The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation

被引：95

作者：

Yamaguchi, Hiroshi ^{[1
]}

Sebera, Jakub ^{[2
]}

Kondo, Jiro ^{[3
]}

Oda, Shuji ^{[1
]}

Komuro, Tomoyuki ^{[1
]}

Kawamura, Takuya ^{[1
]}

Dairaku, Takenori ^{[1
]}

Kondo, Yoshinori ^{[1
]}

Okamoto, Itaru ^{[4
]}

Ono, Akira ^{[4
]}

Burda, Jaroslav V. ^{[5
]}

Kojima, Chojiro ^{[6
]}

Sychrovsky, Vladimir ^{[2
]}

Tanaka, Yoshiyuki ^{[1
]}

机构：

[1] Tohoku Univ, Grad Sch Pharmaceut Sci, Lab Mol Transformat, Aoba Ku, Sendai, Miyagi 9808578, Japan

[2] Acad Sci Czech Republ, Inst Organ Chem & Biochem, CR-16610 Prague 6, Czech Republic

[3] Sophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Chiyoda Ku, Tokyo 1028554, Japan

[4] Kanagawa Univ, Dept Mat & Life Chem, Fac Engn, Kanagawa Ku, Yokohama, Kanagawa 2218686, Japan

[5] Charles Univ Prague, Fac Math & Phys, Dept Chem Phys & Opt, CR-12116 Prague 2, Czech Republic

[6] Osaka Univ, Inst Prot Res, Suita, Osaka 5650871, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / 06期

关键词：

DUPLEX; BINDING; MERCURY(II); IONS; COMPLEXES; CRYSTAL;

D O I：

10.1093/nar/gkt1344

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg-II-mediated T-T base pairs (thymine-Hg-II-thymine, T-Hg-II-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg-II-T base pairs whose chemical structure was determined with the N-15 NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (delta S) for the T-Hg-II-T base pair formation. The positive delta S value arises owing to the Hg-II dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg-II and revealed arrangement of T-Hg-II-T base pairs in metallo-DNA.

引用

页码：4094 / 4099

页数：6

共 53 条

[1] PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Davis, Ian W. ;

Echols, Nathaniel ;

Headd, Jeffrey J. ;

Hung, Li-Wei ;

Kapral, Gary J. ;

Grosse-Kunstleve, Ralf W. ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert ;

Read, Randy J. ;

Richardson, David C. ;

Richardson, Jane S. ;

Terwilliger, Thomas C. ;

Zwart, Peter H. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221

[2]

[Anonymous], X PLOR VERSION 3 1 M

[3] Structure of a copper-mediated base pair in DNA [J].

Atwell, S ;

Meggers, E ;

Spraggon, G ;

Schultz, PG .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2001, 123 (49) :12364-12367

[4] Detection of Mercury-TpT Dinucleotide Binding by Raman Spectra: A Computational Study [J].

Benda, Ladislav ;

Straka, Michal ;

Sychrovsky, Vladimir ;

Bour, Petr ;

Tanaka, Yoshiyuki .

JOURNAL OF PHYSICAL CHEMISTRY A, 2012, 116 (32) :8313-8320

[5] On the role of mercury in the non-covalent stabilisation of consecutive U-HgII-U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids [J].

Benda, Ladislav ;

Straka, Michal ;

Tanaka, Yoshiyuki ;

Sychrovsky, Vladimir .

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, 13 (01) :100-103

[6] METAL ION-BIOMOLECULE INTERACTIONS .12. H-1 AND C-13 NMR EVIDENCE FOR THE PREFERRED REACTION OF THYMIDINE OVER GUANOSINE IN EXCHANGE AND COMPETITION REACTIONS WITH MERCURY(II) AND METHYLMERCURY(II) [J].

BUNCEL, E ;

BOONE, C ;

JOLY, H ;

KUMAR, R ;

NORRIS, AR .

JOURNAL OF INORGANIC BIOCHEMISTRY, 1985, 25 (01) :61-73

[7] Electrontransfer through DNA and metal-containing DNA [J].

Carell, T ;

Behrens, C ;

Gierlich, J .

ORGANIC & BIOMOLECULAR CHEMISTRY, 2003, 1 (13) :2221-2228

[8] DNA-metal base pairs [J].

Clever, Guido H. ;

Kaul, Corinna ;

Carell, Thomas .

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2007, 46 (33) :6226-6236

[9] Antiferromagnetic Coupling of Stacked CuII-Salen Complexes in DNA [J].

Clever, Guido H. ;

Reitmeier, Stephan J. ;

Carell, Thomas ;

Schiemann, Olav .

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2010, 49 (29) :4927-4929

[10]

Frisch M. J., 2016, Gaussian 03 Revision B.03

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