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METHOD FOR ENCODING AND DECODING LIBRARIES
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Encoding
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Our encoding approach relies on the use of secondary amines as tags. The number of these amines required is dependent on the number of compounds in the library. The simplest use of these tags is binary encoding, whereby the presence or absence of an amine is recorded as a 1 or 0. Thus the code {101} contains two of the three amines, and may, for instance, correspond to the incorporation of a particular building block. In the binary encoding scheme the number of possible codes is given by 2n - 1 where n is the number of amine tags that are available. A maximum of three amines is used to encode each building block synthesis. The individual amines will be present at levels from a few picomoles to a few tens of picomoles per analysis. We originally chose 18 tags for encoding three position libraries of up to 250,000 members.5 For many libraries we do not need this many tags; for
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characterization of split-pool encoded combinatorial libraries
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instance, if the nal position is not chemically encoded but, instead, is positionally encoded by simply keeping the pools separate after incorporation of the last building block, then only two sets of codes and 12 amines are needed. In practice, it has been found that it is often not necessary to encode more than two positions. Any unbranched dialkylamine can be used in our encoding scheme. Anilines and benzylamines are excluded. Alpha-branched amines give anomalous encoding ratios due to slower reaction rates. Our initial tags (Table 9.1) were all commercially available, and were chosen for the ability of their dansylated derivatives to be separated on a C18 column. Separation of all 18 tags required 80 minutes because (1) some amines eluted close together, requiring a rather slow gradient to separate them, and (2) several amines were very hydrophobic and needed prolonged elution with neat acetonitrile for elution from the column. To achieve a high-throughput method, we had to signi cantly reduce the decode cycle time. We employed two main strategies. First, systematic analysis of the retention patterns of available amines by experiment and modeling led to predictive models of amine behavior, allowing an ideal set of tags to be identi ed with evenly spaced elution characteristics. This allowed uniform compression of the gradient with minimal loss of resolu-
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Table 9.1. Original Tag Set Number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Amine Name ethylbutylamine methylhexylamine dibutylamine methylheptylamine butylpentylamine dipentylamine butylheptylamine dihexylamine pentyloctylamine propyldecylamine methyldodecylamine bis(2-ethylhexyl)amine dioctylamine butyldodecylamine pentyldodecylamine hexyldodecylamine heptyldodecylamine didecylamine
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method for encoding and decoding libraries
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Table 9.2. Optimized Tag Set Number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Amine Name 2,2,2-trideuteroethylpentylamine 2,2,2-trideuteroethylhexylamine 2,2,2-trideuteroethylheptylamine 2,2,2-trideuteroethyloctylamine 2,2,2-trideuteroethylnonylamine 2,2,2-trideuteroethyldecylamine pentyloctylamine diheptylamine heptyloctylamine dioctylamine pentyldodecylamine hexyldodecylamine heptyldodecylamine didecylamine Molecular Weight 118.2 132.3 146.3 160.3 174.3 188.4 199.4 213.4 227.4 241.4 255.5 269.5 283.5 297.6
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Abbreviation depn dehx dehp deoc denn dedc pnoc hphp hpoc ococ pndo hxdo hpdo dcdc
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tion. Second, changing to a less retentive cyano column allowed all amines to be eluted by the gradient and permitted chromatographic compression to be achieved. In addition the column proportions were changed to allow much faster ow. These factors, and the need for tags of unique molecular weight, led to our second generation tag set as illustrated in Table 9.2. The enhanced throughput is illustrated in Figure 9.2, where all 14 tags are separated in a 4-minute run. 9.2.2. Decoding
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The tags can be released for analysis with strong acid. Single beads were placed in individual tapered glass microvials (National Scienti c, decontaminated before use by heating at 400 C for 2 hours) by an automated beadpicker.19,20 The ligand was removed by prior cleavage, 25 mL of HCl (6N constant boiling grade) was added, and the sealed vials were heated at 135 C for 12 to 16 hours. The HCl was removed from the cooled vial in vacuum. Mass spectroscopy offers the obvious advantage of providing mass information on the molecular species present. If used in conjunction with chromatography (e.g., LC/MS) an additional dimension of data is provided that can assist in decoding. For example, amines are often used as building blocks in library assembly. If for some reason they remain associated with beads during the tag analysis process, they may elute near one of the tags,
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