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Nucleic Acids Research Advance Access originally published online on September 18, 2007
Nucleic Acids Research 2007 35(19):6378-6388; doi:10.1093/nar/gkm708
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Nucleic Acids Research, 2007, Vol. 35, No. 19 6378-6388
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

In vitro selection and characterization of cellulose-binding DNA aptamers

Benjamin J. Boese1 and Ronald R. Breaker2,3,4,*

1Department of Chemical Engineering, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry and 4Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA

*To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 0753; Email: ronald.breaker{at}yale.edu

Received July 30, 2007. Revised August 24, 2007. Accepted August 24, 2007.

Many nucleic acid enzymes and aptamers have modular architectures that allow them to retain their functions when combined with other nucleotide sequences. This modular function facilitates the engineering of RNAs and DNAs that have more complex functions. We sought to create new DNA aptamers that bind cellulose to provide a module for immobilizing DNAs. Cellulose has been used in a variety of applications ranging from coatings and films to pharmaceutical preparations, and therefore DNA aptamers that bind cellulose might enable new applications. We used in vitro selection to isolate aptamers from a pool of random-sequence DNAs and subjected two distinct clones to additional rounds of mutagenesis and selection. One aptamer (CELAPT 14) was chosen for sequence minimization and more detailed biochemical analysis. CELAPT 14 aptamer variants exhibit robust binding both to cellulose powder and paper. Also, an allosteric aptamer construct was engineered that exhibits ATP-mediated cellulose binding during paper chromatography.


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