proton relaxation in pure liquids and in liquids containing paramagnetic gases in solution. Nuovo Cimento C 1:863-873.
    • (1955) Nuovo Cimento C , vol.1 , pp. 863-873
    • Chiarotti, G.1    Cristiani, G.2    Giulotto, L.3
  • 10
    • 80053405018 scopus 로고    scopus 로고
    • Hidden in plain sight: Subtle effects of the 8-oxoguanine lesion on the structure, dynamics, and thermodynamics of a 15-base pair oligodeoxynucleotide duplex
    • Crenshaw, C.M., Wade, J.E., Arthanari, H., Frueh, D., Lane, B.F., and Nunez, M.E. 2011. Hidden in plain sight: Subtle effects of the 8-oxoguanine lesion on the structure, dynamics, and thermodynamics of a 15-base pair oligodeoxynucleotide duplex. Biochemistry 50:8463-8477.
    • (2011) Biochemistry , vol.50 , pp. 8463-8477
    • Crenshaw, C.M.1    Wade, J.E.2    Arthanari, H.3    Frueh, D.4    Lane, B.F.5    Nunez, M.E.6
  • 11
    • 0033006629 scopus 로고    scopus 로고
    • Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR
    • Dhavan, G.M., Lapham, J., Yang, S., and Crothers, D.M. 1999. Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR. J. Mol. Biol. 288:659-671.
    • (1999) J. Mol. Biol , vol.288 , pp. 659-671
    • Dhavan, G.M.1    Lapham, J.2    Yang, S.3    Crothers, D.M.4
  • 12
    • 0033548682 scopus 로고    scopus 로고
    • High base pair opening rates in tracts of GC base pairs
    • Dornberger, U., Leijon, M., and Fritzsche, H. 1999. High base pair opening rates in tracts of GC base pairs. J. Biol. Chem. 274:6957-6962.
    • (1999) J. Biol. Chem , vol.274 , pp. 6957-6962
    • Dornberger, U.1    Leijon, M.2    Fritzsche, H.3
  • 13
    • 0029731421 scopus 로고    scopus 로고
    • DNA melting investigated by differential scanning calorimetry and Raman spectroscopy
    • Duguid, J.G., Bloomfield, V.A., Benevides, J.M., and Thomas, G.J. Jr. 1996. DNA melting investigated by differential scanning calorimetry and Raman spectroscopy. Biophys. J. 71:3350-3360.
    • (1996) Biophys. J , vol.71 , pp. 3350-3360
    • Duguid, J.G.1    Bloomfield, V.A.2    Benevides, J.M.3    Thomas, G.J.4
  • 14
    • 34948859038 scopus 로고    scopus 로고
    • Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA
    • Every, A.E. and Russu, I.M. 2007. Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA. Biopolymers 87:165-173.
    • (2007) Biopolymers , vol.87 , pp. 165-173
    • Every, A.E.1    Russu, I.M.2
  • 15
    • 48149103751 scopus 로고    scopus 로고
    • Influence of magnesium ions on spontaneous opening of DNA base pairs
    • Every, A.E. and Russu, I.M. 2008. Influence of magnesium ions on spontaneous opening of DNA base pairs. J. Phys. Chem. B 112:7689-7695.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 7689-7695
    • Every, A.E.1    Russu, I.M.2
  • 16
    • 84874731309 scopus 로고    scopus 로고
    • Opening dynamics of 8-oxoguanine in DNA
    • Every, A.E. and Russu, I.M. 2013. Opening dynamics of 8-oxoguanine in DNA. J. Mol. Recognit. 26:175-180.
    • (2013) J. Mol. Recognit , vol.26 , pp. 175-180
    • Every, A.E.1    Russu, I.M.2
  • 17
    • 0030037648 scopus 로고    scopus 로고
    • Basecatalysis of imino proton exchange in DNA: Effects of catalyst upon DNA structure and dynamics
    • Folta-Stogniew, E. and Russu, I.M. 1996. Basecatalysis of imino proton exchange in DNA: Effects of catalyst upon DNA structure and dynamics. Biochemistry 35:8439-8449.
