| Budget Amount *help |
¥14,740,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2007: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2006: ¥9,800,000 (Direct Cost: ¥9,800,000)
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| Research Abstract |
Aptamers, short nucleic acid-binding species, have emerged as promising candidates for molecular recognition events on account of their significant ability to bind large number of ligands, including amino acids, ribose-containing cofactors and drugs. High affinity and specificity of these aptamers toward target ligands are generally achieved by a combination of molecular shape complementarity, hydrogen-bonding and stacking interactions. Such binding events typically involve the ligand-induced structural changes of the aptamers, resulting in the formation of unique secondary structures responsible to the ligand binding, for which the internal - or stem-loop structures are representative of active sites for binding events. However, for the further design of both RNA and DNA aptamers for small ligands, little attention has been paid to other types of non-base-pairing moieties despite the potential as binding pockets.
Here we report on a new class of DNA duplex aptamers for selective and st
… More
rong binding to biologically important ligands, where an abasic (AP) site in the duplex is utilized as an active cavity for binding to biologically important ligands, where an abasic (AP) site in the duplex is utilized as an active cavity for binding events. For the AP site-based DNA aptamers, it is strongly expected that, by stacking with two nucleotides flanking the AP site, a target ligand is intercalated into the AP site, and this is accompanied by the formation of hydrogen bonds with a receptor nucleotide opposite the AP site. Indeed, we have successfully developed this type of aptamers with high selectivity for riboflavin (dissociation constant K_d=1.9μM), theophylline (K_d=31μM), caffeine (K_d=20μM), and adenosine (detection range: 10~150μM) in this research project. As compared to typical RNA aptamers, our AP site-based DNA aptamers have some advantages, such as their easy and low-cost synthesis, and higher chemical stability. These features would allow various kinds of analytical applications. Less
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