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Molecules 2009, 14, 1353-1369; doi:10.3390/molecule OPEN ACCESS molecules ISSN 1420-3049 /journal/molecules Review The Shorter the Better: Reducing Fixed Primer Regions of Oligonucleotide Libraries for Aptamer Selection Weihua Pan 1 and Gary A. Clawson 2,* 1 Departments of Pathology, Biochemistry Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA 2 Gittlen Cancer Research Foundation, Hershey Medical Center, Pennsylvania State University, 500 University Drive, Hershey, PA 17033, USA * Author to whom correspondence should be addressed; E-mail: gac4@; Tel.: +1-717-531-5632; Fax: +1-717-531-0661. Received: 20 February 2009; in revised form: 18 March 2009 / Accepted: 25 March 2009 / Published: 27 March 2009 Abstract: Oligonucleotide aptamers are highly structured DNA or RNA molecules, or modified versions thereof, that can bind to targets with specific affinities comparable to antibodies. They are identified through an in vitro selection process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment) to recognize a wide variety of targets, from small molecules to proteins, and from cultured cells to whole organisms. Aptamers possess a number of desirable properties, such as ease of synthesis, stability, robustness, and lack of immunogenicity. Standard SELEX libraries require two primers, one on each side of a central random domain, to amplify the target-bou