Energetics of Z-DNA binding protein-mediated helicity reversals in DNA, RNA, and DNA-RNA duplexes

Journal of Physical Chemistry B

Volumn 117, Issue 44, 2013, Pages 13866-13871

  Bae, Sangsu ^a   Kim, Yuyoung ^a   Kim, Doyoun ^b   Kim, Kyeong Kyu ^b   Kim, Yang Gyun ^c   Hohng, Sungchul ^a  

^a Seoul National University   (South Korea)

^b Sungkyunkwan University School of Medicine   (South Korea)

^c Sungkyunkwan University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEINS; DNA-RNA HYBRIDS; DOUBLE HELIX; MOLECULAR LEVELS; OPERATIONAL MECHANISM; SINGLE-MOLECULE FLUORESCENCES; TECHNICAL LIMITATIONS; THERMODYNAMICS AND KINETICS;

ENERGY TRANSFER; PROTEINS; RNA; STABILIZATION;

DNA;

DNA BINDING PROTEIN; DNA Z; RNA;

ARTICLE; CHEMISTRY; CONFORMATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; METABOLISM; PROTEIN BINDING; TEMPERATURE; THERMODYNAMICS;

DNA, Z-FORM; DNA-BINDING PROTEINS; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RNA; TEMPERATURE; THERMODYNAMICS;

EID: 84887774394     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp409862j     Document Type: Article

References (36)

