Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (253K) Freely available
Right arrow Supplementary Material
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 (12)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hendrickson, C. L.
Right arrow Articles by Benner, S. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hendrickson, C. L.
Right arrow Articles by Benner, S. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 April 2004

Nucleic Acids Research, 2004, Vol. 32, No. 7 2241-2250
© 2004 Oxford University Press

Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine

Cynthia L. Hendrickson, Kevin G. Devine and Steven A. Benner*

Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611-7200, USA

*To whom correspondence should be addressed. Tel: +1 352 392 7773; Fax: +1 352 392 7918; Email: benner{at}chem.ufl.edu
Present addresses:
Kevin G. Devine, Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
Cynthia L. Hendrickson, Nuclear Medicine Department, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA

Received January 11, 2004; Revised and Accepted March 23, 2004

Standard nucleobases all present electron density as an unshared pair of electrons to the minor groove of the double helix. Many heterocycles supporting artificial genetic systems lack this electron pair. To determine how different DNA polymerases use the pair as a substrate specificity determinant, three Family A polymerases, three Family B polymerases and three reverse transcriptases were examined for their ability to handle 3-deaza-2'-deoxyadenosine (c3dA), an analog of 2'-deoxyadenosine lacking the minor groove electron pair. Different polymerases differed widely in their interaction with c3dA. Most notably, Family A and Family B polymerases differed in their use of this interaction to exploit their exonuclease activities. Significant differences were also found within polymerase families. This plasticity in polymerase behavior is encouraging to those wishing to develop a synthetic biology based on artificial genetic systems. The differences also suggest either that Family A and Family B polymerases do not share a common ancestor, that minor groove contact was not used by that ancestor functionally or that this contact was not sufficiently critical to fitness to have been conserved as the polymerase families diverged. Each interpretation is significant for understanding the planetary biology of polymerases.


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
 Nucleic Acids ResHome page
S. Ogata, M. Takahashi, N. Minakawa, and A. Matsuda
Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo- ) DNA polymerase
Nucleic Acids Res., September 1, 2009; 37(17): 5602 - 5609.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Yang, A. M. Sismour, P. Sheng, N. L. Puskar, and S. A. Benner
Enzymatic incorporation of a third nucleobase pair
Nucleic Acids Res., July 26, 2007; 35(13): 4238 - 4249.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Yang, D. Hutter, P. Sheng, A. M. Sismour, and S. A. Benner
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Nucleic Acids Res., December 4, 2006; 34(21): 6095 - 6101.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Kuwahara, J.-i. Nagashima, M. Hasegawa, T. Tamura, R. Kitagata, K. Hanawa, S.-i. Hososhima, T. Kasamatsu, H. Ozaki, and H. Sawai
Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA
Nucleic Acids Res., November 14, 2006; 34(19): 5383 - 5394.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S.-i. Nakano, Y. Uotani, K. Uenishi, M. Fujii, and N. Sugimoto
DNA base flipping by a base pair-mimic nucleoside
Nucleic Acids Res., December 15, 2005; 33(22): 7111 - 7119.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. D. Ahle, S. Barr, A. M. Chin, and T. R. Battersby
Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases
Nucleic Acids Res., June 2, 2005; 33(10): 3176 - 3184.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. S. Meyer, M. Blandino, and T. E. Spratt
Escherichia coli DNA Polymerase I (Klenow Fragment) Uses a Hydrogen-bonding Fork from Arg668 to the Primer Terminus and Incoming Deoxynucleotide Triphosphate to Catalyze DNA Replication
J. Biol. Chem., August 6, 2004; 279(32): 33043 - 33046.
[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.