Cell Surface Targeting

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Cell Surface Targeting
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Two routes
Protein-protein interface
DNA-DNA interface
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DNA-DNA interaction
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Aptamers

• Short DNA/RNA sequences that have high
  specificity and affinity for substrate
• Low generation time

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• Pros
• Potential control of binding kinetics and
  thermodynamics
• Control of relative amounts of substrates that
  bind cell surface
• Swappable
• Cons
• Interaction strength limited by strength of
  aptamer-protein interactions

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Adaptamers

• Anatomy

Aptamer to cell surface
Anti-interesting protein aptamer
Linking region
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First designs
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Assay woes

• Have attempted to run gel shift assays to
  demonstrate protein-aptamer interactions
• These have failed to prove that aptamers are
  binding the proteins
• For the future new assays.

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Control of relative amounts?

• DNA bound cell surface
• ATCATC
• Sequence conjugated to substrate A TAGTAG
• Sequence conjugated to substrate B TAG
• Substrate A binds less often but for longer
  periods of time.
• Precise control of kinetics based on types of
  base-pairs used repeated patterns.