Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency

A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.

Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices

Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine²⁺, spermidine³⁺, and spermine⁴⁺ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine³⁺ (Spd³⁺) cations were performed to study the structuring of Spd³⁺ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm³⁺ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd³⁺ interaction modes, with special attention given to Spd³⁺ conformational changes in the space between the two DNA molecules (caged Spd³⁺). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd³⁺ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.

In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA

Biocompatible hydrophilic polyethylene glycol (PEG) is widely used in biomedical applications, such as drug or gene delivery, tissue engineering or as an antifouling component in biomedical devices. Experimental studies have shown that the size of PEG can weaken polycation-polyanion interactions, like those between branched polyethyleneimine (b-PEI) and DNA in gene carriers, but details of its cause and underlying interactions on the atomic scale are still not clear. To better understand the interaction mechanisms in the formation of polyplexes between b-PEI-PEG based carriers and DNA, we have used a combination of in silico tools and experiments on three multicomponent systems differing in PEG MW. Using the PEI-PEG-squalene-dsDNA systems of the same size, both in the all-atom MD simulations and in experimental in-gel electrophoresis measurements, we found that the binding between DNA and the vectors is highly influenced by the size of PEG, with the binding efficiency increasing with a shorter PEG length. The mechanism of how PEG interferes with the binding between PEI and DNA is explained using a two-step MD simulation protocol that showed that the DNA-vector interactions are influenced by the PEG length due to the hydrogen bond formation between PEI and PEG. Although computationally demanding we find it important to study molecular systems of the same size both in silico and in a laboratory and to simulate the behaviour of the carrier prior to the addition of bioactive molecules to understand the molecular mechanisms involved in the formation of the polyplex.

Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA

Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2-4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.

Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K⁺ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K⁺ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.

Structure-guided DNA-DNA attraction mediated by divalent cations

Probing the role of surface structure in electrostatic interactions, we report the first observation of sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and a poly(AT)-poly(TA) duplex (AT-TA). While AT-TA exhibits non-distinguishable behaviors from random-sequence genomic DNA, AA-TT condenses in all alkaline earth metal ions. We characterized these interactions experimentally and investigated the underlying principles using computer simulations. Both experiments and simulations demonstrate that AA-TT condensation is driven by non-specific ion–DNA interactions. Detailed analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as the major difference between AA-TT and AT-TA, which originates from the continuous and close stacking of nucleobase partial charges. These SEGB cations elicit attraction via spatial juxtaposition with the phosphate backbone of neighboring helices, resulting in an azimuthal angular shift between apposing helices. Our study thus presents a distinct mechanism in which, sequence-directed surface motifs act with cations non-specifically to enact sequence-dependent behaviors. This physical insight allows a renewed understanding of the role of repeating sequences in genome organization and regulation and offers a facile approach for DNA technology to control the assembly process of nanostructures.

Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4

The interactions of natural polyamines (putrescine2+, spermidine3+ and spermine4+) with DNA double helix are studied to characterize their nucleotide sequence pattern preference. Atomistic Molecular Dynamics simulations have been carried out for three systems consisting of the same DNA fragment d(CGCGAATTCGCGAATTCGCG) with different polyamines. The results show that polyamine molecules are localized with well-recognized patterns along the double helix with different residence times. We observed a clear hierarchy in the residence times of the polyamines, with the longest residence time (ca 100ns) in the minor groove. The analysis of the sequence dependence shows that polyamine molecules prefer the A-tract regions of the minor groove - in its narrowest part. The preferable localization of putrescine2+, spermidine3+ and spermine4+ in the minor groove with A-tract motifs is correlated with modulation of the groove width by a specific nucleotide sequences. We did develop a theoretical model pointing to the electrostatic interactions as the main driving force in this phenomenon, making it even more prominent for polyamines with higher charges. The results of the study explain the specificity of polyamine interactions with A-tract region of the DNA double helix which is also observed in experiments.

Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics

Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA-protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA-protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules.

Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg-DNA Interaction

The interaction of the regulatory biologically active peptide Glu-Asp-Arg (EDR) with DNA is considered by spectral, NMR, viscosimetry, and molecular dynamics methods. It was shown that EDR can partly penetrate into the major groove of DNA and affect the base atoms, mainly the N7 and O6 of guanine. It was observed that Mg²⁺ ions can promote DNA-EDR interaction due to their effective screening of the negatively charged phosphate groups of DNA. This action of Mg²⁺ remains in salted solution as well.

Representation of DNA environment: Spiral staircase distribution function

In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg²⁺ or Na⁺ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg²⁺ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na⁺ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.