-
1
-
-
0036308302
-
Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions
-
Rist, M. J., and Marino, J. P. (2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions, Curr. Org. Chem. 6, 775-793.
-
(2002)
Curr. Org. Chem.
, vol.6
, pp. 775-793
-
-
Rist, M.J.1
Marino, J.P.2
-
2
-
-
0346905479
-
Evaluation of fluorescence spectroscopy methods for mapping melted regions of DNA along the transcription pathway
-
Martin, C. T., Újvári, A., and Liu, C. (2003) Evaluation of fluorescence spectroscopy methods for mapping melted regions of DNA along the transcription pathway, Methods Enzymol. 371, 13-33.
-
(2003)
Methods Enzymol.
, vol.371
, pp. 13-33
-
-
Martin, C.T.1
Újvári, A.2
Liu, C.3
-
3
-
-
14644433046
-
One-electron reduction of 2-aminopurine in the aqueous phase. A DFT and pulse radiolysis study
-
Reynisson, J., and Steenken, S. (2005) One-electron reduction of 2-aminopurine in the aqueous phase. A DFT and pulse radiolysis study, Phys. Chem. Chem. Phys. 7, 659-665.
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, pp. 659-665
-
-
Reynisson, J.1
Steenken, S.2
-
4
-
-
23244461855
-
Ultrafast unequilibrated charge transfer: A new channel in the quenching of fluorescent biological probes
-
Wan, C., Xia, T., Becker, H.-C., and Zewail, A. H. (2005) Ultrafast unequilibrated charge transfer: A new channel in the quenching of fluorescent biological probes, Chem. Phys. Lett. 412, 158-163.
-
(2005)
Chem. Phys. Lett.
, vol.412
, pp. 158-163
-
-
Wan, C.1
Xia, T.2
Becker, H.-C.3
Zewail, A.H.4
-
5
-
-
11444261395
-
Fluorescence quenching of 2-aminopurine in dinucleotides
-
Somsen, O. J. G., van Hoek, A., and van Amerongen, H. (2005) Fluorescence quenching of 2-aminopurine in dinucleotides, Chem. Phys. Lett. 402, 61-65.
-
(2005)
Chem. Phys. Lett.
, vol.402
, pp. 61-65
-
-
Somsen, O.J.G.1
Van Hoek, A.2
Van Amerongen, H.3
-
6
-
-
3543088541
-
Stacking-unstacking dynamics of oligodeoxynucleotide trimers
-
Jean, J. M., and Hall, K. B. (2004) Stacking-unstacking dynamics of oligodeoxynucleotide trimers, Biochemistry 43, 10277-10284.
-
(2004)
Biochemistry
, vol.43
, pp. 10277-10284
-
-
Jean, J.M.1
Hall, K.B.2
-
7
-
-
0346158946
-
Ultrafast dynamics in DNA-mediated electron transfer: Base gating and the role of temperature
-
O'Neill, M. A. T., Becker, H.-C., Wan, C., Barton, J. K., and Zewail, A. H. (2003) Ultrafast dynamics in DNA-mediated electron transfer: Base gating and the role of temperature, Angew. Chem., Int. Ed. 42, 5896-5900.
-
(2003)
Angew. Chem., Int. Ed.
, vol.42
, pp. 5896-5900
-
-
O'Neill, M.A.T.1
Becker, H.-C.2
Wan, C.3
Barton, J.K.4
Zewail, A.H.5
-
8
-
-
0037120095
-
Femtosecond charge-transfer dynamics of a modified DNA base: 2-Aminopurine in complexes with nucleotides
-
Fiebig, T., Wan, C., and Zewail, A. H. (2002) Femtosecond charge-transfer dynamics of a modified DNA base: 2-Aminopurine in complexes with nucleotides, ChemPhysChem 3, 781-788.
