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 Showing 1 - 52 of 52 Journals sorted alphabetically Acta Biochimica et Biophysica Sinica       (Followers: 5) Advanced NanoBiomed Research Annual Review of Biophysics       (Followers: 24) Archives of Biochemistry and Biophysics       (Followers: 17) BBA Advances       (Followers: 4) BBA Bioenergetics       (Followers: 5) BBA Biomembranes       (Followers: 11) Biochemical and Biophysical Research Communications       (Followers: 17) Biochemistry and Biophysics Reports Biochimica et Biophysica Acta (BBA) - General Subjects       (Followers: 12) Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids       (Followers: 6) Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease       (Followers: 12) Biochimica et Biophysica Acta (BBA) - Molecular Cell Research       (Followers: 10) Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics       (Followers: 11) Bioinspired, Biomimetic and Nanobiomaterials       (Followers: 3) Biophysical Chemistry       (Followers: 8) Biophysical Journal       (Followers: 46) Biophysical Reports       (Followers: 5) Biophysical Reviews and Letters       (Followers: 5) Biophysics       (Followers: 8) Biophysics Reports BMC Biophysics       (Followers: 4) Cell Biochemistry and Biophysics       (Followers: 6) Current Topics in Biophysics       (Followers: 2) Doklady Biochemistry and Biophysics       (Followers: 1) European Biophysics Journal       (Followers: 4) Food Biophysics       (Followers: 3) Freshwater Biology       (Followers: 31) GSTF Journal of BioSciences IEEE Life Sciences Letters IEEE Nanotechnology Express       (Followers: 18) Indian Journal of Biochemistry and Biophysics (IJBB)       (Followers: 3) International Journal of Biochemistry and Biophysics       (Followers: 1) International Journal of Biophysics Journal of Biopharmaceutical Statistics       (Followers: 23) Journal of Biophotonics       (Followers: 1) Journal of Biophysical Chemistry       (Followers: 3) Journal of Biophysics and Structural Biology       (Followers: 2) Journal of Medicine, Physiology and Biophysics Journal of Physical Chemistry & Biophysics Membranes and Membrane Technologies Nanomedicine Research Journal Nanomedicine: Nanotechnology, Biology and Medicine       (Followers: 5) Natural Products and Bioprospecting       (Followers: 2) Nature Communications       (Followers: 310) PMC Biophysics Progress in Biophysics and Molecular Biology       (Followers: 1) Progress in Physical Geography       (Followers: 11) Quarterly Reviews of Biophysics       (Followers: 3) Radiation and Environmental Biophysics       (Followers: 3) Research & Reviews : A Journal of Life Sciences Statistics in Biopharmaceutical Research       (Followers: 15)
Similar Journals
 European Biophysics JournalJournal Prestige (SJR): 0.604 Citation Impact (citeScore): 2Number of Followers: 4      Hybrid journal (It can contain Open Access articles) ISSN (Print) 1432-1017 - ISSN (Online) 0175-7571 Published by Springer-Verlag  [2537 journals]
• Acoustofluidic interferometric device for rapid single-cell physical
phenotyping

Abstract: High-throughput single-cell analysis based on physical properties (such as morphology or mechanics) is emerging as a powerful tool to inform clinical research, with a great potential for translation towards diagnosis. Here we present a novel microfluidic approach adopting acoustic waves to manipulate and mechanically stimulate single cells, and interferometry to track changes in the morphology and measure size, deformability, and refractive index of non-adherent cells. The method is based on the integration within the acoustofluidic channel of a low-finesse Fabry–Perot resonator, providing very high sensitivity and a speed potentially suitable to obtain the high-throughput necessary to handle the variability stemming from the biological diversity of single cells. The proposed approach is applied to a set of different samples: reference polystyrene beads, algae and yeast. The results demonstrate the capability of the acoustofluidic interferometric device to detect and quantify optomechanical properties of single cells with a throughput suitable to address label-free single-cell clinical analysis.
PubDate: 2022-01-12

