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Thrombin-binding properties of thrombin aptamer derivatives
K Sumikura1, K Yano, K Ikebukuro
1Research Center for Advanced Science and Technology, University of Tokyo, Japan.
Nucleic Acids Symposium Series
|January 1, 1997
Summary
A novel single-stranded DNA with a triple G-quartet structure exhibits significant thrombin-binding activity. This finding challenges the notion that only specific motifs from in vitro selection yield effective thrombin aptamers.
Area of Science:
- Biochemistry
- Molecular Biology
- Biotechnology
Background:
- Thrombin aptamers are short DNA or RNA molecules that bind to thrombin.
- In vitro selection and amplification (SELEX) is a common method for discovering aptamers.
- G-quartet structures are known to contribute to aptamer stability and binding affinity.
Purpose of the Study:
- To synthesize and characterize a single-stranded DNA with a triple G-quartet structure.
- To evaluate the thrombin-binding activity of this novel DNA structure.
- To compare its binding activity with established double G-quartet thrombin aptamers.
Main Methods:
- Chemical synthesis of a single-stranded DNA sequence designed to form a triple G-quartet.
- Thrombin-binding assays conducted at physiological temperature (37°C).
- Comparison of binding affinity and kinetics with a known double G-quartet thrombin aptamer.
Main Results:
- The synthesized triple G-quartet DNA demonstrated comparable thrombin-binding activity to a double G-quartet aptamer.
- The binding activity was observed to be robust at 37°C.
- This suggests alternative structural motifs can achieve high affinity.
Conclusions:
- Single-stranded DNA with triple G-quartet structures can possess significant thrombin-binding capabilities.
- The findings question the exclusive reliance on in vitro selection for identifying optimal aptamer sequences.
- This opens new avenues for aptamer design beyond traditional SELEX methods.