Multivalent interaction is often used in molecular design and leads to engineered multivalent ligands with increased binding avidities toward target molecules. The resulting binding avidity relies critically on the rigid scaffold that joins multiple ligands as the scaffold controls the relative spatial positions and orientations toward target molecules. Currently, no general design rules exist to construct a simple and rigid DNA scaffold for properly joining multiple ligands. Herein, we report a crystal structure-guided strategy for the rational design of a rigid bivalent aptamer with precise control over spatial separation and orientation. Such a pre-organization allows the two aptamer moieties simultaneously to bind to the target protein at their native conformations. The bivalent aptamer binding has been extensively characterized, and an enhanced binding has been clearly observed. This strategy, we believe, could potentially be generally applicable to design multivalent aptamers.

Hydrogen abstractions by NO from symmetric ethers are investigated to determine the rate constants and explore the effect of the functional group on rate constants at different reaction sites. The involved ethers are dimethyl ether (DME), diethyl ether (DEE), dipropyl ether (DPE), and dibutyl ether (DBE). The B3LYP method with a 6-31G(2df,p) basis set is employed to optimize the ground-state geometries and for frequency and intrinsic reaction coordinate calculations. The G4 method is used to calculate the electronic energies for the small ethers (DME and DEE). Given the heavy computational cost of the G4 method, the modified G4MP2 method is applied for larger ethers (DPE and DBE) and also for DME to verify the accuracy of the G4MP2 method by benchmarking with the G4 method. The high-pressure limit rate constants are calculated within the temperature range of 500-2000 K, with the asymmetrical Eckart tunneling correction as well as one-dimensional hindered rotor treatment. The calculated rate constants agree well with the literature data, and the branch ratio analysis suggests that the cis-HONO channel basically dominates the hydrogen abstraction reactions and shows a decrease at high temperatures, followed by HNO and trans-HONO channels; in addition, the hydrogen abstraction at the C site adjacent to the ether bond (α reaction site) accounts for most of the reactions. Furthermore, the total rate constants of the ethers are compared to those of their half-structurally alkanes, and linear Bell-Evans-Polanyi correlations are observed.

No abstract

No abstract

Hydrophobic moieties of amphiphilic DNAs can help DNAs penetrate cell membranes, but the conjugation of hydrophobic moieties to DNAs in solution phase remains challenging. Herein we report a solution-phase synthesis method to conjugate hydrophobic molecules to DNAs. This method is simple and efficient. The resulted amphiphilic DNAs can spontaneously assemble into micelles, which may serve as nanocarriers for cellular delivery of nucleic acids and water-insoluble drugs.