-
(2002)
ChemPhysChem
, vol.3
, pp. 781-788
-
-
Fiebig, T.1
Wan, C.2
Zewail, A.H.3
-
9
-
-
0034896734
-
Probing the structure and dynamics of a DNA hairpin by ultrafast quenching and fluorescence depolarization
-
Larsen, O. F. A., van Stokkum, I. H. M., Gobets, B., van Grondelle, R., and van Amerongen, H. (2001) Probing the structure and dynamics of a DNA hairpin by ultrafast quenching and fluorescence depolarization, Biophys. J. 81, 1115-1126.
-
(2001)
Biophys. J.
, vol.81
, pp. 1115-1126
-
-
Larsen, O.F.A.1
Van Stokkum, I.H.M.2
Gobets, B.3
Van Grondelle, R.4
Van Amerongen, H.5
-
10
-
-
0034687675
-
Femtosecond direct observation of charge transfer between bases in DNA
-
Wan, C., Fiebig, T., Schieman, O., Barton, J. K., and Zewail, A. H. (2000) Femtosecond direct observation of charge transfer between bases in DNA, Proc. Natl. Acad. Sci. U.S.A. 97, 14052-525 14055.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 14052-52514055
-
-
Wan, C.1
Fiebig, T.2
Schieman, O.3
Barton, J.K.4
Zewail, A.H.5
-
11
-
-
0033555454
-
Electron transfer between bases in double helical DNA
-
Kelley, S. O., and Barton, J. K. (1999) Electron transfer between bases in double helical DNA, Science 283, 375.
-
(1999)
Science
, vol.283
, pp. 375
-
-
Kelley, S.O.1
Barton, J.K.2
-
12
-
-
1642533609
-
Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA dupl000s
-
Larsen, O. F. A., van Stokkum, I. H. M., de Weerd, F. L., Vengris, M., Aravindakumar, C. T., van Grondelle, R., Geacintov, N. E., and van Amerongen, H. (2004) Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA dupl000s, Phys. Chem. Chem. Phys. 6, 154-160.
-
(2004)
Phys. Chem. Chem. Phys.
, vol.6
, pp. 154-160
-
-
Larsen, O.F.A.1
Van Stokkum, I.H.M.2
De Weerd, F.L.3
Vengris, M.4
Aravindakumar, C.T.5
Van Grondelle, R.6
Geacintov, N.E.7
Van Amerongen, H.8
-
13
-
-
0035969981
-
Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine
-
Rachofsky, E. L., Seibert, E., Stivers, J. T., Osman, R., and Ross, J. B. (2001) Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine, Biochemistry 40, 957-967.
-
(2001)
Biochemistry
, vol.40
, pp. 957-967
-
-
Rachofsky, E.L.1
Seibert, E.2
Stivers, J.T.3
Osman, R.4
Ross, J.B.5
-
14
-
-
0025845771
-
Dynamics of mismatched base-pairs in DNA
-
Guest, C. R., Hochstrasser, R. A., Sowers, L. C., and Millar, D. P. (1991) Dynamics of mismatched base-pairs in DNA, Biochemistry 30, 3271-3279.
-
(1991)
Biochemistry
, vol.30
, pp. 3271-3279
-
-
Guest, C.R.1
Hochstrasser, R.A.2
Sowers, L.C.3
Millar, D.P.4
-
15
-
-
0024456523
-
Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: Fluorescence, molecular-dynamics, and NMR-studies
-
Nordlund, T. M., Andersson, T. M., Nilsson, L., Rigler, R., Gräslund, A., and McLaughlin, L. W. (1989) Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: Fluorescence, molecular-dynamics, and NMR-studies, Biochemistry 28, 9095-9103.
-
(1989)
Biochemistry
, vol.28
, pp. 9095-9103
-
-
Nordlund, T.M.1
Andersson, T.M.2
Nilsson, L.3
Rigler, R.4
Gräslund, A.5
McLaughlin, L.W.6
-
16
-
-
0037027319
-
2-Aminopurine electronic structure and fluorescence properties in DNA
-
Jean, J. M., and Hall, K. B. (2002) 2-Aminopurine electronic structure and fluorescence properties in DNA, Biochemistry 41, 13152-13161.
