Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (138K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (102)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Stivers, J. T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Stivers, J. T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, Vol 26, Issue 16 3837-3844, Copyright © 1998 by Oxford University Press

ARTICLES

2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects

JT Stivers
Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute and theNational Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. stivers@carb.nist.gov

Metal-ion and sequence dependent changes in the stacking interactions of bases surrounding abasic (AB) sites in 10 different DNA duplexes were examined by incorporating the fluorescent nucleotide probe 2- aminopurine (2-AP), opposite to the site (AB-APopp) or adjacent to the site (AB-APadj) on either strand. A detailed study of the fluorescence emission and excitation spectra of these AB duplexes and their corresponding parent duplexes indicates that AB-APoppis significantly less stacked than 2-AP in the corresponding normal duplex. In general, AB-APadjon the AB strand is stacked, but AB-APadjon the opposite strand shows destabilized stacking interactions. The results also indicate that divalent cation binding to the AB duplexes contributes to destabilizaton of the base stacking interactions of AB-APopp, but has little or no effect on the stacking interactions of AB-APadj. Consistent with these results, the fluorescence of AB-APoppis 18-30- fold more sensitive to an externally added quenching agent than the parent normal duplex. When uracil DNA glycosylase binds to AB-APoppin the presence of 2.5 mM MgCl2, a 3-fold decrease in fluorescence is observed ( K d = 400 +/- 90 nM) indicating that the unstacked 2- APoppbecomes more stacked upon binding. On the basis of these fluorescence studies a model for the local base stacking interactions at these AB sites is proposed.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
B. Liang, E. J. Kahen, K. Calvin, J. Zhou, M. Blanco, and H. Li
Long-distance placement of substrate RNA by H/ACA proteins
RNA, October 1, 2008; 14(10): 2086 - 2094.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Yuan, X. W. Lou, E. Rhoades, H. Chen, and L. A. Archer
T4 DNA ligase is more than an effective trap of cyclized dsDNA
Nucleic Acids Res., August 13, 2007; 35(16): 5294 - 5302.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Kimoto, T. Mitsui, Y. Harada, A. Sato, S. Yokoyama, and I. Hirao
Fluorescent probing for RNA molecules by an unnatural base-pair system
Nucleic Acids Res., August 13, 2007; 35(16): 5360 - 5369.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. Blouin and D. A. Lafontaine
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control
RNA, August 1, 2007; 13(8): 1256 - 1267.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. R.W. Bellamy, K. Krusong, and G. S. Baldwin
A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping
Nucleic Acids Res., March 12, 2007; 35(5): 1478 - 1487.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. Krusong, E. P. Carpenter, S. R. W. Bellamy, R. Savva, and G. S. Baldwin
A Comparative Study of Uracil-DNA Glycosylases from Human and Herpes Simplex Virus Type 1
J. Biol. Chem., February 24, 2006; 281(8): 4983 - 4992.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. R. Horton, X. Zhang, R. Maunus, Z. Yang, G. G. Wilson, R. J. Roberts, and X. Cheng
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion
Nucleic Acids Res., February 9, 2006; 34(3): 939 - 948.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. Malta, G. F. Moolenaar, and N. Goosen
Base Flipping in Nucleotide Excision Repair
J. Biol. Chem., January 27, 2006; 281(4): 2184 - 2194.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. K. Neely, D. Daujotyte, S. Grazulis, S. W. Magennis, D. T. F. Dryden, S. Klimasauskas, and A. C. Jones
Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
Nucleic Acids Res., December 9, 2005; 33(22): 6953 - 6960.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Sandin, L. M. Wilhelmsson, P. Lincoln, V. E. C. Powers, T. Brown, and B. Albinsson
Fluorescent properties of DNA base analogue tC upon incorporation into DNA -- negligible influence of neighbouring bases on fluorescence quantum yield
