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Updated: May 23, 2026
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High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries
Published on: August 12, 2019
Combinatorial and rational synthesis of complex, base-modified aptamer libraries on microarrays
1Institute of Inorganic Chemistry, University of Vienna Vienna 1090 Austria erika.schaudy@univie.ac.at.
RSC Advances
|May 22, 2026
Summary
This study introduces modified nucleotides for aptamer selection using photolithography, enhancing protein binding and revealing sequence-specific affinity patterns for improved aptamer design.
Area of Science:
- Biochemistry
- Molecular Biology
- Chemical Biology
Background:
- Nucleic acid modifications expand functional capabilities, particularly nucleobase modifications for diverse interactions.
- Aptamers, selected via Systematic Evolution of Ligands by EXponential enrichment (SELEX), identify high-affinity binders to targets like proteins.
- Traditional SELEX is limited by four canonical nucleotides and lacks positional control, hindering exploration of sequence-specific binding.
Purpose of the Study:
- To explore photolithographic microarray synthesis for creating oligonucleotide libraries with modified nucleobases.
- To investigate the impact of uracil analogs (dU-Ser, dU-Tyr) on duplex stability and protein binding affinity.
- To demonstrate the utility of oligonucleotide microarrays in mapping affinity patterns within aptamers.
Main Methods:
- Photolithographic synthesis of oligonucleotide microarrays enabling precise placement of modified nucleotides.
- Incorporation of two uracil analogs, dU-Ser and dU-Tyr, at the C5 position.
- Hybridization experiments to assess duplex stability and binding assays using modified streptavidin aptamer libraries.
Main Results:
- Homopolymer strands of dU-Ser and dU-Tyr exhibited enhanced duplex stability compared to uracil (dU) and thymine (dT).
- Permutation libraries of known streptavidin aptamers revealed specific positions where modified uracils enhanced protein binding.
- Identified sequence positions that are sensitive to chemical modifications, impacting aptamer binding.
Conclusions:
- Oligonucleotide microarrays are powerful tools for studying aptamer affinity patterns with high spatial resolution.
- Incorporating base-modified nucleotides into photolithographic synthesis expands the potential for designing high-affinity aptamers.
- This approach facilitates the discovery of sequence-specific binding characteristics crucial for aptamer optimization.