    • (1996) Biochemistry , vol.35 , pp. 8439-8449
    • Folta-Stogniew, E.1    Russu, I.M.2
  • 18
    • 79952083192 scopus 로고    scopus 로고
    • Unique dynamic properties of DNA duplexes containing interstrand cross-links
    • Friedman, J.I., Jiang, Y.L., Miller, P.S., and Stivers, J.T. 2011. Unique dynamic properties of DNA duplexes containing interstrand cross-links. Biochemistry 50:882-890.
    • (2011) Biochemistry , vol.50 , pp. 882-890
    • Friedman, J.I.1    Jiang, Y.L.2    Miller, P.S.3    Stivers, J.T.4
  • 19
    • 0028864424 scopus 로고
    • Studies of base pair kinetics by NMR measurement of proton exchange
    • Gueron, M. and Leroy, J.-L. 1995. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261:383-413.
    • (1995) Methods Enzymol , vol.261 , pp. 383-413
    • Gueron, M.1    Leroy, J.-L.2
  • 20
    • 0023256126 scopus 로고
    • A single model of DNA base-pair opening drives imino proton exchange
    • Gueron, M., Kochoyan, M., and Leroy, J.L. 1987. A single model of DNA base-pair opening drives imino proton exchange. Nature 328:89-92.
    • (1987) Nature , vol.328 , pp. 89-92
    • Gueron, M.1    Kochoyan, M.2    Leroy, J.L.3
  • 22
    • 0025325784 scopus 로고
    • Processes of base-pair opening and proton exchange in Z-DNA
    • Kochoyan, M., Leroy, J.L., and Gueron, M. 1990. Processes of base-pair opening and proton exchange in Z-DNA. Biochemistry 29:4799-4805.
    • (1990) Biochemistry , vol.29 , pp. 4799-4805
    • Kochoyan, M.1    Leroy, J.L.2    Gueron, M.3
  • 24
    • 75849143765 scopus 로고    scopus 로고
    • Measurement of hydrogen exchange times of the RNA imino protons using by phase-modulated CLEAN chemical exchange spectroscopy
    • Lee, Y.M., Lee, E.H., Seo, Y.J., Kang, Y.M., Ha, J.H., Kim, H.E., and Lee, J.H. 2009. Measurement of hydrogen exchange times of the RNA imino protons using by phase-modulated CLEAN chemical exchange spectroscopy. Bull. Korean Chem. Soc. 30:2197-2198.
    • (2009) Bull. Korean Chem. Soc , vol.30 , pp. 2197-2198
    • Lee, Y.M.1    Lee, E.H.2    Seo, Y.J.3    Kang, Y.M.4    Ha, J.H.5    Kim, H.E.6    Lee, J.H.7
  • 25
    • 0026674753 scopus 로고
    • Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes
    • Leijon, M. and Groeslund, A. 1992. Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes. Nucleic Acids Res. 20:5339-5343.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5339-5343
    • Leijon, M.1    Groeslund, A.2
  • 26
    • 0026598551 scopus 로고
    • Proton exchange in DNAluzopeptin and DNA-echinomycin bisintercalation complexes:Rates and processes of base-pair opening
    • Leroy, J.L., Gao, X., Misra, V., Gueron, M., and Patel, D.J. 1992. Proton exchange in DNAluzopeptin and DNA-echinomycin bisintercalation complexes:Rates and processes of base-pair opening. Biochemistry 31:1407-1415.
    • (1992) Biochemistry , vol.31 , pp. 1407-1415
    • Leroy, J.L.1    Gao, X.2    Misra, V.3    Gueron, M.4    Patel, D.J.5
  • 27
    • 0031286135 scopus 로고    scopus 로고
    • Understanding radiation damping in a simple way
    • Mao, X.-A. and Ye, C.-H. 1997. Understanding radiation damping in a simple way. Concepts Magn. Reson. 9:173-187.
