|
1
|
Ito Y, Kondo H, Shiota Y, Yoshizawa K. Theoretical Analysis of the Reaction Mechanism of Biotin Carboxylase. J Chem Theory Comput 2008; 4:366-74. [DOI: 10.1021/ct700260f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuko Ito
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroki Kondo
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
|
2
|
Zhang RY, Pang DW, Zhang ZL, Yan JW, Yao JL, Tian ZQ, Mao BW, Sun SG. Investigation of Ordered ds-DNA Monolayers on Gold Electrodes. J Phys Chem B 2002. [DOI: 10.1021/jp025817o] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong-Ying Zhang
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Dai-Wen Pang
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Zhi-Ling Zhang
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Jia-Wei Yan
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Jian-Lin Yao
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Zhong-Qun Tian
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Bing-Wei Mao
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| | - Shi-Gang Sun
- Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China, and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
|
3
|
Liu M, Yang L, Deng W, Su M, Wang C, Lin SB, Kan LS, Bai C. Effect of selective substitution of 5-bromocytosine on conformation of DNA triple helices. J Biomol Struct Dyn 1998; 15:895-903. [PMID: 9619512 DOI: 10.1080/07391102.1998.10508211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Three triplex DNAs containing 5-bromocytosine[BrC] were studied by vibrational spectroscopy and molecular modelling. Firstly, three oligodeoxypyrimidines of 5'-(TC)3-T4-(BrCT)3 [CBrC], 5'-(TBrC)3-T4-(CT)3 [BrCC] and 5'-(TBrC)3-T4-(BrCT)3 [BrCBrC] were synthesized and then reacted with an oligodeoxypurine of 5'-(AG)3 at pH=4.5 in phosphate buffer respectively to form three comparative hairpin triplex named CY,YC and YY. The results of FT-Raman and IR revealed that YY is almost in A-like form, CY and YC are combinations of A-like form and B-like form, but A-form dominates in CY while B-form is equivalent as A-form in YC. The result is consistent with the theoretical analysis.
Collapse
Affiliation(s)
- M Liu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing
| | | | | | | | | | | | | | | |
Collapse
|
|
4
|
Fang Y, Wei Y, Bai C, Tang Y, Lin SB, Kan LS. Hydrated water molecules of pyrimidine/purine/pyrimidine DNA triple helices as revealed by FT-IR spectroscopy: a role of cytosine methylation. J Biomol Struct Dyn 1997; 14:485-93. [PMID: 9172648 DOI: 10.1080/07391102.1997.10508147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hydrated water molecules of pyrimidine/purine/pyrimidine DNA hairpin triplex was studied by a comparison of triplex (CC.AG6) formed by a host oligodeoxypyrimidine of 5'-d(TC)3T4(CT)3(CC) with a target hexadeoxypurine 5'-d(AG)3(AG6) strand and by triplexes (MM.AG6, MC.AG6, and CM.AG6) formed by oligonucleotides with the exact sequences as above except 5-methylcytosine replaced all (MM), 5' end half (MC), and 3' end half (CM) cytosine bases in CC via FT-IR spectroscopy in hydrated film. Results revealed that: (i) all these triplexes have a similar hydration pattern, in which water molecules probably bound in the N7 sites of adenines and guanines in the Crick-Hoogsteen groove, and to the methyl group of thymidines in the Watson-Hoogsteen groove. There are also some bound water molecules found at the O2 sites of thymines in both Watson-Crick and Crick-Hoogsteen grooves. (ii) In the CC.AG6 triplex the S-type sugars are always dominant in all hydrated states, whereas in MM.AG6 triplex the relative population of the N-type sugars is very close to that of the S-type between 86% and 66% of humidity. Furthermore, the sugar conformation in two partially modified triplexes (CM.AG6, and MC.AG6) are dominant by the N-type at lower humidity. This phenomenon might reflect that the degree of bound water varies among the binding sites of bases. (iii) The effect of introducing a methyl group on cytosine is to generate a spine of hydrophobic region in MM (MC and MC). The enlarging hydrophobic area not only increase the stability in solution, and also the stability in sodium hydrated films of the pyrimidine/purine/pyrimidine hairpin triplexes.
Collapse
Affiliation(s)
- Y Fang
- Institute of Chemistry, Academia Sinica, Beijing, China
| | | | | | | | | | | |
Collapse
|
|
5
|
Fang Y, Wei Y, Bai C, Kan LS. Surface-Enhanced Fourier Transform Raman Scattering from a DNA Triple Helix Poly[dA]·2Poly[dT] at a Silver Electrode: Beyond the Short-Range Mechanism. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9623150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ye Fang
- Institute of Chemistry, Academia Sinica, Beijing 100080, China
| | - Ying Wei
- Institute of Chemistry, Academia Sinica, Beijing 100080, China
| | - Chunli Bai
- Institute of Chemistry, Academia Sinica, Beijing 100080, China
| | - Lou-sing Kan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| |
Collapse
|