• Isothermal titration calorimetry in the single-injection mode with
imperfect mixing

Abstract: Isothermal titration calorimetry (ITC) is now a method of choice to obtain thermodynamic information about the interaction between two molecular partners. Most often, the method in use is the so-called multiple-injection method (MIM) consisting in distinct short-time injections of the titrant separated by sufficient delay to reach equilibrium before each new injection. However, an alternative single-injection method (SIM) exists. It consists in a unique continuous injection and, despite the fact that it is quite simple and generally faster than MIM, it is very little used. The goal of this work is to reconsider its theoretical basis. A new equation taking into account the effect of dilution resulting from the continuous titration process is obtained. It allows to consider efficiently the continuum of possibilities from perfect to imperfect mixing of the cell content. It is shown that, to good approximation, imperfect mixing can be accounted for by considering the cell volume as an adjustable parameter. Most likely, this should lead to an artificial increase of it, although one cannot reject the possibility of a decrease. The processing of experimental data on the interaction of Ba++ with 18-crown-6 from led to an increase by 6.9%, which resulted in a much better fit of the titration curve and improved results on the association constant Ka and enthalpy variation ∆H. A criterion is also obtained on the maximum injection rate to be used for maintaining quasi-equilibrium during the whole titration for the association–dissociation mechanism $${\text{A}}\;{ + }\;{\text{B}}\;\; \rightleftarrows \;\;{\text{C}}$$ .
PubDate: 2022-01-08

• Correction to: Thermodynamics of protein folding: methodology, data
analysis and interpretation of data

PubDate: 2021-12-21

• Clostridium perfringens Beta2 toxin forms highly cation-selective channels
in lipid bilayers

Abstract: Clostridium perfringens is a potent producer of a variety of toxins. Well studied from these are five toxins (alpha, Beta (CPB), epsilon, iota and CPE) that are produced by seven toxinotype strains (A–G) of C. perfringens. Besides these toxins, C. perfringens produces also another toxin that causes necrotizing enterocolitis in piglets. This toxin termed consensus Beta2 toxin (cCPB2) has a molecular mass of 27,620 Da and shows only little homology to CPB and no one to the other toxins of C. perfringens. Its primary action on cells remained unknown to date. cCPB2 was heterogeneously expressed as fusion protein with GST in Escherichia coli and purified to homogeneity. Although cCPB2 does not exhibit the typical structure of beta-stranded pore-forming proteins and contains no indication for the presence of amphipathic alpha-helices we could demonstrate that cCPB2 is a pore-forming component with an extremely high activity in lipid bilayers. The channels have a single-channel conductance of about 700 pS in 1 M KCl and are highly cation-selective as judged from selectivity measurements in the presence of salt gradients. The high cation selectivity is caused by the presence of net negative charges in or near the channel that allowed an estimate of the channel size being about 1.4 nm wide. Our measurements suggest that the primary effect of cCPB2 is the formation of cation-selective channels followed by necrotic enteritis in humans and animals. We searched in databases for homologs of cCPB2 and constructed a cladogram representing the phylogenetic relationship to the next relatives of cCPB2.
PubDate: 2021-12-02

• Correction to: Reproducibility and accuracy of microscale thermophoresis
in the NanoTemper Monolith: a multi laboratory benchmark study

PubDate: 2021-12-01

• Effective inhibition of insulin amyloid fibril aggregation by nickel(II)
complexes containing heterocyclic thiosemicarbazones

Abstract: The sensitivity of protein molecular structures makes them susceptible to aggregation in conditions unfavorable for the maintenance of their native folds. The aggregation of proteins leads to many disorders, but the inhibition of amyloid fibril formation using metal-containing small molecules is gaining popularity. Herein we report the effect of nickel(II) complexes (N1, N2, N3, and N4) bearing thiosemicarbazones on the inhibition of amyloid fibril formation by insulin. The interactions of the complexes with amyloid fibrils were investigated using various biophysical techniques, including light scattering, intrinsic fluorescence assay, thioflavin T (ThT) assay, and Fourier transform-infrared spectroscopy. The results revealed that the phenyl-substituted N3 was an efficient inhibitor of amyloid fibril formation and maintained the insulin in its native structure despite conditions promoting fibrillation. Graphic abstract Nickel(II) complexes containing indole based thiosemicarbazones were efficient in inhibiting the amyloid fibril formation and maintaining the insulin in its native structure in unfavorable conditions.
PubDate: 2021-12-01

