Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability

Single-molecule measurements of double-stranded DNA condensation

Electrostatically driven double-stranded DNA (dsDNA) condensation is critical in regulating many biological processes, including bacteriophage and virus replication and the packaging of chromosomal DNA in sperm heads. Here, we review single-molecule measurements of dsDNA condensed by cationic proteins, polypeptides, and small multivalent cations. Optical tweezers (OT) measurements of dsDNA collapsed by cationic condensing agents reveal a critical condensing force unique to each condensing agent that is tunable with condensing agent concentration and ionic strength. DNA globules visualized via atomic force microscopy, transmission electron microscopy, and cryoelectron microscopy reveal condensed dsDNA adopting several conformations including highly ordered toroids with a measurable central hole and, more recently, the maximally dense, yarn-ball-like structures observed with dsDNA condensed by the HIV-1 nucleocapsid protein. The combination of these approaches provides multifaceted insight into the shape and size of electrostatically condensed dsDNA globules and the kinetics of their formation and dissolution. We also review the physics of dsDNA condensation, including recent studies that show dsDNA globule size is tunable with ionic strength. Overall, this review provides important insights into understanding dsDNA condensate-regulated biological processes, as well as potential uses for gene delivery.

Contrasting effects of mismatch locations on Z-DNA formation under bending force

Z-DNA is a non-canonical, left-handed helical structure that plays crucial roles in various cellular processes. DNA mismatches, which involve the incorporation of incorrect Watson-Crick base pairs, are present in all living organisms and contribute to the mechanism of Z-DNA formation. However, the impact of mismatches on Z-DNA formation remains poorly understood. Moreover, the combined effect of DNA mismatches and bending, a common biological phenomenon observed in vivo, has not yet been explored due to technological limitations. Here, using single-molecule FRET, we show that a mismatch inside the Z-DNA region, i.e., the CG repeat region, hinders Z-DNA formation. In stark contrast, however, a mismatch in the B-Z junction facilitates Z-DNA formation. When the bending force is applied on double stranded DNA, a mismatch in the B-Z junction releases the bending stress more effectively than one in the CG repeat region. These findings provide mechanical insights into the role of DNA mismatches and bending forces in regulating Z-DNA formation, whether promoting or inhibiting it in biological environments.

Polymers in Physics, Chemistry and Biology: Behavior of Linear Polymers in Fractal Structures

We start presenting an overview on recent applications of linear polymers and networks in condensed matter physics, chemistry and biology by briefly discussing selected papers (published within 2022-2024) in some detail. They are organized into three main subsections: polymers in physics (further subdivided into simulations of coarse-grained models and structural properties of materials), chemistry (quantum mechanical calculations, environmental issues and rheological properties of viscoelastic composites) and biology (macromolecules, proteins and biomedical applications). The core of the work is devoted to a review of theoretical aspects of linear polymers, with emphasis on self-avoiding walk (SAW) chains, in regular lattices and in both deterministic and random fractal structures. Values of critical exponents describing the structure of SAWs in different environments are updated whenever available. The case of random fractal structures is modeled by percolation clusters at criticality, and the issue of multifractality, which is typical of these complex systems, is illustrated. Applications of these models are suggested, and references to known results in the literature are provided. A detailed discussion of the reptation method and its many interesting applications are provided. The problem of protein folding and protein evolution are also considered, and the key issues and open questions are highlighted. We include an experimental section on polymers which introduces the most relevant aspects of linear polymers relevant to this work. The last two sections are dedicated to applications, one in materials science, such as fractal features of plasma-treated polymeric materials surfaces and the growth of polymer thin films, and a second one in biology, by considering among others long linear polymers, such as DNA, confined within a finite domain.

From straight to curved: A historical perspective of DNA shape

DNA is the macromolecule responsible for storing the genetic information of a cell and it has intrinsic properties such as deformability, stability and curvature. DNA Curvature plays an important role in gene transcription and, consequently, in the subsequent production of proteins, a fundamental process of cells. With recent advances in bioinformatics and theoretical biology, it became possible to analyze and understand the involvement of DNA Curvature as a discriminatory characteristic of gene-promoting regions. These regions act as sites where RNAp (ribonucleic acid-polymerase) binds to initiate transcription. This review aims to describe the formation of Curvature, as well as highlight its importance in predicting promoters. Furthermore, this article provides the potential of DNA Curvature as a distinguishing feature for promoter prediction tools, as well as outlining the calculation procedures that have been described by other researchers. This work may support further studies directed towards the enhancement of promoter prediction software.

