Modifications to MerMade 192 High Throughput synthesizers for Efficient Aptamer Synthesis Dipak Goyal, Paul J. Hatala Archemix Corp., 300 Third Street, Cambridge MA 02129 Jeff Strauss, Jeff Scheumack BioAutomation Corp., 8408 Kenning Court, Plano TX

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Modifications to MerMade 192 High Throughput
synthesizers for Efficient Aptamer Synthesis
Dipak Goyal, Paul J. HatalaArchemix Corp., 300
Third Street, Cambridge MA 02129 Jeff Strauss,
Jeff ScheumackBioAutomation Corp., 8408 Kenning
Court, Plano TX 75024
RESULTS
ABSTRACT Aptamers are oligonucleotides that bind
protein targets with high affinity and
specificity, thereby disrupting protein-protein
interactions. Typically, candidates for
pharmaceutical development range in length from
15-40 nucleotides, and can be heavily
substituted. However, since the discovery
process is SELEX based, the initial synthetic
constructs may contain molecules greater than 80
nucleotides in length. In order to facilitate
the drug discovery process, high throughput
oligonucleotide synthesis is essential. We
report the modifications to a MerMade 192 high
throughput synthesizer that allow for the
parallel synthesis of a wide range of substituted
oligonucleotides (15mer to gt 80mer). This work
is a collaborative effort undertaken by Archemix
Corp. and Bioautomation Inc. INTRODUCTION The
MM192, Figure 1, is configured with 10 amidite
ports with customization up to 20 amidite ports.
Each amidite channel is supported with activator
channel, ensuring supply of controlled
amidite/activator mixture. The ancillary reagent
supply can be configured with 12 channels of
acetonitrile, deblock, oxidizer, and capping.
With these options, the MM192 is not only a high
throughput synthesizer, but has the reagent
options to make high-quality DNA/RNA/LNA
aptamers. BioAutomation has modified the MM192
software/hardware to fulfill the high degree of
complexity in both substitution and size required
by Archemix Corporation. Furthermore, in order to
obtain highly efficient oligomer synthesis,
consistent contact times are required for all
lengths of oligonucleotide. BioAutomation has
prepared a custom software solution to ensure
consistent contact times across a wide variety of
chemistries and lengths.
METHODS In order to test the software
modifications on the MerMade 192, 96
oligonucleotides were synthesized. Starting with
a 15-mer, each well added an additional
2-deoxyribose monomer, ending a 110-mer as shown
in Figure 3. The oligonucleotides were cleaved
and deprotected under standard conditions and
then subjected to high-throughput mass
spectrometry and analytical anion exchange HPLC.
The results are shown in Table 1 and Figure 5.
Figure 3. Schematic of plate showing positions of
corresponding lengths of aptamers
Table 1. High throughput mass spectrometry results
26Mer
74Mer
Maintaining the critical contact time was
achieved by a software modification that adds an
additional acetonitrile wash for completed
columns making each column experience the same
vacuum during draining step. Figure 4
illustrates the stepwise addition of reagents.
38Mer
86Mer
50Mer
98Mer
62Mer
110Mer
Figure 5. Selected analytical SAX-HPLC Data
A
B
C
CONCLUSION Based on the high throughput MS and
analytical SAX-HPLC results, the software upgrade
provided consistent contact time across a large
increase in oligonucleotide length, without loss
of purity. ACKNOWLEDGEMENTS The authors
appreciate the many important contributions of
Jim McArdle.
Figure 2. 96 Well plate for high throughput
synthesis
D
E
Figure 4. Screen shots depicting stepwise
addition of reagents A) Extra acetonitrile
wash, B)deblocking, C) Complete acetonitrile
wash, D) Extra acetonitrile wash, E) Coupling
Figure 1. MerMade 192 synthesizer