Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes

Journal of Fluorescence

Volumn 19, Issue 6, 2009, Pages 1111-1118

  Banerjee, Debapriya ^a   Makhal, Abhinandan ^a   Pal, Samir Kumar ^a  

^a S N BOSE NATIONAL CENTRE FOR BASIC SCIENCES   (India)

Author keywords

Femtosecond resolved hydration dynamics; Hoechst; Sequence dependent molecular recognition

Indexed keywords

FEMTOSECONDS; HOECHST; HYDRATION DYNAMICS; SEQUENCE-DEPENDENT;

DICHROISM; DNA; DYNAMICS; GENES; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; NUCLEIC ACIDS; PROTEINS;

HYDRATION;

DNA; HISTONE; PIBENZIMOL; WATER;

ANIMAL; ARTICLE; CATTLE; CHEMISTRY; CIRCULAR DICHROISM; CONFORMATION; FLUORESCENCE; FLUORESCENCE POLARIZATION; KINETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; ROTATION;

ANIMALS; BASE SEQUENCE; BISBENZIMIDAZOLE; CATTLE; CIRCULAR DICHROISM; DNA; FLUORESCENCE; FLUORESCENCE POLARIZATION; HISTONES; KINETICS; NUCLEIC ACID CONFORMATION; ROTATION; WATER;

EID: 72149104057     PISSN: 10530509     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10895-009-0512-9     Document Type: Article

References (30)