• DNA–MBF1 study using molecular dynamics simulations

Abstract: Regulatory factor MBF1 is highly conserved between species and has been described as a cofactor and transcription factor. In plants, several reports associate MBF1 with heat stress response. Nevertheless, the specific physical processes involved in the MBF1–DNA interaction are still far from clearly understood. We thus performed extensive molecular dynamics simulations of DNA with a homology-based modethel of the MBF1 protein. Based on recent experimental data, we proposed two B-DNA sequences, analyzing their interaction with our model of the Arabidopsis MBF1c protein (AtMBF1c) at three different temperatures: 293, 300, and 320 K, maintaining a constant pressure of 1 bar. The simulations suggest that MBF1 binds directly to the DNA, supporting the idea of its role as a transcription factor. We identified two different conformations of the MBF1 protein when bound, and characterized the specific groups of amino acids involved in the formation of the DNA–MBF1 complex. These regions of amino acids are bound mostly to the minor groove of DNA by the attraction of positively charged residues and the negatively charged backbone, but subject to the compatibility of shapes, much in the sense of a lock-and-key mechanism. We found that only with a sequence rich in CTAGA motifs at 300 K does MBF1 bind to DNA in the DNA-binding domain Cro/C1-type HTH predicted. In the rest of the systems tested, we observed non-specific DNA–MBF1 interactions. This study complements findings previously reported by others on the role of CTAGA as a DNA-binding element for MBF1c at a heat stress temperature.
PubDate: 2021-12-01

• Observations of three “re-entrant” twisted structures in
double-stranded DNA dispersion particles

Abstract: In this work we report on observations of new twisted (cholesteric-like) structures in liquid-crystalline dispersion particles with a hexagonal packing of double-stranded (ds) DNA molecules. Heating up to 80 °C of the DNA dispersion formed in a aqueous-salt solution with a high osmotic pressure (concentration) of poly(ethylene glycol) induces the formation of a new, optically active, spirally twisted structure of these molecules ("re-entrant" cholesteric structure (rest-A structure)). Cooling of this dispersion up to 22 °C is accompanied by the formation of an additional "re-entrant" cholesteric structure (rest-B). Modification of particles of the ds DNA dispersion (with rest-B structure) by replacing Na+ cations by multi-charged Gd3+ cations results in the third " re-entrant" structure (rest-C) despite a high density packing of ds nucleic acid molecules. Graphical abstract
PubDate: 2021-11-28

• Quantifying force transmission through fibroblasts: changes of traction
forces under external shearing

Abstract: Mammalian cells have evolved complex mechanical connections to their microenvironment, including focal adhesion clusters that physically connect the cytoskeleton and the extracellular matrix. This mechanical link is also part of the cellular machinery to transduce, sense and respond to external forces. Although methods to measure cell attachment and cellular traction forces are well established, these are not capable of quantifying force transmission through the cell body to adhesion sites. We here present a novel approach to quantify intracellular force transmission by combining microneedle shearing at the apical cell surface with traction force microscopy at the basal cell surface. The change of traction forces exerted by fibroblasts to underlying polyacrylamide substrates as a response to a known shear force exerted with a calibrated microneedle reveals that cells redistribute forces dynamically under external shearing and during sequential rupture of their adhesion sites. Our quantitative results demonstrate a transition from dipolar to monopolar traction patterns, an inhomogeneous distribution of the external shear force to the adhesion sites as well as dynamical changes in force loading prior to and after the rupture of single adhesion sites. Our strategy of combining traction force microscopy with external force application opens new perspectives for future studies of force transmission and mechanotransduction in cells.
PubDate: 2021-10-28