Nucleic Acids Res., September 7, 2005; 33(16): 5019 - 5025.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. B. Gaied, N. Glasser, N. Ramalanjaona, H. Beltz, P. Wolff, R. Marquet, A. Burger, and Y. Mély
8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2'-deoxyribosyl-2-aminopurine with improved properties
Nucleic Acids Res., February 17, 2005; 33(3): 1031 - 1039.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. C. Engman, P. Sandin, S. Osborne, T. Brown, M. Billeter, P. Lincoln, B. Norden, B. Albinsson, and L. M. Wilhelmsson
DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
Nucleic Acids Res., September 27, 2004; 32(17): 5087 - 5095.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T.-J. Su, B. A. Connolly, C. Darlington, R. Mallin, and D. T. F. Dryden
Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase
Nucleic Acids Res., April 23, 2004; 32(7): 2223 - 2230.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. K. Shchyolkina, D. N. Kaluzhny, O. F. Borisova, M. E. Hawkins, R. L. Jernigan, T. M. Jovin, D. J. Arndt-Jovin, and V. B. Zhurkin
Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin
Nucleic Acids Res., January 22, 2004; 32(2): 432 - 440.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Rai, T. D. Cole, E. Thompson, D. P. Millar, and S. Linn
Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex DNA sequences
Nucleic Acids Res., May 1, 2003; 31(9): 2323 - 2332.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. A. O'Neill and J. K. Barton
Inaugural Article: Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA
PNAS, December 24, 2002; 99(26): 16543 - 16550.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. S. Christine, A. W. MacFarlane IV, K. Yang, and R. J. Stanley
Cyclobutylpyrimidine Dimer Base Flipping by DNA Photolyase
J. Biol. Chem., October 4, 2002; 277(41): 38339 - 38344.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
I. Wong, A. J. Lundquist, A. S. Bernards, and D. W. Mosbaugh
Presteady-state Analysis of a Single Catalytic Turnover by Escherichia coli Uracil-DNA Glycosylase Reveals a "Pinch-Pull-Push" Mechanism
J. Biol. Chem., May 24, 2002; 277(22): 19424 - 19432.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. L. Jiang, K. Kwon, and J. T. Stivers
Turning On Uracil-DNA Glycosylase Using a Pyrene Nucleotide Switch
J. Biol. Chem., November 2, 2001; 276(45): 42347 - 42354.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Cheng and R. J. Roberts
AdoMet-dependent methylation, DNA methyltransferases and base flipping
Nucleic Acids Res., September 15, 2001; 29(18): 3784 - 3795.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. R. W. Bellamy and G. S. Baldwin
A kinetic analysis of substrate recognition by uracil-DNA glycosylase from herpes simplex virus type 1
Nucleic Acids Res., September 15, 2001; 29(18): 3857 - 3863.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Rist and J. Marino
Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence
Nucleic Acids Res., June 1, 2001; 29(11): 2401 - 2408.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Pompizi, A. Haberli, and C. J. Leumann
Oligodeoxynucleotides containing conformationally constrained abasic sites: a UV and fluorescence spectroscopic investigation on duplex stability and structure
Nucleic Acids Res., July 15, 2000; 28(14): 2702 - 2708.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
B. Singer and B. Hang
Nucleic acid sequence and repair: role of adduct, neighbor bases and enzyme specificity
Carcinogenesis, June 1, 2000; 21(6): 1071 - 1078.
[Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
W. M. Lindstrom Jr., J. Flynn, and N. O. Reich
Reconciling Structure and Function in HhaI DNA Cytosine-C-5 Methyltransferase
J. Biol. Chem., February 18, 2000; 275(7): 4912 - 4919.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
G. Vilkaitis, A. Dong, E. Weinhold, X. Cheng, and S. Klimasauskas
Functional Roles of the Conserved Threonine 250 in the Target Recognition Domain of HhaI DNA Methyltransferase
J. Biol. Chem., December 1, 2000; 275(49): 38722 - 38730.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. Kwon and J. T. Stivers
Fluorescence Spectroscopy Studies of Vaccinia Type IB DNA Topoisomerase. CLOSING OF THE ENZYME CLAMP IS FASTER THAN DNA CLEAVAGE
J. Biol. Chem., January 4, 2002; 277(1): 345 - 352.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. M. Jean and K. B. Hall
2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
PNAS, January 2, 2001; 98(1): 37 - 41.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.