Identification of Amplified Compounds

The main objective of library analysis is to detect changes in concentration of individual library members. This will allow determining if the library has reached equilibrium and if molecular amplification is being produced by addition of the template. 

In some libraries, changes in concentration can be detected by direct analysis of the DCLs through NMR or MS however, more complex libraries can require the previous separation through chromatographic techniques. 

in particular with ESI, has been an important tool for the analysis of DCLs of receptors. Its utility has been shown by analyzing libraries of potential receptors based on imines [56], hydrazones [60, 114], disulfides [76], acetals [44], and esters [35]. When the libraries are more complex, high resolution may be necessary. Furthermore, MS-MS enables analysis in cases involving sequence isomers [114] and regioisomers [70]. 

ESI-MS has also proved to be a powerful technique for the study of intermo-lecular processes. This characteristic has allowed the use of ESI-MS to detect intermolecular interactions that drive molecular amplification in DCLs. This has been used mainly for DCLs templated with cation guests like acetylcholine or cinchona alkaloids [61, 63, 66]. 

Independent of the analytical methodology used, detecting good binders within a DCL requires the comparison of AFs for the various library members, rather than absolute differences in concentration (these two metrics are equivalent in libraries where all library members have similar concentration in the absence of 

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Next, the RBDCL was screened against the TAMRA-labeled DNA sequences. As seen in Fig. 3.11, only one pool of resin showed significant fluorescence. This pool contained the monomer Cys-Ser-Ser-Quin, and as such the homodisulfide (Cys-Ser-Ser-Quin) was selected as the best binder. Equilibrium dialysis experiments confirmed that (Cys-Ser-Ser-Quin) bound the target DNA Sequence 2 with a dissociation constant of 2.8 tM. While it is certainly true that identification of amplified compounds from large solution-phase DCLs is possible, given sufficiently... 

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