Aptamers truncation

J. Akitomi, S. Kato, Y. Yoshida, K. Horii, M. Furuichi, ValFold program for the aptamer truncation process, Bioinformation 7 (1) (2011)38-40. 

The cloned sequences often (but not always) have obvious secondary structures in common, leading to visual truncations by which the fixed sequences and other unnecessary sequences from the random regions are eliminated from the aptamer, often resulting in slightly increased affinity over the starting full-length aptamer. When visual truncation is not possible, experimental truncation is done instead. After truncation the aptamer may be further altered by substituting nuclease-resistant purines for the normal... 

As a second step to characterize the aptamers, the primer domains from the library can be deleted from main aptamer and truncated aptamers are tested for ligand binding capability. We use M-fold program (available from http //www. bioinfo.rpi.edu/applications/mfold/) to predict the secondary structures of each aptamer (10). The shortened and optimized aptamer sequences can be decorated with fluoro-phores for custom biosensing applications. 

W.M. Rockey, F.J. Hernandez, S.Y. Huang, S. Cao, C.A. Howell, Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling, Nucleic Acid Ther. 21 (5) (2011) 299-314. 

Experimental examinations can be used instead of structural simulations to determine the essential sequence. In fact, experimental approaches are more commonly used. These procedures require the mass synthesis and analysis of shortened aptamer sequences. Chemical syntheses, boundary analyses, and enzymatic probing and footprinting can be used to generate the shortened sequences. The disadvantage of utilizing an experimental approach is that the iterative process of truncating aptamers and measuring aptamer activity requires weeks to months to survey a small population and may become very costly. 

The specific delivery of aptamer-siRNA chimeras into targeted cells was further proven to result in the apoptosis of cancer cells in vivo." Because systemic delivery of the aptamer-siRNA chimeras will be ideal to combat metastasized cancer, the efficiency of the chimeric molecules has to be optimized. To increase the potency of antitumor activity of the AlO-Plkl chimera, modifications such as truncating the sequence from 71 nt to 39 nt, structural modifications to increase the efficiency of processing the siRNA by cellular machinery, and PEGylation of the 5 -terminus to increase the half-life in serum to improve in vivo kinetics have been utilized." ... 

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