Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine

Artificial DNA: PNA and XNA

Volumn 5, Issue FEB, 2014, Pages

  Chen, Frederic Y H ^a   Park, Soyoung ^b   Otomo, Haruka ^b   Sakashita, Sohei ^b   Sugiyama, Hiroshi ^b,c,d  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b KYOTO UNIVERSITY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

8 methylguanine; B Z transition; CD spectra; Z form DNA

Indexed keywords

8 METHYLGUANIDINE; METHYLGUANIDINE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; 8-METHYLGUANINE; DNA B; DNA Z; GUANINE; OLIGODEOXYRIBONUCLEOTIDE; 8 METHYLGUANINE; GUANINE DERIVATIVE; OLIGOMER;

ARTICLE; CHIRALITY; CIRCULAR DICHROISM; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; DNA SYNTHESIS; SOLVATION; STRUCTURE ANALYSIS; ANALOGS AND DERIVATIVES; CHEMISTRY; NUCLEOTIDE SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA MODIFICATION; MOLECULAR MODEL;

BASE SEQUENCE; CIRCULAR DICHROISM; DNA, B-FORM; DNA, Z-FORM; GUANINE; OLIGODEOXYRIBONUCLEOTIDES;

EID: 84899435739     PISSN: 1949095X     EISSN: 19490968     Source Type: Journal    
DOI: 10.4161/adna.28226     Document Type: Article

References (18)

1. Rich A, Nordheim A, Wang AHJ. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem 1984; 53: 791-846; PMID: 6383204; http://dx. doi. org/10. 1146/annurev. bi. 53. 070184. 004043.
2. Rich A, Zhang S. Timeline: Z-DNA: the long road to biological function. Nat Rev Genet 2003; 4: 566-72; PMID: 12838348; http://dx. doi. org/10. 1038/nrg1115.
3. Ha SC, Lowenhaupt K, Rich A, Kim Y-G, Kim KK. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. J Am Chem Soc 2009; 131: 11485-91; PMID: 19637911.
4. Kang Y-M, Bang J, Lee E-H, Ahn H-C, Seo Y-J, Kim KK, Kim Y-G, Choi B-S, Lee J-H. NMR spectroscopic elucidation of the B-Z transition of a DNA double helix induced by the Z alpha domain of human ADAR1. J Am Chem Soc 2009; 131: 11485-91; PMID: 19637911; http://dx. doi. org/10. 1021/ja902654u.
5. Yang L, Wang S, Tian T, Zhou X. Advancements in Z-DNA: development of inducers and stabilizers for B to Z transition. Curr Med Chem 2012; 19: 557-68; PMID: 22204344; http://dx. doi. org/10. 2174/092986712798918806.
6. Sugiyama H, Kawai K, Matsunaga A, Fujimoto K, Saito I, Robinson H, Wang AH. Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions. Nucleic Acids Res 1996; 24: 1272-8; PMID: 8614630; http://dx. doi. org/10. 1093/nar/24. 7. 1272.
7. Xu Y, Ikeda R, Sugiyama H. 8-Methylguanosine: a powerful Z-DNA stabilizer. J Am Chem Soc 2003; 125: 13519-24; PMID: 14583048; http://dx. doi. org/10. 1021/ja036233i.
8. Moradi M, Babin V, Roland C, Sagui C. Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study. Nucleic Acids Res 2013; 41: 33-43; PMID: 23104380; http://dx. doi. org/10. 1093/nar/gks1003.
9. Pohl FM, Jovin TM. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol 1972; 67: 375-96; PMID: 5045303; http://dx. doi. org/10. 1016/0022-2836(72)90457-3.
10. Ornstein RL, Rein R, Breen DL, Macelroy RD. An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking. Biopolymers 1978; 17: 2341-60; http://dx. doi. org/10. 1002/bip. 1978. 360171005.
11. Huguet JM, Bizarro CV, Forns N, Smith SB, Bustamante C, Ritort F. Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci U S A 2010; 107: 15431-6; PMID: 20716688; http://dx. doi. org/10. 1073/pnas. 1001454107.
12. Soumpasis DM. Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions. Proc Natl Acad Sci U S A 1984; 81: 5116-20; PMID: 6591181; http://dx. doi. org/10. 1073/pnas. 81. 16. 5116.
13. Saenger W, Hunter WN, Kennard O. DNA conformation is determined by economics in the hydration of phosphate groups. Nature 1986; 324: 385-8; PMID: 3785407; http://dx. doi. org/10. 1038/324385a0.
14. Sindhikara DJ, Hirata F. Analysis of biomolecular solvation sites by 3D-RISM theory. J Phys Chem B 2013; 117: 6718-23; PMID: 23675899; http://dx. doi. org/10. 1021/jp4046116.
15. Du Q, Beglov D, Roux B. Solvation free energy of polar and nonpolar molecules in water: an extended interaction site integral equation theory in three dimensions. J Phys Chem B 2000; 104: 796-805; http://dx. doi. org/10. 1021/jp992712l.
16. Maruyama Y, Yoshida N, Hirata F. Electrolytes in biomolecular systems studied with the 3D-RISM/RISM theory. Interdiscip Sci 2011; 3: 290-307; PMID: 22179763; http://dx. doi. org/10. 1007/s12539-011-0104-7.
17. Lee Y-K, Lee J, Choi JH, Seok C. Contribution of counterion entropy to the salt-induced transition between B-DNA and Z-DNA. Bull Korean Chem Soc 2012; 33: 3719-26; http://dx. doi. org/10. 5012/bkcs. 2012. 33. 11. 3719.
18. Westman E, Strömberg R. Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, 3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). Nucleic Acids Res 1994; 22: 2430-1; PMID: 7518583; http://dx. doi. org/10. 1093/nar/22. 12. 2430.