-
(2002)
Biochemistry
, vol.41
, pp. 13152-13161
-
-
Jean, J.M.1
Hall, K.B.2
-
17
-
-
0035793105
-
2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
-
Jean, J. M., and Hall, K. B. (2001) 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking, Proc. Natl. Acad. Sci. U.S.A. 98, 37-41.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 37-41
-
-
Jean, J.M.1
Hall, K.B.2
-
18
-
-
0000189651
-
Density-functional thermochemistry. 3. The role of exact exchange
-
Becke, A. D. (1993) Density-functional thermochemistry. 3. The role of exact exchange, J. Chem. Phys. 98, 5648-5652.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
19
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density
-
Lee, C. T., Yang, W. T., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density, Phys. Rev. B 37, 785-789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.T.1
Yang, W.T.2
Parr, R.G.3
-
20
-
-
0000703066
-
Toward a systematic molecular-orbital theory for excited-states
-
Foresman, J. B., Head-Gordon, M., Pople, J. A., and Frisch, M. J. (1992) Toward a systematic molecular-orbital theory for excited-states, J. Phys. Chem. 96, 135-149.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 135-149
-
-
Foresman, J.B.1
Head-Gordon, M.2
Pople, J.A.3
Frisch, M.J.4
-
21
-
-
1242338125
-
Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides
-
Berry, D. A., Jung, K. Y., Wise, D. S., Sercel, A. D., Pearson, W. H., Mackie, H., Randolph, J. B., and Somers, R. L. (2004) Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides, Tetrahedron Lett. 45, 2457-2461.
-
(2004)
Tetrahedron Lett.
, vol.45
, pp. 2457-2461
-
-
Berry, D.A.1
Jung, K.Y.2
Wise, D.S.3
Sercel, A.D.4
Pearson, W.H.5
Mackie, H.6
Randolph, J.B.7
Somers, R.L.8
-
22
-
-
33344477201
-
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation
-
10.1261/rna.2165806
-
Tinsley, R. A., and Walter, N. G. (2006) Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation, RNA (10.1261/rna.2165806).
-
(2006)
RNA
-
-
Tinsley, R.A.1
Walter, N.G.2
-
23
-
-
33746609515
-
-
Wavefunction Inc., Irvine, CA
-
Spartan02 (2002) Wavefunction Inc., Irvine, CA.
-
(2002)
Spartan02
-
-
-
24
-
-
17144414126
-
Properties of a new fluorescent cytosine analogue, pyrrolocytosine
-
Thompson, K. C., and Miyake, N. (2005) Properties of a new fluorescent cytosine analogue, pyrrolocytosine, J. Phys. Chem. B 109, 6012-6019.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6012-6019
-
-
Thompson, K.C.1
Miyake, N.2
-
25
-
-
0039530337
-
-
Sándorfy, C., Ed. Kluwer Academic Publishers, Dordrecht, The Netherlands
-
Sándorfy, C. (1999) in The role of Rydberg states in spectroscopy and photochemistry (Sándorfy, C., Ed.) Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
(1999)
The Role of Rydberg States in Spectroscopy and Photochemistry
-
-
Sándorfy, C.1
-
26
-
-
0141704726
-
-
Gaussian, Inc., Pittsburgh, PA
-
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J. J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2003) Gaussian 03, revision B.04, Gaussian, Inc., Pittsburgh, PA.
