The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site

Journal of Nucleic Acids

Volumn 2011, Issue , 2011, Pages

  Fujimoto, Takeshi ^a   Nakano, Shu Ichi ^a   Miyoshi, Daisuke ^a   Sugimoto, Naoki ^a  

^a KONAN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; GUANINE QUADRUPLEX;

ARTICLE; CIRCULAR DICHROISM; DNA STABILITY; DNA STRUCTURE; GENETIC STABILITY; MOLECULAR BIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID BASE SUBSTITUTION; PREDICTION; PRIORITY JOURNAL; STRUCTURE ANALYSIS; THERMODYNAMICS; THERMOSTABILITY;

EID: 84865087281     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.4061/2011/857149     Document Type: Article

References (50)

1. Zimmerman S. B., Minton A. P., Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annual Review of Biophysics and Biomolecular Structure 1993 22 27 65 2-s2.0-0027318513 (Pubitemid 23180316)
2. Minton A. P., The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. Journal of Biological Chemistry 2001 276 14 10577 10580 2-s2.0-0035815743 10.1074/jbc.R100005200 (Pubitemid 38089223)
3. Ellis R. J., Minton A. P., Cell biology: join the crowd. Nature 2003 425 6953 27 28 2-s2.0-0041822089 10.1038/425027a (Pubitemid 37101701)
4. Medalia O., Weber I., Frangakis A. S., Nicastro D., Gerisch G., Baumeister W., Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 2002 298 5596 1209 1213 2-s2.0-0037044862 10.1126/science.1076184 (Pubitemid 35285482)
5. Ellis R. J., Macromolecular crowding: an important but neglected aspect of the intracellular environment. Current Opinion in Structural Biology 2001 11 1 114 119 2-s2.0-0035253217 10.1016/S0959-440X(00)00172-X (Pubitemid 32155560)
6. Davis-Searles P. R., Saunders A. J., Erie D. A., Winzor D. J., Pielak G. J., Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annual Review of Biophysics and Biomolecular Structure 2001 30 271 306 2-s2.0-0034987618 10.1146/annurev.biophys.30.1.271 (Pubitemid 32566165)
7. Wenner J. R., Bloomfield V. A., Crowding effects on EcoRV kinetics and binding. Biophysical Journal 1999 77 6 3234 3241 2-s2.0-0032762645
8. Sasaki Y., Miyoshi D., Sugimoto N., Regulation of DNA nucleases by molecular crowding. Nucleic Acids Research 2007 35 12 4086 4093 2-s2.0-34547613317 10.1093/nar/gkm445 (Pubitemid 47244629)
9. Spink C. H., Chaires J. B., Selective stabilization of triplex DNA by poly(ethylene glycols). Journal of the American Chemical Society 1995 117 51 12887 12888 2-s2.0-0029198316
10. Goobes R., Minsky A., Thermodynamic aspects of triplex DNA formation in crowded environments. Journal of the American Chemical Society 2001 123 50 12692 12693 2-s2.0-0035915355 10.1021/ja016577d (Pubitemid 33140400)
11. Nakano S., Karimata H., Ohmichi T., Kawakami J., Sugimoto N., The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. Journal of the American Chemical Society 2004 126 44 14330 14331 2-s2.0-7744221005 10.1021/ja0463029 (Pubitemid 39463597)
12. Miyoshi D., Karimata H., Sugimoto N., Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. Journal of the American Chemical Society 2006 128 24 7957 7963 2-s2.0-33745374520 10.1021/ja061267m (Pubitemid 43945737)
13. Miyoshi D., Nakamura K., Tateishi-Karimata H., Ohmichi T., Sugimoto N., Hydration of watson crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. Journal of the American Chemical Society 2009 131 10 3522 3531 2-s2.0-67749110113 10.1021/ja805972a
14. 3). Journal of the American Chemical Society 2010 132 48 17105 17107 2-s2.0-78650109518 10.1021/ja105259m
15. Olsen C. M., Lee H. T., Marky L. A., Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops. Journal of Physical Chemistry B 2009 113 9 2587 2595 2-s2.0-65249160660 10.1021/jp806853n