• Morphological, fractal, and textural features for the blood cell
classification: the case of acute myeloid leukemia

Abstract: Microscopic examination of stained peripheral blood smears is, nowadays, an indispensable tool in the evaluation of patients with hematological and non-hematological diseases. While a rapid automated quantification of the regular blood cells is available, recognition and counting of immature white blood cells (WBC) still relies mostly on the microscopic examination of blood smears by an experienced observer. Recently, there are efforts to improve the prediction by various machine learning approaches. An open dataset collection including the recently digitalized single-cell images for 200 patients, from peripheral blood smears at 100 × magnification, was used. We studied different morphological, fractal, and textural descriptors for WBC classification, with an aim to indicate the most reliable parameters for the recognition of certain cell types. Structural properties of both the mature and non-mature leukocytes obtained from (i) acute myeloid leukemia patients, or (ii) non-malignant controls, were studied in depth, with a sample size of about 25 WBC per group. We quantified structural and textural differences and, based on the statistical ranges of parameters for different WBC types, selected eight features for classification: Cell area, Nucleus-to-cell ratio, Nucleus solidity, Fractal dimension, Correlation, Contrast, Homogeneity, and Energy. Classification Precision of up to 100% (80% on average) was achieved.
PubDate: 2021-10-12
DOI: 10.1007/s00249-021-01574-w

• Partial structure, dampened mobility, and modest impact of a His tag in
the SARS-CoV-2 Nsp2 C-terminal region

Abstract: Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many viruses use their own IDPs to “hack” these processes to deactivate host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational preferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2, whose C-terminal region (CtR) is predicted to be disordered, interacts with human proteins that regulate translation initiation and endosome vesicle sorting. Molecules that block these interactions could be valuable leads for drug development. The 13Cβ and backbone 13CO, 1HN, 13Cα, and 15N nuclei of Nsp2’s 45-residue CtR were assigned and used to characterize its structure and dynamics in three contexts; namely: (1) retaining an N-terminal His tag, (2) without the His tag and with an adventitious internal cleavage, and (3) lacking both the His tag and the internal cleavage. Two five-residue segments adopting a minor extended population were identified. Overall, the dynamic behavior is midway between a completely rigid and a fully flexible chain. Whereas the presence of an N-terminal His tag and internal cleavage stiffen and loosen, respectively, neighboring residues, they do not affect the tendency of two regions to populate extended conformations.
PubDate: 2021-10-11
DOI: 10.1007/s00249-021-01575-9

• Thermodynamics of semi-specific ligand recognition: the binding of
dipeptides to the E.coli dipeptide binding protein DppA

Abstract: This investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ( $$\Delta {C}_{p}^{o}$$ ) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.
PubDate: 2021-10-05
DOI: 10.1007/s00249-021-01572-y

• Structure and mechanism of secondary sulfonamide binding to carbonic
anhydrases

Abstract: Zinc-containing metalloenzyme carbonic anhydrase (CA) binds primary sulfonamides with extremely high, up to picomolar, affinity by forming a coordination bond between the negatively charged amino group and the zinc ion and making hydrogen bonds and hydrophobic contacts with other parts of the inhibitor molecule. However, N-methyl-substituted, secondary or tertiary sulfonamides bind CA with much lower affinity. In search for an explanation for this diminished affinity, a series of secondary sulfonamides were synthesized and, together with analogous primary sulfonamides, the affinities for 12 recombinant catalytically active human CA isoforms were determined by the fluorescent thermal shift assay, stopped-flow assay of the inhibition of enzymatic activity and isothermal titration calorimetry. The binding profile of secondary sulfonamides as a function of pH showed the same U-shape dependence seen for primary sulfonamides. This dependence demonstrated that there were protein binding-linked protonation reactions that should be dissected for the estimation of the intrinsic binding constants to perform structure-thermodynamics analysis. X-ray crystallographic structures of secondary sulfonamides and computational modeling dissected the atomic contributions to the binding energetics. Graphic abstract Secondary sulfonamides bind to carbonic anhydrases via coordination bond between the negatively charged nitrogen of alkylated amino group and Zn(ii) in the active site of CA. The binding reaction is linked to deprotonation of the amino group and protonation of the Zn(ii)-bound hydroxide. To perform the structure-thermodynamics analysis, contributions of these linked reactions must be subtracted to determine the intrinsic energetics. In this aspect, the secondary sulfonamides are similar to primary sulfonamides as CA inhibitors.
PubDate: 2021-10-01
DOI: 10.1007/s00249-021-01561-1