    • (1997) Concepts Magn. Reson , vol.9 , pp. 173-187
    • Mao, X.-A.1    Ye, C.-H.2
  • 28
    • 0000201502 scopus 로고
    • Radiation damping effects of transverse relaxation time measurements
    • Mao, X.-A., Guo, J.-X., and Ye, C.-H. 1994a. Radiation damping effects of transverse relaxation time measurements. Chem. Phys. Lett. 227:65-68.
    • (1994) Chem. Phys. Lett , vol.227 , pp. 65-68
    • Mao, X.-A.1    Guo, J.-X.2    Ye, C.-H.3
  • 29
    • 0000201496 scopus 로고
    • Radiation damping effects on spin-lattice relaxation time measurements
    • Mao, X.-A., Guo, J.-X., and Ye, C.-H. 1994b. Radiation damping effects on spin-lattice relaxation time measurements. Chem. Phys. Lett. 222:417-421.
    • (1994) Chem. Phys. Lett , vol.222 , pp. 417-421
    • Mao, X.-A.1    Guo, J.-X.2    Ye, C.-H.3
  • 30
    • 0000706229 scopus 로고
    • The 1-1 hard pulse: A simple and effective method ofwater resonance suppression in FT 1H NMR
    • Marius Clore, G., Kimber, B.J., and Gronenborn, A.M. 1983. The 1-1 hard pulse: A simple and effective method ofwater resonance suppression in FT 1H NMR. J. Magn. Res. 54:170-173.
    • (1983) J. Magn. Res , vol.54 , pp. 170-173
    • Marius Clore, G.1    Kimber, B.J.2    Gronenborn, A.M.3
  • 31
    • 0026737976 scopus 로고
    • Kinetics and energetics of base-pair opening in 5'-d (CGCGAATTCGCG)-3' and a substituted dodecamer containing G-T mismatches
    • Moe, J.G. and Russu, I.M. 1992. Kinetics and energetics of base-pair opening in 5'-d (CGCGAATTCGCG)-3' and a substituted dodecamer containing G-T mismatches. Biochemistry 31:8421-8428.
    • (1992) Biochemistry , vol.31 , pp. 8421-8428
    • Moe, J.G.1    Russu, I.M.2
  • 32
    • 0542406119 scopus 로고
    • Selective excitation in Fourier transform nuclear magnetic resonance
    • Morris, G.A. and Freeman, R. 1978. Selective excitation in Fourier transform nuclear magnetic resonance. J. Magn. Res. 29:433-462.
    • (1978) J. Magn. Res , vol.29 , pp. 433-462
    • Morris, G.A.1    Freeman, R.2
  • 33
    • 79952074754 scopus 로고    scopus 로고
    • Dynamics of uracil and 5-fluorouracil in DNA
    • Parker, J.B. and Stivers, J.T. 2010. Dynamics of uracil and 5-fluorouracil in DNA. Biochemistry 50:612-617.
    • (2010) Biochemistry , vol.50 , pp. 612-617
    • Parker, J.B.1    Stivers, J.T.2
  • 34
    • 0034924446 scopus 로고    scopus 로고
    • Investigation of unusual DNA motifs
    • Phan, A.-T., Gueron, M., and Leroy, J.-L. 2000. Investigation of unusual DNA motifs. Methods Enzymol. 338:341-371.
    • (2000) Methods Enzymol , vol.338 , pp. 341-371
    • Phan, A.-T.1    Gueron, M.2    Leroy, J.-L.3
  • 35
    • 0027997526 scopus 로고
    • DNA lesions: A thermodynamic perspective
    • Plum, G. and Breslauer, K.J. 1994. DNA lesions: A thermodynamic perspective. Ann. N.Y. Acad. Sci. 726:45-56.