16. Arora A., Maiti S., Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents. Journal of Physical Chemistry B 2009 113 25 8784 8792 2-s2.0-67649218406 10.1021/jp809486g
17. Rajendran A., Nakano S., Sugimoto N., Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH. Chemical Communications 2010 46 8 1299 1301 2-s2.0-76349107608 10.1039/b922050j
18. Nakano S., Karimata H. T., Kitagawa Y., Sugimoto N., Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes. Journal of the American Chemical Society 2009 131 46 16881 16888 2-s2.0-70450159038 10.1021/ja9066628
19. Todd A. K., Johnston M., Neidle S., Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Research 2005 33 9 2901 2907 2-s2.0-20144369806 10.1093/nar/gki553 (Pubitemid 41511229)
20. Allsopp R. C., Vaziri H., Patterson C., Goldstein S., Younglai E. V., Futcher A. B., Greider C. W., Harley C. B., Telomere length predicts replicative capacity of human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 1992 89 21 10114 10118 2-s2.0-0026460896 10.1073/pnas.89.21.10114
21. Klobutcher L. A., Swanton M. T., Donini P., Prescott D. M., All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3′ terminus. Proceedings of the National Academy of Sciences of the United States of America 1981 78 5 3015 3019 2-s2.0-0019568388
22. Williamson J. R., G-quartet structures in telomeric DNA. Annual Review of Biophysics and Biomolecular Structure 1994 23 703 730 2-s2.0-0028173870
23. Huppert J. L., Balasubramanian S., Prevalence of quadruplexes in the human genome. Nucleic Acids Research 2005 33 9 2908 2916 2-s2.0-20144364292 10.1093/nar/gki609 (Pubitemid 41511230)
24. Blackburn E. H., Challoner P. B., Identification of a telomeric DNA sequence in Trypanosoma brucei. Cell 1984 36 2 447 457 2-s2.0-0021256990 (Pubitemid 14126233)
25. Blackburn E. H., Structure and function of telomeres. Nature 1991 350 6319 569 573 2-s2.0-0025731583 10.1038/350569a0 (Pubitemid 21912269)
26. Patel D. J., Phan A. T., Kuryavyi V., Human telomere, oncogenic promoter and 5′ -UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Research 2007 35 22 7429 7455 2-s2.0-38049030699 10.1093/nar/gkm711
27. Vallur A. C., Maizels N., Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions. Proceedings of the National Academy of Sciences of the United States of America 2008 105 43 16508 16512 2-s2.0-55949086124 10.1073/pnas.0805327105
28. Szostak J. W., Blackburn E. H., Cloning yeast telomeres on linear plasmid vectors. Cell 1982 29 1 245 255 2-s2.0-0019949718 (Pubitemid 12027686)
29. Greider C. W., Blackburn E. H., The telomere terminal transferase of tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell 1987 51 6 887 898 2-s2.0-0023663881
30. Baker E. S., Lee J. T., Sessler J. L., Bowers M. T., Cyclo[n]pyrroles: size and site-specific binding to G-quadruplexes. Journal of the American Chemical Society 2006 128 8 2641 2648 2-s2.0-33644653403 10.1021/ja0564968 (Pubitemid 43327943)
31. Seenisamy J., Bashyam S., Gokhale V., Vankayalapati H., Sun D., Siddiqui-Jain A., Streiner N., Shin-ya K., White E., Wilson W. D., Hurley L. H., Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure. Journal of the American Chemical Society 2005 127 9 2944 2959 2-s2.0-20044382992 10.1021/ja0444482 (Pubitemid 40349873)
32. Shirude P. S., Gillies E. R., Ladame S., Godde F., Shin-ya K., Huc I., Balasubramanian S., Macrocyclic and helical oligoamides as a new class of G-quadruplex ligands. Journal of the American Chemical Society 2007 129 39 11890 11891 2-s2.0-34848865663 10.1021/ja073775h (Pubitemid 47512006)
