Cell-SELEX Identifies a “Sticky” RNA Aptamer Sequence
Table 1
Analysis of the cell-SELEX sequences.
(a) Major sequences obtained from the high throughput sequencing (HTS) analysis of MiaPaCa2 (R1 to R7) cell-SELEX
Clone
R1%
R2%
R3%
R4%
R5%
R6%
R7%
M7-14
63.5
79.8
77.0
68.0
79.4
82.9
78.8
P7-1
6.03
7.90
10.2
13.8
7.22
4.38
7.60
P7-1.1
1.00
0.70
1.18
3.91
1.89
2.79
2.80
(b) Sequences of clones from MiaPaCa-2 (R7) cell-SELEX
Clone
% of pool
M7-14
86
P7-1
13
(c) Sequences of clones from Panc-1 (R7) cell-SELEX
Clone
% of pool
M7-14
45
P7-1
45
P7-14
9
(a) HTS data analysis of sequences (rounds R1 through R7) obtained from the MiaPaCa-2 cell-SELEX identified three major sequences designated as M7-14, P7-1, and P7-1.1. The percentages of sequences identified in each rounds are tabulated. The variable region of the aptamers are represented in red, the flanking constant regions of the aptamers are in black, and the nucleotide residues that varied between all clones “mutations” are represented in blue. All the “mutations” were restricted outside the motif sequence region (red bold font), emphasizing the selection pressure to conserve the motif sequence and the structure. The aptamer cluster for all the sequences that were obtained from the HTS is presented in the Supplementary File (S2). (b) Sequences of the clones identified from round 7 (R7) of the MiaPaCa-2 cell-SELEX and their percentage of representations in the R7 sequence pool. (c) Sequences of the clones identified from round 7 (R7) of the Panc-1 cell-SELEX and their percentage of representations in the R7 sequence pool.
