Flexibility of single-stranded DNA measured by single-molecule FRET

Intramolecular Folding of PolyT Oligonucleotides Induced by Cooperative Binding of Silver(I) Ions

Ag⁺-bridged T-Ag⁺-T was recently discovered in a Ag⁺-DNA nanowire crystal, but it was reported that Ag⁺ had little to no affinity to T nucleobases and T-rich oligonucleotides in solution. Therefore, the binding mode for the formation of this type of novel metallo base pair in solution is elusive. Herein, we demonstrate that Ag⁺ can interact with polyT oligonucleotides once the concentration of Ag⁺ in solution exceeds a threshold value. The threshold value is independent of the concentration of the polyT oligonucleotide but is inversely proportional to the length of the polyT oligonucleotide. The polyT oligonucleotides are intramolecularly folded due to their positively cooperative formation and the stack of T-Ag⁺-T base pairs, resulting in the 5'- and 3'-ends being in close proximity to each other. The intramolecular Ag⁺-folded polyT oligonucleotide has a higher thermal stability than the duplex and can be reversibly modulated by cysteine.

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

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique

Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.

Simple, rapid, and sensitive on-site detection of Hg2+ in water samples through combining portable evanescent wave optofluidic biosensor and fluorescence resonance energy transfer principle

Rapid and sensitive detection of Hg²⁺ in the environment and drinking water is vital because of its non-degradability, bioaccumulation, and high toxicity. Herein, we report a portable evanescent wave optofluidic biosensor (EWOB) for simple sensitive detection of Hg²⁺ using fluorescence labeled poly-A DNA strand (CY-A14) and quencher labeled poly-T DNA strand (BQ-T14) as signal reporter and biorecognition element, respectively. Both CY-A14 and Hg²⁺ can competitively bind with BQ-T14 based on DNA hybridization and the specifical binding of Hg²⁺ and T bases of DNA to form T-Hg²⁺-T mismatch structure, respectively. Higher concentration of Hg²⁺ lead to less CY-A14 bound to BQ-T14 and thus a higher fluorescence intensity. The influence of several key environmental factors on Hg²⁺ biosensor, such as pH, temperature, and ionic strength, was investigated in details because they were essential for practical applications of Hg²⁺ biosensor. Under optimal conditions, a detection cycle for a single sample, including the measurement and regeneration, was less than 10 min with a Hg²⁺ detection limit of 8.5 nM. The high selectivity of the biosensor was showed by evaluating its response to various potentially interfering metal ions. Our results clearly demonstrated that the portable EWOB could serve as a powerful tool for rapid and sensitive on-site detection of Hg²⁺ in real water samples. The EWOB is also potentially applicable to detect other heavy metal ions or small molecule targets for which DNA/aptamers could be applied as specific biosensing probes.

Assessment of AMBER Force Fields for Simulations of ssDNA

Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

Direct observation of effect of crowding induced macromolecular hydration on molecular breathing in the stem of Fork-DNA by single-molecule FRET microspectroscopy

The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.

Molecular flexibility of DNA as a key determinant of RAD51 recruitment

The timely activation of homologous recombination is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. Biochemically, human RAD51 polymerises faster on single‐stranded DNA (ssDNA) compared to double‐stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? In this study, we tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By directly fitting a mechanistic model to our experimental data, we demonstrate that the RAD51 polymerisation rate positively correlates with the flexibility of DNA. Once the RAD51‐DNA complex is formed, however, RAD51 remains stably bound independent of DNA flexibility, but rapidly dissociates from flexible DNA when RAD51 self‐association is perturbed. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in rapidly recruiting repair factors that multimerise at sites of DNA damage.

In-Situ Configuration Studies on Segmented DNA Origami Nanotubes

One-dimensional nanotubes are of considerable interest in materials and biochemical sciences. A particular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs, templating of other materials into linear arrays and the construction of artificial membrane channels. However, little is known about the structures of assembled DNA nanotubes in solution. Here we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informative in the context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomic force microscopy (AFM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). In particular, the SAXS data revealed important structural information on these DNA nanotubes, such as the in-solution diameters (≈25 nm), which could be obtained only with difficulty by use of other methods. Our results establish SAXS as a reliable structural analysis method for long DNA nanotubes and could assist in the rational design of these structures.

Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength

A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH₂, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl₂ or MgSO₄ cations. At 10 mM MgCl₂ or MgSO₄, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH₂. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH₂, MgCl₂ and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

Incorporation of STED technique into single-molecule spectroscopy to break the concentration limit of diffusing molecules in single-molecule detection

Incorporation of STED into ALEX-FRET increases the concentration limit of single-molecule detection by 100-fold to 5 nM.

Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation

A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.