Electrostatic confinement and manipulation of DNA molecules for genome analysis

Manipulation and analysis of large DNA molecules by controlling their dynamics using micro and nanogaps

Manipulation and analysis methods for large DNAs are critical for epidemiological, clinical, diagnostic, and fundamental research on bacteria, membrane vesicles, plants, yeast, and human cells. However, the physical properties of large DNAs often challenge their manipulation and analysis with high accuracy and speed using conventional methods such as gel electrophoresis and column-based methods. This review presents the approaches that leverage micrometer- and nanometer-sized gaps within microchannels to control the dynamics and conformations of large DNAs, thereby overcoming these challenges. By designing gap structures and migration conditions based on the relationship between gap parameters and the physical characteristics of large DNAs-such as diameter and persistence length-these methods enable swifter and more precise manipulation and analysis of large DNAs, including size separation, concentration, purification, and single-molecule analysis.

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers

This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.

Concentration of lambda concatemers using a 3D printed device

Identifying significant variations in genomes can be cumbersome, as the variations span a multitude of base pairs and can make genome assembly difficult. However, large DNA molecules that span the variation aid in assembly. Due to the DNA molecule's large size, routine molecular biology techniques can break DNA. Therefore, a method is required to concentrate large DNA. A bis-acrylamide roadblock was cured in a proof-of-principle 3D printed device to concentrate DNA at the interface between the roadblock and solution. Lambda concatemer DNA was stained with YOYO-1 and loaded into the 3D printed device. A dynamic range of voltages and acrylamide concentrations were tested to determine how much DNA was concentrated and recovered. The fluorescence of the original solution and the concentrated solution was measured, the recovery was 37% of the original sample, and the volume decreased by a factor of 3 of the original volume.

DNA Visualization Using Fluorescent Proteins

DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.

21 Fluorescent Protein-Based DNA Staining Dyes

Fluorescent protein-DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins.

Multidimensional insights into the repeated electromagnetic field stimulation and biosystems interaction in aging and age-related diseases

We provide a multidimensional sequence of events that describe the electromagnetic field (EMF) stimulation and biological system interaction. We describe this process from the quantum to the molecular, cellular, and organismal levels. We hypothesized that the sequence of events of these interactions starts with the oscillatory effect of the repeated electromagnetic stimulation (REMFS). These oscillations affect the interfacial water of an RNA causing changes at the quantum and molecular levels that release protons by quantum tunneling. Then protonation of RNA produces conformational changes that allow it to bind and activate Heat Shock Transcription Factor 1 (HSF1). Activated HSF1 binds to the DNA expressing chaperones that help regulate autophagy and degradation of abnormal proteins. This action helps to prevent and treat diseases such as Alzheimer's and Parkinson's disease (PD) by increasing clearance of pathologic proteins. This framework is based on multiple mathematical models, computer simulations, biophysical experiments, and cellular and animal studies. Results of the literature review and our research point towards the capacity of REMFS to manipulate various networks altered in aging (Reale et al. PloS one 9, e104973, 2014), including delay of cellular senescence (Perez et al. 2008, Exp Gerontol 43, 307-316) and reduction in levels of amyloid-β peptides (Aβ) (Perez et al. 2021, Sci Rep 11, 621). Results of these experiments using REMFS at low frequencies can be applied to the treatment of patients with age-related diseases. The use of EMF as a non-invasive therapeutic modality for Alzheimer's disease, specifically, holds promise. It is also necessary to consider the complicated and interconnected genetic and epigenetic effects of the REMFS-biological system's interaction while avoiding any possible adverse effects.

Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

Characteristic time for the end monomers of a spherically confined polymer to find a nano-pore

Translocation of a polymer through a nano-pore is relevant in a variety of contexts such as passage of RNAs through a nuclear pore and transportation of proteins across a membrane. An essential step in polymer translocation is for the end monomers to search the pore. This process requires a characteristic time, referred to as the "attempt time" in this work. Here, we study the attempt time τ of a confined polymer inside a spherical surface by combining a scaling approach and Langevin dynamics simulations. For a moderately to strongly confined polymer, our results suggest that τ ∼ R^3.67 for R > P and τ ∼ R^2.67 for R < P, where R is the radius of the spherical surface and P is the persistence length of the polymer. All simulation data obtained for an intermediate range of the volume fraction of monomers ϕ(≲ 0.2) tend to collapse onto each other. This implies that τ does not explicitly depend on ϕ, in agreement with the theoretical predictions. These results will be useful for interpreting translocation as a two-step process: the initial attempt to find the pore and eventual pore crossing.

CO2-Driven diffusiophoresis for maintaining a bacteria-free surface

Dissolution and dissociation of CO2 in an aqueous phase induce diffusiophoretic motion of suspended particles with a nonzero surface charge. We report CO2-driven diffusiophoresis of colloidal particles and bacterial cells in a circular Hele-Shaw geometry. Combining experiments and model calculations, we identify the characteristic length and time scales of CO2-driven diffusiophoresis in relation to system dimensions and CO2 diffusivity. The motion of colloidal particles driven by a CO2 gradient is characterized by measuring the average velocities of particles as a function of distance from the CO2 sources. In the same geometrical configurations, we demonstrate that the directional migration of wild-type V. cholerae and a mutant lacking flagella, as well as S. aureus and P. aeruginosa, near a dissolving CO2 source is diffusiophoresis, not chemotaxis. Such a directional response of the cells to CO2 (or an ion) concentration gradient shows that diffusiophoresis of bacteria is achieved independent of cell shape, motility and the Gram stain (cell surface structure). Long-time experiments suggest potential applications for bacterial diffusiophoresis to cleaning systems or anti-biofouling surfaces, by reducing the population of the cells near CO2 sources.

Dynamics of a driven confined polyelectrolyte solution

The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement.

DNA binding fluorescent proteins as single-molecule probes

DNA binding fluorescent proteins are useful probes for a broad range of biological applications.

Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer

Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.

TAMRA-polypyrrole for A/T sequence visualization on DNA molecules

Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.

A simple dialysis device for large DNA molecules

The potential of genomic DNA is realized when new modalities are invented that manipulate large DNAs with minimal breakage or loss of sample. Here, we describe a polydimethylsiloxane-polycarbonate membrane device to remove small molecules from a sample while retaining large DNAs. Dialysis rates dramatically change as DNA size in kb (M) increases and DNA dimensions become comparable to pore size, and chain characteristics go from rod-like to Gaussian. Consequently, we describe empirical rates of dialysis, R, as a function of M as falling into two regimes: DNAs ≤ 1 kb show R(M) ∼e ^{- t/τ} _M (t = time, τ_M = time constant), while DNAs ≥1.65 kb slowly passage with R(M) ∼M ^-1.68; such partitioning potentiates single-molecule imaging.

Structure and proton conduction in sulfonated poly(ether ether ketone) semi-permeable membranes: a multi-scale computational approach

The design of polymeric membranes for proton or ionic exchange highly depends on the fundamental understanding of the physical and molecular mechanisms that control the formation of the conduction channels. There is an inherent relation between the dynamical structure of the polymeric membrane and the electrostatic forces that drive membrane segregation and proton transport. Here, we used a multi-scale computational approach to analyze the morphology of sulfonated poly(ether ether ketone) membranes at the mesoscale. A self-consistent description of the electrostatic phenomenon was adopted, where discrete polymer chains and a continuum proton field were embedded in a continuum fluid. Brownian dynamics was used for the evolution of the suspended polymer molecules, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the proton concentration field. We varied the polymer concentration, the degree of sulfonation and the level of confinement to find relationships between membrane structure and proton conduction. Our results indicate that the reduced mobility of polymer chains, at concentrations above overlap, and a moderate degree of sulfonation - i.e., 30% - are essential elements for membrane segregation and proton domain connectivity. These conditions also ensure that the membrane structure is not affected by size or by potential gradients. Importantly, our analysis shows that membrane conductivity and current are linearly dependent on polymer concentration and quadratically dependent on the degree of sulfonation. We found that the optimal polymeric membrane design requires a polymer concentration above overlap and a degree of sulfonation around 50%. These conditions promote a dynamical membrane morphology with a constant density of proton channels. Our results and measurements agree with previous experimental works, thereby validating our model and observations.

Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules

As the interest in DNA nanotechnology increases, so does the need for larger and more complex DNA structures. In this work, we describe two methods of using large, double-stranded (ds) DNA to self-assemble sequence-specific, nonrepetitive microscale structures. A model system restructures T7 DNA (40 kb) through sequence-specific biotinylation followed by intramolecular binding to a 40 nm diameter neutravidin bead to create T7 "rosettes". This model system informed the creation of "nodal DNA" where "nodes" with single-stranded DNA flaps are attached to a large dsDNA insert so that a complementary oligonucleotide "strap" bridges the two nodes for restructuring to form a DNA "bolo". To do this in high yield, several methodologies were developed, including a protection/deprotection scheme using RNA/RNase H and dialysis chambers, which remove excess straps while retaining large DNA molecules. To assess these restructuring processes, the DNA was adsorbed onto supported lipid bilayers, allowing for a visual assay of their structure using single-molecule fluorescence microscopy. Good agreement between the expected and observed fluorescence intensity measurements of the individual features of restructured DNA for both the DNA rosettes and bolos gives us a high degree of confidence that both processes give sequence-specific restructuring of large, dsDNA molecules to create microscale objects.

Development of 3D printed mesofluidic devices to elute and concentrate DNA

To understand structural variation for personal genomics, an extensive ensemble of large DNA molecules will be required to span large structural variations. Nanocoding, a whole-genome analysis platform, can analyze large DNA molecules for the construction of physical restriction maps of entire genomes. However, handling of large DNA is difficult and a system is needed to concentrate large DNA molecules, while keeping the molecules intact. Insert technology was developed to protect large DNA molecules during routine cell lysis and molecular biology techniques. However, eluting and concentrating DNA molecules has been difficult in the past. Utilizing 3D printed mesofluidic device, a proof of principle system was developed to elute and concentrate lambda DNA molecules at the interface between a solution and a poly-acrylamide roadblock. The matrix allowed buffer solution to move through the pores in the matrix; however, it slowed down the progression of DNA in the matrix, since the molecules were so large and the pore size was small. Using fluorescence intensity of the insert, 84% of DNA was eluted from the insert and 45% of DNA was recovered in solution from the eluted DNA. DNA recovered was digested with a restriction enzyme to determine that the DNA molecules remained full length during the elution and concentration of DNA.

Measuring the wall depletion length of nanoconfined DNA

Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.

Discrete and Continuum Models for the Salt in Crowded Environments of Suspended Charged Particles

Electrostatic forces greatly affect the overall dynamics and diffusional activities of suspended charged particles in crowded environments. Accordingly, the concentration of counter- or co-ions in a fluid-''the salt"-determines the range, strength, and order of electrostatic interactions between particles. This environment fosters engineering routes for controlling directed assembly of particles at both the micro- and nanoscale. Here, we analyzed two computational modeling schemes that considered salt within suspensions of charged particles, or polyelectrolytes: discrete and continuum. Electrostatic interactions were included through a Green's function formalism, where the confined fundamental solution for Poisson's equation is resolved by the general geometry Ewald-like method. For the discrete model, the salt was considered as regularized point-charges with a specific valence and size, while concentration fields were defined for each ionic species for the continuum model. These considerations were evolved using Brownian dynamics of the suspended charged particles and the discrete salt ions, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the concentration fields. The salt/particle models were considered as suspensions under slit-confinement conditions for creating crowded "macro-ions", where density distributions and radial distribution functions were used to compare and differentiate computational models. Importantly, our analysis shows that disparate length scales or increased system size presented by the salt and suspended particles are best dealt with using concentration fields to model the ions. These findings were then validated by novel simulations of a semipermeable polyelectrolyte membrane, at the mesoscale, from which ionic channels emerged and enable ion conduction.

Distribution of label spacings for genome mapping in nanochannels

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.