-
(2003)
Gaussian 03, Revision B.04
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Montgomery Jr., J.A.7
Vreven, T.8
Kudin, K.N.9
Burant, J.C.10
Millam, J.M.11
Iyengar, S.S.12
Tomasi, J.J.13
Barone, V.14
Mennucci, B.15
Cossi, M.16
Scalmani, G.17
Rega, N.18
Petersson, G.A.19
Nakatsuji, H.20
Hada, M.21
Ehara, M.22
Toyota, K.23
Fukuda, R.24
Hasegawa, J.25
Ishida, M.26
Nakajima, T.27
Honda, Y.28
Kitao, O.29
Nakai, H.30
Klene, M.31
Li, X.32
Knox, J.E.33
Hratchian, H.P.34
Cross, J.B.35
Adamo, C.36
Jaramillo, J.37
Gomperts, R.38
Stratmann, R.E.39
Yazyev, O.40
Austin, A.J.41
Cammi, R.42
Pomelli, C.43
Ochterski, J.W.44
Ayala, P.Y.45
Morokuma, K.46
Voth, G.A.47
Salvador, P.48
Dannenberg, J.J.49
Zakrzewski, V.G.50
Dapprich, S.51
Daniels, A.D.52
Strain, M.C.53
Farkas, O.54
Malick, D.K.55
Rabuck, A.D.56
Raghavachari, K.57
Foresman, J.B.58
Ortiz, J.V.59
Cui, Q.60
Baboul, A.G.61
Clifford, S.62
Cioslowski, J.63
Stefanov, B.B.64
Liu, G.65
Liashenko, A.66
Piskorz, P.67
Komaromi, I.68
Martin, R.L.69
Fox, D.J.70
Keith, T.71
Al-Laham, M.A.72
Peng, C.Y.73
Nanayakkara, A.74
Challacombe, M.75
Gill, P.M.W.76
Johnson, B.77
Chen, W.78
Wong, M.W.79
Gonzalez, C.80
Pople, J.A.81
more..
-
27
-
-
0003594187
-
-
Swiss Center for Scientific Computing, Manno, Switzerland
-
Flükiger, P., Lüthi, H. P., Portmann, S., and Weber, J. (2000) MOLEKEL 4.0, Swiss Center for Scientific Computing, Manno, Switzerland.
-
(2000)
MOLEKEL 4.0
-
-
Flükiger, P.1
Lüthi, H.P.2
Portmann, S.3
Weber, J.4
-
29
-
-
0000045103
-
Calculations and characterization of the electronic spectra of DNA bases based on ab initio MP2 geometries of different tautomeric forms
-
Broo, A., and Holmén, A. (1997) Calculations and characterization of the electronic spectra of DNA bases based on ab initio MP2 geometries of different tautomeric forms, J. Phys. Chem. A 101, 3589-3600.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3589-3600
-
-
Broo, A.1
Holmén, A.2
-
30
-
-
0035121180
-
CASSCF investigation of electronic excited states of 2-aminopurine
-
Rachofsky, E. L., Ross, J. B. A., Krauss, M., and Osman, R. (2001) CASSCF investigation of electronic excited states of 2-aminopurine, J. Phys. Chem. A 105, 190-197.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 190-197
-
-
Rachofsky, E.L.1
Ross, J.B.A.2
Krauss, M.3
Osman, R.4
-
31
-
-
28544448728
-
Single-reference ab initio methods for the calculation of excited states of large molecules
-
Dreuw, A., and Head-Gordon, M. (2005) Single-reference ab initio methods for the calculation of excited states of large molecules, Chem. Rev. 105, 4009-4037.
-
(2005)
Chem. Rev.
, vol.105
, pp. 4009-4037
-
-
Dreuw, A.1
Head-Gordon, M.2
-
32
-
-
33344455128
-
The application of CAMB3LYP to the charge-transfer band problem of the zincbacteriochlorin-bacteriochlorin complex
-
Kobayashi, R., and Amos, R. D. (2006) The application of CAMB3LYP to the charge-transfer band problem of the zincbacteriochlorin-bacteriochlorin complex, Chem. Phys. Lett. 420, 106-109.
-
(2006)
Chem. Phys. Lett.
