Aptamers are short RNA ⁄ DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA ⁄ DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.Key words: bioinformatics, mechanism-based drug design, molecular recognition, structure-based drug design Received 18 October 2010, revised 24 February 2011 and accepted for publication 1 April 2011 Aptamers, short RNA ⁄ DNA sequences, are selected through an experimental technique known as systematic evolution of ligands by exponential enrichment (SELEX) to bind to specific biomolecular targets including small molecules, proteins, nucleic acids, phospholipids as well as complex structures such as cells, tissues, bacteria, and other organisms. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology with recognized therapeutic and diagnostic clinical applications (1-5). SELEX consists of a number of rounds of in vitro selection in which the RNA ⁄ DNA pool is incubated with the binding target. The non-binding or loosely binding sequences are discarded, while the binding sequences are expanded using the polymerase chain reaction method to provide a pool of sequences for the next round of testing. In practice, multiple rounds of selection and expansion are required before unique tightly binding sequences can be identified. Additionally, isolated aptamers will often need to be reengineered to reduce their sequence length and impart additional favorable biological properties. These issues pose a challenge for the efficient identification of correct aptamers.Over the past several years, various research groups have attempted...

The phospholipid phosphatidylserine (PS) is an early marker exploited for detecting apoptosis (PS externalization in the cell membrane bilayer) and one factor that is associated with increased amyloid plaque deposition in transmissible spongiform encephalopathies (TSEs). PS can therefore be considered as a promising target for diagnosis or treatment of diseases. Aptamers (short nucleic acid sequences) are a particularly attractive class of materials among those currently considered for targeting PS. Here we applied an entropy based seed-and-grow strategy to design a DNA aptamer template to bind specifically to PS. The binding properties of designed aptamers were investigated computationally and experimentally. The studies identify the sequence, 5'-AAAGAC-3', as the preferred template for further modifications and studies toward its practical implementations.

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We and others have observed that substrates for copper-containing amine oxidases cause substrate inhibition at high concentrations. Through use of a novel "pseudoquantitative" rapid equilibrium approach, kinetic analyses with human and bovine enzymes indicate that these effects are consistent with substrates binding to oxidised and reduced enzyme forms. Small cations compete with binding of substrates to oxidised and reduced enzyme, influencing both substrate turnover and substrate inhibition patterns. Cations reduce affinity of the resting bovine enzyme for spermidine, but not benzylamine, indicating that the predominant effect of cations on substrate oxidation results from binding to an anionic site outside the active site. However, binding of cations to the active site of the reduced form of both enzymes attenuates substrate inhibition with both spermidine and benzylamine. Our observations have significant practical implications for researchers assaying kinetic behaviour of these enzymes, and particularly those developing novel inhibitors of human copper-containing amine oxidases.

The need to monitor cancer therapy-induced cellular and tissue changes using noninvasive imaging techniques continues to stimulate both basic and clinical research. Monitoring changes in cellular proliferative capacity that occur after treatment with radiation and/or chemotherapy has the potential to provide longitudinal information on the cellular dynamics of tumors before, during, and after therapeutic intervention. Cells can lose their reproductive potential through one of several mechanisms, including apoptosis and autophagy (which are forms of programmed cell death), premature senescence, or necrosis. When a tumor responds to therapy, current imaging methods do not provide information about the exact mechanism of cell death executed. We are now beginning to develop the molecular imaging tools that will enable us to noninvasively image cell death mechanisms both in experimental models and in the clinical cancer environment. Studies with these imaging tools will contribute to a better understanding of therapeutic responses and assist in the design and evaluation of more effective treatments. This review examines the state-of-the-art in the use of (radio)tracers for the purpose of imaging mechanisms of tumor cell inactivation (cell death) in animal models and in clinical trials.