1. PE Pjura K Grzeskowiak RE Dickerson 1987 Binding of Hoechst 33258 to the minor groove of B-DNA J Mol Biol 197 257 271 10.1016/0022-2836(87)90123-9 10.1016/0022-2836(87)90123-9 1:CAS:528:DyaL1cXivVGr 2445998 (Pubitemid 17152378)
2. 2 An examination of propeller twist and minor-groove water structure at 2•2 Å resolution J Mol Biol 226 1161 1173 10.1016/0022-2836(92)91059-X 10.1016/0022-2836(92)91059-X 1:CAS:528:DyaK3sXjsVGrsQ%3D%3D 1518049
3. 2and its complex with propamidine from NMR and molecular modelling Biochim Biophys Acta 1350 205 220 1:CAS:528: DyaK2sXktlOisg%3D%3D 9048890
4. 2 duplex: calorimetric and spectroscopic studies J Mol Biol 271 244 257 10.1006/jmbi.1997.1170 10.1006/jmbi.1997.1170 1:CAS:528:DyaK2sXls12rs78%3D 9268656 (Pubitemid 27344746)
5. 2: volumetric, calorimetric, and spectroscopic characterizations Biochemistry 44 9785 9794 10.1021/bi047374f 10.1021/bi047374f 1:CAS:528:DC%2BD2MXlt12nurY%3D 16008363 (Pubitemid 40994372)
6. PL Privalov AI Dragan C Crane-Robinson KJ Breslauer DP Remeta CASA Minetti 2007 What drives proteins into the major or minor grooves of DNA? J Mol Biol 365 1 9 10.1016/j.jmb.2006.09.059 10.1016/j.jmb.2006.09.059 1:CAS:528:DC%2BD28Xht1KnsrvM 17055530 (Pubitemid 44821203)
7. SK Pal L Zhao AH Zewail 2003 Water at DNA surfaces: ultrafast dynamics in minor groove recognition Proc Natl Acad Sci USA 100 8113 8118 10.1073/pnas.1433066100 10.1073/pnas.1433066100 1:CAS:528:DC%2BD3sXlsFGns7o%3D 12815094 (Pubitemid 36842507)
8. SK Pal AH Zewail 2004 Dynamics of water in biological recognition Chem Rev 104 2099 2123 10.1021/cr020689l 10.1021/cr020689l 1:CAS:528: DC%2BD2cXisFaqs7k%3D 15080722
9. D Vlieghe J Sponer LV Meervelt 1999 Crystal structure of d(GGCCAATTGG) complexed with DAPI reveal novel binding mode Biochemisty 38 16443 16451 10.1021/bi9907882 10.1021/bi9907882 1:CAS:528:DyaK1MXnsFOnsrY%3D (Pubitemid 30007496)
10. JR Quintana AA Lipanov RE Dickerson 1991 Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G Biochemistry 30 10294 10306 10.1021/bi00106a030 10.1021/bi00106a030 1:CAS:528:DyaK3MXlvFOku70%3D 1718416
11. AW Wood CM Nunn A Czarny DW Boykin S Neidle 1995 Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2 Nucleic Acids Res 23 3678 3684 10.1093/nar/23.18.3678 10.1093/nar/23.18.3678 1:CAS:528:DyaK2MXoslynsbs%3D 7478996
12. DG Brown MR Sanderson E Garman S Neidle 1992 Crystal structure of a berenil-d(CGCAAATTTGCG) complex: an example of drug-DNA recognition based on sequence-dependent structural features J Mol Biol 226 481 490 10.1016/0022-2836(92)90962-J 10.1016/0022-2836(92)90962-J 1:CAS:528: DyaK3sXisVKqtbw%3D 1640462
13. N Spink DG Brown JV Skelly S Neidle 1994 Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex Nucleic Acids Res 22 1607 1612 10.1093/nar/22.9.1607 10.1093/nar/22.9.1607 1:CAS:528:DyaK2cXlslSntLs%3D 7515488
14. R Jin KJ Breslauer 1988 Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)] poly[d(AT)]duplex Proc Natl Acad Sci USA 85 8939 8942 10.1073/pnas.85.23.8939 10.1073/pnas.85.23. 8939 1:CAS:528:DyaL1MXhtVyisbs%3D 2461559 (Pubitemid 19001820)
15. D Banerjee SK Pal 2007 Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove J Phys Chem B 111 10833 10838 10.1021/jp074697n 10.1021/jp074697n 1:CAS:528:DC%2BD2sXosVCrs7o%3D 17676797 (Pubitemid 47497629)
16. O'Connor DV, Philips D (1984) Time correlated single photon counting. Academic, London
17. D Banerjee SK Pal 2007 Simultaneous binding of minor groove binder and intercalator to dodecamer DNA: importance of relative orientation of donor and acceptor in FRET J Phys Chem B 111 5047 5052 10.1021/jp0715427 10.1021/jp0715427 1:CAS:528:DC%2BD2sXksFart7Y%3D 17455977 (Pubitemid 46854488)
18. D Banerjee SK Pal 2006 Ultrafast charge transfer and solvation of DNA minor groove binder: Hoechst 33258 in restricted environments Chem Phys Lett 432 257 262 10.1016/j.cplett.2006.10.018 10.1016/j.cplett.2006.10.018 1:CAS:528:DC%2BD28Xht1Wltb3O (Pubitemid 44773740)
19. R Sarkar SK Pal 2007 Interaction of Hoechst 33258 and ethidium with histone1-DNA condensates Biomacromolecules 8 3332 3339 10.1021/bm700690p 10.1021/bm700690p 1:CAS:528:DC%2BD2sXhtFSjt7jE 17902690 (Pubitemid 350193731)
20. D Zhong SK Pal AH Zewail 2001 Femtosecond studies of protein-DNA binding and dynamics: histone I ChemPhysChem 2 219 227 10.1002/1439-7641(20010417)2: 4<219::AID-CPHC219>3.0.CO;2-K 10.1002/1439-7641(20010417)2:4<219::AID- CPHC219>3.0.CO;2-K 1:CAS:528:DC%2BD3MXjtFykuro%3D
21. 2 by Hoechst 33258: a high field NMR study Biochemistry 29 10181 10190 10.1021/bi00496a005 10.1021/bi00496a005 1:CAS:528:DyaK3cXlvVKksLg%3D 1703003
22. Privé GG, Yanagi K, Dickerson RE (1991) Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J Mol Biol 217:177-199
23. DG Alexeev AA Lipanov IY Skuratovskii 1987 Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove Nature 325 821 823 10.1038/325821a0 10.1038/325821a0 1:CAS:528:DyaL2sXhtleqt70%3D 3821870 (Pubitemid 17056482)
24. JKA Kamal T Xia SK Pal L Zhao AH Zewail 2004 Enzyme functionality and solvation of subtilisin carlsberg: From hours to femtoseconds Chem Phys Lett 387 209 215 10.1016/j.cplett.2004.02.011 10.1016/j.cplett.2004.02.011 1:CAS:528:DC%2BD2cXitl2mt7s%3D
25. SK Pal L Zhao T Xia AH Zewail 2003 Site and sequence selective ultrafast hydration of DNA Proc Natl Acad Sci USA 100 13746 13751 10.1073/pnas.2336222100 10.1073/pnas.2336222100 1:CAS:528:DC%2BD3sXpsFGisr4%3D 14603035 (Pubitemid 37499137)
26. W Gu BP Schoenborn 1995 Molecular dynamics simulation of hydration in myoglobin Proteins 22 20 26 10.1002/prot.340220104 10.1002/prot.340220104 1:CAS:528:DyaK2MXmtl2lsrg%3D 7675783
27. V Ramakrishnan 1997 Histone structure and the organization of the nucleosome Annu Rev Biophys Biomol Struct 26 83 112 10.1146/annurev.biophys.26. 1.83 10.1146/annurev.biophys.26.1.83 1:CAS:528:DyaK2sXktFCjtb8%3D 9241414 (Pubitemid 27255368)
28. TJ Richmond CA Davey 2003 The structure of DNA in the nucleosome core Nature 423 145 150 10.1038/nature01595 10.1038/nature01595 1:CAS:528: DC%2BD3sXjsVOrtb0%3D 12736678 (Pubitemid 36569532)
29. A Laigle L Chinsky PY Turpin J Liquier E Taillandier 1982 In vitro recognition of DNA base pairs by histones in histone-DNA complexes and reconstituted core particles: an ultraviolet resonance Raman study Nucleic Acids Res 10 7395 7404 10.1093/nar/10.22.7395 10.1093/nar/10.22.7395 1:CAS:528:DyaL3sXjtVShtw%3D%3D 7155896
30. JH Moon SK Kim U Sehlstedt A Rodger B Norden 1996 DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258 Biopolymers 38 593 606 10.1002/(SICI)1097-0282(199605)38:5<593::AID- BIP5>3.0.CO;2-N 10.1002/(SICI)1097-0282(199605)38:5<593::AID-BIP5>3.0. CO;2-N 1:CAS:528:DyaK28Xit1OjtLg%3D 8722229 (Pubitemid 26119645)