, vol.420
, pp. 106-109
-
-
Kobayashi, R.1
Amos, R.D.2
-
33
-
-
0035799966
-
Excited-state energy transfer processes in phenylene- and biphenylene-linked and directly-linked zinc-(II) and free-base hybrid diporphyrins
-
Cho, H. S., Jeong, D. H., Yoon, M.-C., Kim, Y. H., Kim, Y.-R., Kim, D., Jeoung, S. C., Kim, S. K., Aratani, N., Shinmori, H., and Osuka, A. (2001) Excited-State Energy Transfer Processes in Phenylene- and Biphenylene-Linked and Directly-Linked Zinc-(II) and Free-Base Hybrid Diporphyrins, J. Phys. Chem. A 105, 4200-4210.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 4200-4210
-
-
Cho, H.S.1
Jeong, D.H.2
Yoon, M.-C.3
Kim, Y.H.4
Kim, Y.-R.5
Kim, D.6
Jeoung, S.C.7
Kim, S.K.8
Aratani, N.9
Shinmori, H.10
Osuka, A.11
-
34
-
-
0000162043
-
Theoretical determination of electron affinity and ionization potential of DNA and RNA bases
-
Russo, N., Toscano, M., and Grand, A. (2000) Theoretical determination of electron affinity and ionization potential of DNA and RNA bases, J. Comput. Chem. 21, 1243-1250.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1243-1250
-
-
Russo, N.1
Toscano, M.2
Grand, A.3
-
35
-
-
0029773892
-
Theoretical studies of GG-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5′-localization of HOMO of stacked GG bases in B-from DNA
-
Sugiyama, H., and Saito, I. (1996) Theoretical studies of GG-specific photocleavage of DNA via electron transfer: significant lowering of ionization potential and 5′-localization of HOMO of stacked GG bases in B-from DNA, J. Am. Chem. Soc. 118, 7063-7068.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 7063-7068
-
-
Sugiyama, H.1
Saito, I.2
-
36
-
-
0035969959
-
Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence
-
Rachofsky, E. L., Osman, R., and Ross, J. B. A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence. Biochemistry 40, 946-956.
-
(2001)
Biochemistry
, vol.40
, pp. 946-956
-
-
Rachofsky, E.L.1
Osman, R.2
Ross, J.B.A.3
-
37
-
-
36849126497
-
Relationship between absorption intensity and fluorescence lifetime of molecules
-
Strickler, S. J., and Berg, R. A., (1962) Relationship between absorption intensity and fluorescence lifetime of molecules, J. Chem. Phys. 37, 814-822.
-
(1962)
J. Chem. Phys.
, vol.37
, pp. 814-822
-
-
Strickler, S.J.1
Berg, R.A.2
-
38
-
-
0003516749
-
-
Oxford University Press, New York
-
Atkins, P. W., and de Paula, J. (2001) Physical Chemistry, 7th ed., Oxford University Press, New York.
-
(2001)
Physical Chemistry, 7th Ed.
-
-
Atkins, P.W.1
De Paula, J.2
-
39
-
-
0014669561
-
Fluorescence studies of nucleotides and polynucleotides
-
Ward, D. C., Reich, E., and Stryer, L. (1969) Fluorescence studies of nucleotides and polynucleotides, J. Biol. Chem. 244, 1228-1237.
-
(1969)
J. Biol. Chem.
, vol.244
, pp. 1228-1237
-
-
Ward, D.C.1
Reich, E.2
Stryer, L.3
-
40
-
-
0031011001
-
Electronic transition moments of 2-aminopurine
-
Holmén, A., Nordén, B., and Albinsson, B. (1997) Electronic transition moments of 2-aminopurine, J. Am. Chem. Soc. 119, 3114-3121.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 3114-3121
-
-
Holmén, A.1
Nordén, B.2
Albinsson, B.3
-
41
-
-
9144265600
-
Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements
-
Neely, R. K., Magennis, S. W., Dryden, D. T. F., and Jones, A. C. (2004) Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements, J. Phys. Chem. B 108, 17606-17610.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 17606-17610
-
-
Neely, R.K.1
Magennis, S.W.2
Dryden, D.T.F.3
Jones, A.C.4
-
42
-
-
14644388252
-
Electronic spectra of 2-aminopurine and 2,6-diaminopurine: Phototautomerism and fluorescence reabsorption
-
Santhosh, C., and Mishra, P. C. (1991) Electronic spectra of 2-aminopurine and 2,6-diaminopurine: Phototautomerism and fluorescence reabsorption, Spectrochim. Acta 47A, 1685-1693.
-
(1991)
Spectrochim. Acta
, vol.47 A
, pp. 1685-1693
-
-
Santhosh, C.1
Mishra, P.C.2
|