1. Rich, A. DNA Comes in Many Forms Gene 1993, 135, 99-109
2. Pohl, F. M.; Jovin, J. M. Salt-Induced Co-operative Conformational Change of a Synthetic DNA: Equilibrium and Kinetic Studies with Poly (dG-dC) J. Mol. Biol. 1972, 67, 375-396
3. Thamann, T. J.; Lord, R. C.; Wang, A. H. -J.; Rich, A. The High Salt Form of Poly(dG-dC)·Poly(dG-dC) Is Left-Handed Z-DNA: Raman Spectra of Crystals and Solutions Nucleic Acids Res. 1981, 9, 5443-5457
4. Wang, A. H.-J.; Quigley, G. J.; Kolpak, F. J.; Crawford, J. L.; Van Boom, J. H.; Van Der Marel, G.; Rich, A. Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution Nature 1979, 282, 680-686
5. Haniford, D. B.; Pulleyblank, D. E. Facile Transition of Poly[d(TG)·d(CA)] into a Left-Handed Helix in Physiological Conditions Nature 1983, 302, 632-634
6. Rich, A.; Nordheim, A.; Wang, A. H. -J. The Chemistry and Biology of Left-Handed Z-DNA Annu. Rev. Biochem. 1984, 53, 197-846
7. Peck, L. J.; Nordheim, A.; Rich, A.; Wang, J. C. Flipping of Cloned d(pCpG)n·d(pCpG)n DNA Sequences From Right- to Left-Handed Helical Structure by Salt, Co(III), or Negative Supercoiling Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 4560-4564
8. Fuertes, M. A.; Cepeda, V.; Alonso, C.; Pérez, J. M. Molecular Mechanisms for the B-Z Transition in the Example of Poly[d(G-C)·d(G-C)] Polymers. A Critical Review Chem. Rev. 2006, 106, 2045-2064
9. Wu, Z.; Tian, T.; Yu, J.; Weng, X.; Liu, Y.; Zhou, Z. Formation of Sequence-Independent Z-DNA Induced by a Ruthenium Complex at Low Salt Concentrations Angew. Chem., Int. Ed. 2011, 50, 11962-11967
10. Behe, M.; Zimmerman, S.; Felsenfeld, G. Changes In the Helical Repeat of Poly(dG-m5dC)·Poly(dG-m5dC) and Poly(dG-dC)·Poly(dG-dC) Associated with the B-Z Rransition Nature 1981, 293, 233-235
11. Rahmouni, A. R.; Wells, R. D. Stabilization of Z-DNA in Vivo by Localized Supercoiling Science 1989, 246, 358-363
12. Herbert, A.; Lowenhaupt, K.; Spitzner, J.; Rich, A. Chicken Double-Stranded RNA Adenosine Deaminase Has Apparent Specificity for Z-DNA Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 7550-7554
13. Hamada, H.; Kakunaga, T. Potential Z-DNA Forming Sequences Are Highly Dispersed in the Human Genome Nature 1982, 298, 396-398
14. Schroth, G. P.; Chou, P. J.; Ho, P. S. Mapping Z-DNA in the Human Genome. Computer-Aided Mapping Reveals a Nonrandom Distribution of Potential Z-DNA-Forming Sequences in Human Genes J. Biol. Chem. 1992, 267, 11846-11855
15. Rich, A.; Zhang, S. Z-DNA: The Long Road to Biological Function Nat. Rev. Genet. 2003, 4, 566-572
16. Schwartz, T.; Behlke, J.; Lowenhaupt, K.; Heinemann, U.; Rich, A. Structure of the DLM-1-Z-DNA Complex Reveals a Conserved Family of Z-DNA-Binding Proteins Nat. Struct. Biol. 2001, 8, 761-765
17. Rothenburg, S.; Deigendesch, N.; Dittmar, K.; Koch-Nolte, F.; Haag, F.; Lowenhaupt, K.; Rich, A. A PKR-Like Eukaryotic Initiation Factor 2α Kinase from Zebrafish Contains Z-DNA Binding Domains Instead of dsRNA Binding Domains Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 1602-1607
18. Kim, Y. -G.; Muralinath, M.; Brandt, T.; Pearcy, M.; Hauns, K.; Lowenhaupt, K.; Jacobs, B. L.; Rich, A. A Role for Z-DNA Binding in Vaccinia Virus Pathogenesis Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6974-6979
19. Ha, S. C.; Lokanath, N. K.; Van Quyen, D.; Wu, C. A.; Lowenhaupt, K.; Rich, A.; Kim, Y. -G.; Kim, K. K. A Poxvirus Protein Forms a Complex with Left-Handed Z-DNA: Crystal Structure of a Yatapoxvirus Zα Bound to DNA Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14367-14372
20. Takaoka, A.; Wang, Z.; Choi, M. K.; Yanai, H.; Negishi, H.; Ban, T.; Lu, Y.; Miyagishi, M.; Kodama, T.; Honda, K. DAI (DLM-1/ZBP1) is a Cytosolic DNA Sensor and an Activator of Innate Immune Response Nature 2007, 448, 501-505
21. Brown, B. A., II; Lowenhaupt, K.; Wilbert, C. M.; Hanlon, E. B.; Rich, A. The Zα Domain of the Editing Enzyme dsRNA Adenosine Deaminase Binds Left-Handed Z-RNA as well as Z-DNA Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13532-13586
22. Schwartz, T.; Rould, M. A.; Lowenhaupt, K.; Herbert, A.; Rich, A. Crystal Structure of the Zα Domain of the Human Editing Enzyme ADAR1 Bound to Left-Handed Z-DNA Science 1999, 284, 1841-1845
23. Ha, S. C.; Lowenhaupt, K.; Rich, A.; Kim, Y. -G.; Kim, K. K. Crystal Structure of a Junction between B-DNA and Z-DNA Reveals Two Extruded Bases Nature 2005, 437, 1183-1186
24. Lee, Y. -M; Kim, H. -E.; Park, C. -J.; Lee, A. -R.; Ahn, H. -C.; Cho, S. J.; Choi, K. -H.; Choi, B. -S.; Lee, J. -H. NMR Study on the B-Z Junction Formation of DNA Duplexes Induced by Z-DNA Binding Domain of Human ADAR1 J. Am. Chem. Soc. 2012, 134, 5276-5283
25. Bothe, J. R.; Lowenhaupt, K.; Al-Hashimi, H. M. Sequence-Specific B-DNA Flexibility Modulates Z-DNA Formation J. Am. Chem. Soc. 2011, 133, 2016-2018
26. Bae, S.; Kim, D.; Kim, K. K.; Kim, Y. -G.; Hohng, S. Intrinsic Z-DNA Is Stabilized by the Conformational Selection Mechanism of Z-DNA-Binding Proteins J. Am. Chem. Soc. 2011, 133, 668-671
27. Bae, S.; Son, H.; Kim, Y. -G.; Hohng, S. Z-DNA Stabilization Is Dominated by the Hofmeister Effect Phys. Chem. Chem. Phys. 2013, 15, 15829-15832
28. Roy, R.; Hohng, S.; Ha, T. A Practical Guide to Single-Molecule FRET Nat. Methods 2008, 5, 507-516
29. Shi, X.; Lim, J.; Ha, T. Acidification of the Oxygen Scavenging System in Single-Molecule Fluorescence Studies: In Situ Sensing with a Ratiometric Dual-Emission Probe Anal. Chem. 2010, 82, 6132-6138
30. Hanggi, P.; Talkner, P.; Borkovec, M. Reaction-Rate Theory: 50 Years after Kramers Rev. Mod. Phys. 1990, 62, 251-341
31. Peck, L. J.; Wang, J. C. Energetics of B-to-Z Transition in DNA Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 6206-6210
32. Kim, D.; Reddy, S.; Kim, D. Y.; Rich, A.; Lee, S.; Kim, K. K.; Kim, Y. -G. Base Extrusion Is Found at Helical Junctions between Right- and Left-Handed Forms of DNA and RNA Nucleic Acids Res. 2009, 37, 4353-4359
33. Zhang, L.; Kasif, S.; Cantor, C. R.; Broude, N. E. GC/AT-Content Spikes as Genomic Punctuation Marks Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16855-16860
34. Khuu, P.; Sandor, M.; Deyoung, J.; Ho, P. S. Phylogenomic Analysis of the Emergence of GC-Rich Transcription Elements Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 16528-16533
35. Li, H.; Xiao, J.; Li, J.; Lu, L.; Feng, S.; Dröge, P. Human Genomic Z-DNA Segments Probed by the Zα Domain of ADAR1 Nucleic Acids Res. 2009, 37, 2737-2746
36. Cer, R. Z.; Bruce, K. H.; Mudunuri, U. S.; Yi, M.; Volfovsky, N.; Luke, B. T.; Bacolla, A.; Collins, J. R.; Stephens, R. M.; Non-B, D. B. A Database of Predicted Non-B DNA-Forming Motifs in Mammalian Genomes Nucleic Acids Res. 2011, 39, D383-D391