α-Synuclein Disrupts Vesicle Fusion by Two Mutant-Specific Mechanisms

Synaptic accumulation of α-synuclein (α-Syn) oligomers and their interactions with VAMP2 have been reported to be the basis of synaptic dysfunction in Parkinson's disease (PD). α-Syn mutants associated with familial PD have also been known to be capable of interacting with VAMP2, but the exact mechanisms resulting from those interactions to eventual synaptic dysfunction are still unclear. Here, we investigate the effect of α-Syn mutant oligomers comprising A30P, E46K, and A53T on VAMP2-embedded vesicles. Specifically, A30P and A53T oligomers cluster vesicles in the presence of VAMP2, which is a shared mechanism with wild type α-Syn oligomers induced by dopamine. On the other hand, E46K oligomers reduce the membrane mobility of the planar bilayers, as revealed by single-particle tracking, and permeabilize the membranes in the presence of VAMP2. In the absence of VAMP2 interactions, E46K oligomers enlarge vesicles by fusing with one another. Our results clearly demonstrate that α-Syn mutant oligomers have aberrant effects on VAMP2-embedded vesicles and the disruption types are distinct depending on the mutant types. This work may provide one of the possible clues to explain the α-Syn mutant-type dependent pathological heterogeneity of familial PD.

Self-Attractive Semiflexible Polymers under an External Force Field

The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in two spatial dimensions and placed in contact with a heat bath described by the Brownian multi-particle collision method. For strong self-attraction the equilibrium conformations range from compact structures to double-stranded chains, and to rods when increasing the stiffness. Under the external field at small rigidities, the initial close-packed chain is continuously unwound by the force before being completely elongated. For double-stranded conformations the transition from the folded state to the open one is sharp being steeper for larger stiffnesses. The discontinuity in the transition appears in the force-extension relation, as well as in the probability distribution function of the gyration radius. The relative deformation with respect to the equilibrium case along the direction normal to the force is found to decay as the inverse of the applied force.

"Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy

Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to occur on similar timescales as one-dimensional (1D) diffusion of proteins on DNA if effective in stalling these proteins as they scan DNA. We examined the flexibility and dynamics of DNA oligomers containing 3 base pair (bp) mismatched sites specifically recognized in vitro by nucleotide excision repair protein Rad4 (yeast ortholog of mammalian XPC). A previous Forster resonance energy transfer (FRET) study mapped DNA conformational distributions with cytosine analog FRET pair primarily sensitive to DNA twisting/unwinding deformations (Chakraborty et al. Nucleic Acids Res. 46: 1240-1255 (2018)). These studies revealed B-DNA conformations for nonspecific (matched) constructs but significant unwinding for mismatched constructs specifically recognized by Rad4, even in the absence of Rad4. The timescales of these unwinding fluctuations, however, remained elusive. Here, we labeled DNA with Atto550/Atto647N FRET dyes suitable for fluorescence correlation spectroscopy (FCS). With these probes, we detected higher FRET in specific, mismatched DNA compared with matched DNA, reaffirming unwinding/bending deformations in mismatched DNA. FCS unveiled the dynamics of these spontaneous deformations at ~ 300 µs with no fluctuations detected for matched DNA within the ~ 600 ns-10 ms FCS time window. These studies are the first to visualize anomalous unwinding/bending fluctuations in mismatched DNA on timescales that overlap with the < 500 µs "stepping" times of repair proteins on DNA. Such "flexible hinge" dynamics at lesion sites could arrest a diffusing protein to facilitate damage interrogation and recognition.

DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions

Z-DNA, a noncanonical helical structure of double-stranded DNA (dsDNA), plays pivotal roles in various biological processes, including transcription regulation. Mechanical stresses on dsDNA, such as twisting and stretching, help to form Z-DNA. However, the effect of DNA bending, one of the most common dsDNA deformations, on Z-DNA formation is utterly unknown. Here, we show that DNA bending induces the formation of Z-DNA, that is, more Z-DNA is formed as the bending force becomes stronger. We regulated the bending force on dsDNA by using D-shaped DNA nanostructures. The B-Z transition was observed by single-molecule fluorescence resonance energy transfer. We found that as the bending force became stronger, Z-DNA was formed at lower Mg²⁺ concentrations. When dsDNA contained cytosine methylations, the B-Z transition occurred at 78 mM Mg²⁺ (midpoint) in the absence of the bending force. However, the B-Z transition occurred at a 28-fold lower Mg²⁺ concentration (2.8 mM) in the presence of the bending force. Monte Carlo simulation suggested that the B-Z transition stabilizes the bent form via the formation of the B-Z junction with base extrusion, which effectively releases the bending stress on DNA. Our results clearly show that the bending force facilitates the B-Z transition under physiological salt conditions.

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.