Adsorption Behaviors of DNA/Cation Complexes on Amino and Silica Chip Surfaces: A Dual Polarization Interferometry Study

The adsorption of DNA/Ca²⁺, DNA/Cu²⁺, and DNA/Co­(NH₃)₆³⁺ complexes on amino and silica chip surfaces were investigated using dual polarization interferometry. A more compact DNA/cation complex layer formed on the amino chip surface compared with that on the silica chip surface at the same cation condition. The real-time mass, thickness, and density changes were monitored during the adsorption process. The overall results show that the approaching complexes can cause the conformation rearrangement of the preadsorbed complexes and the preadsorbed complexes affect the deposition pattern of the approaching complexes during the adsorption of DNA/Ca²⁺ and DNA/Cu²⁺ complexes on both chip surfaces. The relatively strong electrostatic repulsion between the approaching and adsorbed complexes results in multiple mass loading rate changes and loose attachment of the approaching complexes. The weak repulsion between the DNA/Co­(NH₃)₆³⁺ complexes cannot induce this kind of conformation rearrangement. Thus, no multiple mass loading rate changes were observed. Meanwhile, the preadsorbed DNA/Co­(NH₃)₆³⁺ complex can also affect the deposition pattern of the approaching complex because of the geometric resistance. Therefore, this study will help better understand the conformation change and deposition pattern of complexes with different charge conditions during the adsorption process on the solid–liquid interface

Synchronized Assembly of Gold Nanoparticles Driven by a Dynamic DNA-Fueled Molecular Machine

A strategy for gold nanoparticle (AuNP) assembly driven by a dynamic DNA-fueled molecular machine is revealed here. In this machine, the aggregation of DNA-functionalized AuNPs is regulated by a series of toehold-mediated strand displacement reactions of DNA. The aggregation rate of the AuNPs can be regulated by controlling the amount of oligonucleotide catalyst. The versatility of the dynamic DNA-fueled molecular machine in the construction of two-component “OR” and “AND” logic gates has been demonstrated. This newly established strategy may find broad potential applications in terms of building up an “interface” that allows the combination of the strand displacement-based characteristic of DNA with the distinct assembly properties of inorganic nanoparticles, ultimately leading to the fabrication of a wide range of complex multicomponent devices and architectures

Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations

<div><p>Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies.</p></div

pH-Controlled Resettable Modular DNA Strand-Displacement Circuits

Sophisticated dynamic molecular systems with diverse functions have been fabricated by using the fundamental tool of toehold-mediated strand displacement (TMSD) in the field of dynamic DNA nanotechnology. However, simple approaches to reset these TMSD-based dynamic systems are lacking due to the difficulty in creating kinetically favored pathways to implement the backward resetting reactions. Here, we develop a facile proton-driven strategy to achieve complete resetting of a modular DNA circuit by integrating a pH-responsive intermolecular CG-C+ triplex DNA and an i-motif DNA into the conventional DNA substrate. The pH-programmed strategy allows modular DNA components to specifically associate/dissociate to promote the forward/backward TMSD reactions, thereby enabling the modular DNA circuit to be repeatedly operated at a constant temperature without generating any DNA waste products. Leveraging this tractable approach, we further constructed two resettable DNA logic gates used for logical computation and two resettable catalytic DNA systems with good performance in signal transduction and amplification

List of simulations involved in this work.

a<p>In these two structures, loop bases are deleted and just G-quartets left.</p

Structural dynamics of hybrid_bsc0 loops.

<p>(a), distance and angle between two thymine bases T and T of double chain reversal loop. (b), The RMSD of TTA loop in [3+1] hybrid structure, and the NMR experimental structure was chosen as reference. (c), angle between T and T and angle between T and A.</p

TTA loops conformations discussed in this work.

<p>Thymine in blue, adenine in green and guanine in yellow. Hydrogen bonds are drawn in gray dash lines, and all bonds connected with hydrogen are hidden.</p

Details of hydrogen bonds between loop bases and between loop base and quartet base.

<p>Results under parm99 force field are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071380#pone.0071380.s005" target="_blank">Table S2</a>.</p>a<p>This hydrogen bond formed after 250 ns in the simulation, so just last 700 ns of the trajectory was used to count the hydrogen bond.</p

The probability distribution of the RMSD of G-quartets in anti_bsc0 and hybrid_bsc0 models (solid lines), and in anti_stem and hybrid_stem (dash lines).

<p>The probability distribution of the RMSD of G-quartets in anti_bsc0 and hybrid_bsc0 models (solid lines), and in anti_stem and hybrid_stem (dash lines).</p

Scheme of two hTel G-quadruplex structures involved in this work.

<p><i>Syn</i> and <i>anti</i> glycosidic bond orientations are drawn in white and gray. From layer 1 to layer 3 are three G-quartets named from the orient of the first strand of G-quadruplexes.</p