Highly Specific Recognition of Guanosine Using Engineered Base‐Excised Aptamers

Abstract

Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base‐excision strategy to engineer existing aptamers to bind guanosine. Both a Na+‐binding aptamer and the classical adenosine aptamer have been manipulated as base‐excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16‐deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non‐SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.

Rational Design of Abasic Site-Containing DNA Triplexes To Bind Small Molecules with Low Nanomolar Dissociation Constants

“…This situation is quite different from the SELEX-resulting in aptamer, which often requires a relatively large number of conserved bases in addition to their overall 2D/3D structures. Similarly, the designed Apt G , Apt Ga , and Apt Ga1 outperformed the previously reported two guanosine-binding aptamers (which have K d values of 32 and 780 μM, respectively). , …”

“…20 A vacancy-bearing DNA scaffolds like duplex, G-quadruplex, or other structures acted as an aptamer to bind free purine nucleosides. 21,22 Here, we have extended this strategy to abasic site-containing DNA triplexes. To this end, we have de novo-designed DNA structures (aptamers) that can recognize and bind to specific ligands with high affinities.…”

“…DNA has also been extensively explored for construction of nanostructures. − Structural features at the nano-scale can be readily realized. − To achieve functions (e.g., binding or catalysis), the structural features at the angstrom level are often needed, but realization of such a high precision is scarce for arbitrarily designed nucleic acids. , Previously, the double-stranded DNAs containing abasic site have been reported for the aptamer design of small molecules, riboflavin and theophylline . A vacancy-bearing DNA scaffolds like duplex, G-quadruplex, or other structures acted as an aptamer to bind free purine nucleosides. , Here, we have extended this strategy to abasic site-containing DNA triplexes. To this end, we have de novo -designed DNA structures (aptamers) that can recognize and bind to specific ligands with high affinities.…”

AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing

“…This will be particularly useful for biosensing and engineering dynamic biomimetic systems. This strategy should be easily adapted to certain aptamers that recognize natural bases, such as guanosine-binding DNA aptamers and ATP-binding RNA aptamers. , It is also possible to extend this strategy to aptamers that recognize non-DNA/RNA ligands if the ligands can conjugate to DNAs. However, it is important to note that the molecular design of this strategy is based on the detailed structural information on aptamer–ligand complexes.…”