Aptamer: A9L
Target: Recombinant Prostate-Specific Membrane Antigen (PSMA) of prostate cancer cells
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGGCCGAAAAAGACCUGACUUCUAUACUAAGUCUACGUCCC3'
Sequence length: 41
GC content: 0.4878048780487805
Affinity: Kd ~ 5
Pool type: 5′-GGGAGGACGAUGCGG-40N-CAGACGACUCGCCCGA-3'
Pool random region: 40
Binding buffer/conditions: HBSMCIT [HBSMC [HEPES buffered saline (pH 7.4), 1 mm MgCl2, and 1 mm CaCl2], 0.01% I-block (Tropix Inc., Bedford, MA), and 0.05% Tween 20]
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: RNA Turncation: To generate the A9 truncations, the sequence of full-length A9 as previously reported (Lupold et al., 2002) (5′-GGGAGGACGAUGCGGACCGAAAAAGACCUGACUUCUAUACUAAGUCUACGUUCCCAGACGACUCGCCCGA-3′) was loaded into the program RNAStructure 4.6 (MATHEWS, 2006; Mathews et al., 2007). Using a computer-guided “rational truncation” approach, bases were removed from the 5′ and 3′ ends such that the predicted secondary structure of the remaining oligonucleotide was as similar as possible to that of full-length A9. Where necessary, base changes were made at the 5′ and 3′ ends to maintain a 5′-GGG transcription start codon and a complementary 3′-CCC. To create the illustrations, the secondary structures were rendered with the program VARNA 3.7 (Darty et al., 2009).

Based on the data just provided, we hypothesized that a further truncation of A9g which retains suridine at position 39 should result in an RNA aptamer with comparable PSMA inhibitory activity to A9g. To test this hypothesis, we removed the most distal G-C base-pair of A9g (A9L; 41 mer). We also introduced a base change at the first position to maintain the 5′-GGG T7 RNA polymerase transcription start (Fig. 5C; left panel). As predicted, A9L was equally as effective as A9g at inhibiting PSMA enzymatic activity (Fig. 5C; right panel). Elimination of additional bases from the 5′ or 3′ termini (eg, A9h; 37 mer) abrogated inhibition of PSMA enzymatic activity (Fig. 5C; right panel). These findings were consistent with altered folding of these shorter RNAs as predicted by using the RNA secondary structure prediction algorithm (RNAStructure 4.6) and loss of sequence elements (eg, U at position 39) required for function.
Application as quoted in the referenced paper: Therapeutic: " Given the therapeutic potential of the PSMA RNA aptamers for applications including inhibition of PSMA's pro-carcinogenic properties (Silver et al., 1997; Lapidus et al., 2000; Colombatti et al., 2009; Yao et al., 2010) and delivery of small molecule drugs/toxins (Bagalkot et al., 2006; Dhar et al., 2008, 2011), therapeutic siRNAs (McNamara et al., 2006; Dassie et al., 2009; Pastor et al., 2010), and nanoparticles (Farokhzad et al., 2004) to prostate cancer cells, further optimization to facilitate large-scale chemical synthesis of these RNAs is compelling. Toward this end, we have employed computational RNA structural modeling and RNA/protein docking models to guide the truncation of the A9 PSMA RNA aptamer. This analysis resulted in a truncated derivative of the A9 aptamer (A9L, 41mer), which, due to its reduced length, is now amenable to large-scale chemical synthesis. Importantly, A9L retains PSMA binding activity/specificity and functionality. Specifically, we show that A9L inhibits PSMA's enzymatic activity and, when directly applied to cells expressing PSMA, is effectively internalized.."
Additional information: pool modified with 2′F-CTP, 2′F-UTP, ATP, GTP. DNA library/pool was used as a template to generate the RNA pool used in the selection. A T7 promoter sequence might be necessary to use this DNA library/pool as a template to generate the RNA pool in the selection..
Many of the information was extracted from parent paper which may include pool type and binding buffer.
Reference (2011,Nucleic Acid Ther): Rockey, W. M., Hernandez, F. J., Huang, S. Y., Cao, S., Howell, C. A., Thomas, G. S., Liu, X. Y., Lapteva, N., Spencer, D. M., McNamara, J. O., Zou, X., Chen, S. J., & Giangrande, P. H. (2011). Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic acid therapeutics, 21(5), 299–314. https://doi.org/10.1089/nat.2011.0313