• Structure and dynamics of sodium alginate as elucidated by chemical shift
anisotropy and site-specific spin–lattice relaxation time measurements

Abstract: The biocompatible, biodegradable, linear copolymer sodium alginate is fabricated from $$1 \to 4$$ linked $$\beta$$ -d-mannuronic acid (M block) and $$\alpha$$ -l-guluronic acid (G-block). It has wide applications in drug delivery, cell encapsulation, and commercial application in the textile, cosmetics, paper, food, biomedical, and pharmaceutical industries. The structure and dynamics of sodium alginate were here investigated by measuring chemical shift anisotropy (CSA) parameters, spin–lattice relaxation time, and molecular correlation time. The principal components of the CSA tensor were determined by two-dimensional phase-adjusted spinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) SSNMR. The alternating M and G blocks of both equatorial and axial links are associated with greater overall flexibility. The molecular correlation time of the carboxyl carbon of both G and M blocks is faster than for the anomeric carbon and pyranose carbon. This is further experimental evidence of the coexistence of two different dynamics within the polysaccharide chains of sodium alginate, which was previously established by 1H–13C dipolar profile analysis. The relaxation time of the para-crystalline region of sodium alginate is comparable with that of chitosan, but it is much shorter than that of cellulose and chitin. The order of the molecular correlation time of sodium alginate and chitosan is also the same. Hence, it can be concluded that sodium alginate exhibits greater flexibility than cellulose and chitin. These types of investigation into the local electronic configuration and nuclear spin dynamics at various carbon nuclei sites of the biopolymer at atomic-scale resolution will help in the design of biomimetic materials.
PubDate: 2021-10-01
DOI: 10.1007/s00249-021-01559-9

• The importance of hydrophobic interactions in the structure of
transcription systems

Abstract: Hydrophobic forces play a crucial role in both the stability of B DNA and its interactions with proteins. In the present study, we postulate that the hydrophobic effect is an essential component in establishing specificity in the interaction transcription factor proteins with their consensus DNA sequence partners. The PDB coordinates of more than 50 transcription systems have been used to analyze the hydrophobic attraction of proteins towards their DNA consensus. This analysis includes computing the hydrophobic energy of the interacting molecules by means of their hydrophobic moments. Hydrophobic moments have successfully been used in previous studies involving self-assembly protein systems. In the present case, in spite of some variability, we found specificity in transcription factors when interacting with their respective consensus DNA sequences. By applying our model of biological membrane pattern for hydrophobic interactions, we postulate that hydrophobic forces constitute the necessary intermediate interaction between the unspecific electrostatic attraction for DNA phosphate groups and the very short-range interaction promoting hydrogen bonds. We conclude that hydrophobic interactions serve as the intermediate force guiding transcriptions factors towards the proper hydrogen bonds to their DNAs.
PubDate: 2021-10-01
DOI: 10.1007/s00249-021-01557-x

• Reflectometry and molecular dynamics study of the impact of cholesterol
and melatonin on model lipid membranes