33. Yaku H., Murashima T., Miyoshi D., Sugimoto N., Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes. Chemical Communications 2010 46 31 5740 5742 2-s2.0-77955213299 10.1039/c0cc00956c
34. van Steensel B., Smogorzewska A., De Lange T., TRF2 protects human telomeres from end-to-end fusions. Cell 1998 92 3 401 413 2-s2.0-0032489012 10.1016/S0092-8674(00)80932-0 (Pubitemid 28093017)
35. Lindahl T., Instability and decay of the primary structure of DNA. Nature 1993 362 6422 709 715 2-s2.0-0027278557 10.1038/362709a0 (Pubitemid 23125973)
36. Lindahl T., Nyberg B., Rate of depurination of native deoxyribonucleic acid. Biochemistry 1972 11 19 3610 3618 2-s2.0-0015504248
37. Tchou J., Kasai H., Shibutani S., Chung M. H., Laval J., Grollman A. P., Nishimura S., 8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity. Proceedings of the National Academy of Sciences of the United States of America 1991 88 11 4690 4694 2-s2.0-0025774845 (Pubitemid 21914607)
38. Esposito V., Martino L., Citarella G., Virgilio A., Mayol L., Giancola C., Galeone A., Effects of abasic sites on structural, thermodynamic and kinetic properties of quadruplex structures. Nucleic Acids Research 2009 38 6 2069 2080 2-s2.0-77951228598 10.1093/nar/gkp1087
39. 3 sequences containing guanine abasic sites. Biochemical and Biophysical Research Communications 2010 399 2 203 208 10.1016/j.bbrc.2010.07.055
40. Sugimoto N., Nakano S., Katoh M., Matsumura A., Nakamuta H., Ohmichi T., Yoneyama M., Sasaki M., Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 1995 34 35 11211 11216 2-s2.0-0029134549 10.1021/bi00035a029
41. Nakano S., Kanzaki T., Sugimoto N., Influences of Ribonucleotide on a duplex conformation and its thermal stability: study with the chimeric RNA-DNA strands. Journal of the American Chemical Society 2004 126 4 1088 1095 2-s2.0-0942276311 10.1021/ja037314h (Pubitemid 38140739)
42. Mergny J. L., Li J., Lacroix L., Amrane S., Chaires J. B., Thermal difference spectra: a specific signature for nucleic acid structures. Nucleic Acids Research 2005 33 16 e138 2-s2.0-25144483978
43. 3] G-tetraplex. Structure 1993 1 4 263 282 2-s2.0-0027918585 (Pubitemid 2031126)
44. Sugimoto N., Nakano M., Nakano S., Thermodynamics - structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 2000 39 37 11270 11281 2-s2.0-0034687124 10.1021/bi000819p
45. Vasilevskaya V. V., Khokhlov A. R., Matsuzawa Y., Yoshikawa K., Collapse of single DNA molecule in poly(ethylene glycol) solutions. The Journal of Chemical Physics 1995 102 16 6595 6602 2-s2.0-36449006012
46. Chen Z., Zheng K. W., Hao Y. H., Tan Z., Reduced or diminished stabilization of the telomere G-quadruplex and inhibition of telomerase by small chemical ligands under molecular crowding condition. Journal of the American Chemical Society 2009 131 30 10430 10438 2-s2.0-68049109541 10.1021/ja9010749
47. Sági J., Hang B., Singer B., Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases. Chemical Research in Toxicology 1999 12 10 917 923 2-s2.0-0343195221 10.1021/tx990088y (Pubitemid 29498364)
48. Sági J., Guliaev A. B., Singer B., 15-Mer DNA duplexes containing an abasic site are thermodynamically more stable with adjacent purines than with pyrimidines. Biochemistry 2001 40 13 3859 3868 2-s2.0-0035799355 10.1021/bi0024409 (Pubitemid 32280422)
49. Gelfand C. A., Plum G. E., Grollman A. P., Johnson F., Breslauer K. J., Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry 1998 37 20 7321 7327 2-s2.0-0032546530 10.1021/bi9803372 (Pubitemid 28235215)
50. Goobes R., Kahana N., Cohen O., Minsky A., Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochemistry 2003 42 8 2431 2440 2-s2.0-0037418563 10.1021/bi026775x (Pubitemid 36255217)