    • (1994) Ann. N.Y. Acad. Sci , vol.726 , pp. 45-56
    • Plum, G.1    Breslauer, K.J.2
  • 36
    • 31444443924 scopus 로고    scopus 로고
    • NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases
    • Priyakumar, U.D. and MacKerell, A.D. 2006. NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J. Am. Chem. Soc. 128:678-679.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 678-679
    • Priyakumar, U.D.1    MacKerell, A.D.2
  • 37
    • 0035146646 scopus 로고    scopus 로고
    • Forceinduced melting of the DNA double helix 1. Thermodynamic analysis
    • Rouzina, I. and Bloomfield, V.A. 2001. Forceinduced melting of the DNA double helix 1. Thermodynamic analysis. Biophys. J. 80:882-893.
    • (2001) Biophys. J , vol.80 , pp. 882-893
    • Rouzina, I.1    Bloomfield, V.A.2
  • 38
    • 3943107573 scopus 로고    scopus 로고
    • Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints
    • Sancar, A., Lindsey-Boltz, L.A., Unsal-Kacmaz, K., and Linn, S. 2004. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Ann. Rev. Biochem. 73:39-85.
    • (2004) Ann. Rev. Biochem , vol.73 , pp. 39-85
    • Sancar, A.1    Lindsey-Boltz, L.A.2    Unsal-Kacmaz, K.3    Linn, S.4
  • 39
    • 33751196656 scopus 로고
    • Diffusion and nuclear spin relaxation in water
    • Simpson, J.H. and Carr, H.Y. 1958. Diffusion and nuclear spin relaxation in water. Phys. Rev. 111:1201-1202.
    • (1958) Phys. Rev , vol.111 , pp. 1201-1202
    • Simpson, J.H.1    Carr, H.Y.2
  • 41
    • 58149363306 scopus 로고
    • Suppression of radiation damping in multidimensional NMR experiments using magnetic field gradients
    • Sklenar, V. 1995. Suppression of radiation damping in multidimensional NMR experiments using magnetic field gradients. J. Magn. Res. A 114:132-135.
    • (1995) J. Magn. Res. A , vol.114 , pp. 132-135
    • Sklenar, V.1
  • 42
    • 0035979354 scopus 로고    scopus 로고
    • Imino proton exchange and base-pair kinetics in RNA duplexes
    • Snoussi, K. and Leroy, J.L. 2001. Imino proton exchange and base-pair kinetics in RNA duplexes. Biochemistry 40:8898-8904.
    • (2001) Biochemistry , vol.40 , pp. 8898-8904
    • Snoussi, K.1    Leroy, J.L.2
  • 43
    • 84887080183 scopus 로고    scopus 로고
    • Site-specific stabilization of DNA by a tethered major groove amine, 7-Aminomethyl-7-deaza-2ä≤ deoxyguanosine
    • Szulik, M.W., Voehler, M.W., Ganguly, M., Gold, B., and Stone, M.P. 2013. Site-specific stabilization of DNA by a tethered major groove amine, 7-Aminomethyl-7-deaza-2ä≤ deoxyguanosine. Biochemistry 52:7659-7668.
    • (2013) Biochemistry , vol.52 , pp. 7659-7668
    • Szulik, M.W.1    Voehler, M.W.2    Ganguly, M.3    Gold, B.4    Stone, M.P.5
  • 44
    • 77950029639 scopus 로고    scopus 로고
    • Comparison of spin-lattice relaxation measurements made in the presence of strong radiation damping
    • Taylor, R.E. and Peterson, R.D. 2010. Comparison of spin-lattice relaxation measurements made in the presence of strong radiation damping. J. Mol. Struct. 970:155-159.
    • (2010) J. Mol. Struct , vol.970 , pp. 155-159
    • Taylor, R.E.1    Peterson, R.D.2
  • 46
    • 0040184162 scopus 로고    scopus 로고
    • Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: Evidence for a secondary long-lived open state of the base pair
    • Warmlander, S., Sen, A., and Leijon, M. 2000. Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: Evidence for a secondary long-lived open state of the base pair. Biochemistry 39:607-615.
    • (2000) Biochemistry , vol.39 , pp. 607-615
    • Warmlander, S.1    Sen, A.2    Leijon, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.