Abstract: The effect of melatonin and/or cholesterol on the structural properties of a model lipid bilayer prepared from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) has been investigated both experimentally and via molecular dynamics (MD) simulations. Neutron reflectometry experiments performed with single supported membranes revealed changes in lipid bilayer thickness upon the introduction of additional components. While the presence of cholesterol led to an increase in membrane thickness, the opposite effect was observed in the case of melatonin. The results obtained are in a good agreement with MD simulations which provided further information on the organization of components within the systems examined, indicating a mechanism underlying the membranes’ thickness changes due to cholesterol and melatonin that had been observed experimentally. Cholesterol and melatonin preferentially accumulate in different membrane regions, presumably affecting the conformation of lipid hydrophobic moieties differently, and in turn having distinct impacts on the structure of the entire membrane. Our findings may be relevant for understanding the effects of age-related changes in cholesterol and melatonin concentrations, including those in the brains of individuals with Alzheimer’s disease.
PubDate: 2021-10-01
DOI: 10.1007/s00249-021-01564-y

• ‘Chain and running’ induced by mechanical interactions among cells of
different phenotypes in the Bacillus subtilis biofilm

Abstract: In either a living system or a non-living system, the interaction among its constituent cells or particles is a fundamental aspect at all scales. For example, during the Bacillus subtilis biofilm formation, cells differentiate into multiple phenotypes to adapt to the environments; few hours after the initial inoculation, we find the phenotype of matrix-producing cells form “chain” structure surrounding the phenotype of the “running” motile cells. We use “chain” to characterize the structure of matrix-producing cells, and “running” to characterize the proliferation and growth of motile cells. Due to a large number of cells in the biofilm, it is impossible to construct a traditional kinetic model to describe the causal link between the single-cell movement and the colony behavior. Here, we obtain cell state information and cell group shape information through experiments; after the image analysis, we get the key interaction rules between cells, and then, we simulate the comparable movement of two cell types and the resulting colony geometry using the multi-agent model. Our work makes a better understanding of the relationship between the macroscopic shape of colonies and microscopic mechanical interactions among cells in the early stage of biofilm growth.
PubDate: 2021-10-01
DOI: 10.1007/s00249-021-01562-0

• Correction to: Lipoic acid nanoforms based on phosphatidylcholine:
production and characteristics

PubDate: 2021-09-22
DOI: 10.1007/s00249-021-01571-z

• Insight into dual fluorescence effects induced by molecular aggregation
occurring in membrane model systems containing 1,3,4-thiadiazole
derivatives

Abstract: This work reports on biophysical insights into the excited state intramolecular proton transfer (ESIPT) processes taking place in three 1,3,4-thiadiazole derivatives that served as model compounds, on which electronic absorption, fluorescence, Fourier-transform infrared spectroscopy (FTIR), surface plasmon resonance (SPR) and electrochemical impedance spectroscopy (EIS) studies were performed. The fluorescence spectra recorded in various solvents revealed an interesting dual fluorescence effect. In molecules in their monomeric form, the effect is associated with the ESIPT phenomenon, and may be further enhanced by aggregation-related effects, such as aggregation-induced emissions. Other spectroscopic studies on the selected molecules in a liposomal medium as a model revealed that, in a biomimetic environment, they can exist in both monomeric and aggregated forms. In both cases, however, the effects observed are closely related to the lipid’s main phase transition temperature and the structure of the molecule. Introduction of specific substituents to the phenyl moiety either allows or prevents proton transfer from occurring in the excited state. The hydrophobicity changes in a lipid environment may result in an emergence of specific molecular forms and therefore either facilitate or hinder ESIPT processes. SPR and EIS confirmed the significant hydrophobicity changes in the model lipid systems, while FTIR measurements revealed a notable influence of 1,3,4-thiadiazoles on the fluidity of liposomal membranes. The results obtained clearly show that the thiadiazole derivatives are very good model molecules for studying hydrophobic-hydrophilic environments, and particularly with polymers or liposomes used as drug delivery systems.
PubDate: 2021-09-13
DOI: 10.1007/s00249-021-01569-7

• Direct visualization of local activities of long DNA strands via
image–time correlation

Abstract: Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5–10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of $$\upmu m$$ ) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image–time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.
PubDate: 2021-09-09
DOI: 10.1007/s00249-021-01570-0

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