End-to-end attraction of duplex DNA

Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev
Nucleic Acids Res 40(9) 3812-21 (2012)
DOI:10.1093/nar/gkr1220  PMID:22241779  BibTex

Highlight

DNA–DNA interactions are essential to many biological processes, including DNA replication, recombination and compaction. While side-by-side interactions between two or more DNA molecules have been the subject of many studies, end-to-end interaction of duplex DNA and its role in cell biology and DNA nanotechnology remains almost entirely unexplored. Recent experiments dem­onstrated spont­aneous end-to-end association of short duplex DNA fragments into long rod-like structures. To determine the microscopic origin, magnitude and range of forces driving this spectacular self-assembly, we carried out the first direct study of end-to-end association using the all-atom molecular dynamics method. Our state-of-the-art free energy calculations combined with brute-force simulations of spontaneous self-assembly revealed the standard binding free energy and kinetic rate constants for the end-to-end interaction. We found the end-to-end force to be strong, short-range, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction was discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems. This work is described in a report appearing in Nucleic Acids Research.

Abstract

Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

We performed simulations of a pair of DNA fragments that were axially aligned and initially seperated. As shown in the animation, the pair of DNA fragments collapsed rapidly into an end-to-end assembly. We repeated this simulation 19 times and found rapid collapse in all cases. Here, the 5'-ends of the DNA fragments terminated in a hydroxyl group. The azimuthal angle of the end-to-end assembly was usually around either 0 or 180 degrees (compare to 34 degrees in canonical DNA). These two configurations roughly maximized the contact area between the bases of the two DNA fragments.

The terminal chemistry of the DNA fragments significantly affected the configuration of the end-to-end assembly. Here we show one of twenty trajectories of two DNA framgents with 5'-phosphorylated ends collapsing into an end-to-end assembly, which favors a continuous 5'-to-3' direction across the junction. Hence, the end-to-end assembly closely resembles a single, canonical DNA molecule.

The axial aligment restraints present in the above simulations may have artificially contributed to the stability of the end-to-end assembly. When the axial alignment restraints were removed, an end-to-end assembly remained stably bound for over 600 nanoseconds of simulation. In the  simulation depicted in this animation, the 5'-ends of the DNA terminated in hydroxyl groups.

Steered molecular dynamics was used to probe the energetics of end-to-end attraction. A spring was tethered to the center of mass (CoM) of the terminal nucleotides of each DNA fragment. The rest length of the spring was increased, inducing rupture via shearing of the terminal base pairs. In other simulations we used several different pulling schemes that all induced rupture through the same pathway: shearing of the terminal nucleotides.

These simulations allowed us to estimate an upper bound of the binding free energy for the end-to-end assembly of roughly 8 kcal/mol. A series of umbrella sampling simulations confirmed that the standard binding free energy is in the range of 6.3 ± 1 kcal/mol.

Our enhanced-sampling simulations indicated that end-to-end association of DNA fragments is associated with a very large free energy well. To ensure that our predictions were indeed correct, we performed a brute-force simulation of 458 DNA fragments in a cubic volume 23.8 Å on each side. The DNA fragments, which were not in contact initially, aggregated into chains containing up to 11 DNA fragments in length during the 260 ns simulation. Initially, the unit cell containing all the DNA fragments is depicted. Subsequently, the assembly of the longest 10 aggregates is animated. Since aggregates can span across the periodic boundary of the system, neighboring periodic images of the unit cell are shown.

The simulation confirmed that the free energy associated with end-to-end association of DNA fragments is very large.