SELEX 344 Subject

The TAR RNA target sequence, the 2 -amino RNA library and the appended aldehydes were subjected to the DCC SELEX system. The screen selected a 19-nt sequence with U-NH appended at position 9 and unmodified at positions 6 and 7 (Eig. 3.20). Importantly, it was shown that different sequences were identified when control selections were carried out in the absence of aldehydes, proving that the imino-conjugated nucleic acids are being selected. 

Figure 1 illustrates how SELEX is used to select an RNA species that binds tightly to ATR In step (1), a random mixture of RNA polymers is subjected to unnatural selection by passing it through a resin to which ATP is attached. The practical limit for the complexity of an RNA mixture in SELEX is about 1015 different sequences, which allows for the complete randomization of 25 nucleotides (425 = 1015). When longer RNAs are used, the RNA pool used to initiate the search does not include all possible sequences. RNA polymers that pass through the column are discarded those that bind to ATP are washed from the column with salt solution and collected. The collected RNA polymers are amplified by reverse transcriptase to make many DNA complements to the selected RNAs then an RNA polymerase makes many RNA complements of the resulting DNA molecules. This new pool of RNA is subjected to the same selection procedure, and the cycle is repeated a dozen or more times. At the end, only a few aptamers, in this... 

NECEEM-based Non-SELEX. The essence of the procedure and the results of a binding assay are shown in Figure 9.9. The equilibrium mixture of the naive DNA library and the target is prepared and subjected to the first step of NECEEM-based partitioning. The first enriched library is collected in a vial with several microliters of the target solution. The mixture is incubated to establish the first aptamer-emiched equilibrium mixture. The... 

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