Methods in Modern Biophysics

Nölting, Bengt

doi:10.1007/978-3-662-05367-6

Cited by 13 publications

(6 citation statements)

References 336 publications

(390 reference statements)

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“…At present, many different experimental methods for studying the structure and dynamics of DNA have been developed. The most important are X-ray diffraction analysis, neutron scattering, infrared (IR) spectroscopy, hydrogen-deuterium(-tritium) exchange, resonant microwave absorption and nuclear magnetic resonance (NMR) [150,151]. In spite of this, fluorescence correlation spectroscopy of molecular beacons is the only technique that allows studying the kinetics of the denaturation bubble in DNA [152][153][154].…”

Section: Conclusion and Discussionmentioning

confidence: 99%

A review on nonlinear DNA physics

et al. 2020

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The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

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Section: Conclusion and Discussionmentioning

confidence: 99%

A review on nonlinear DNA physics

et al. 2020

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“…Why should we wish to perform such experiments which, as a rule, require measurements of tiny signals in environments of significant noise, in all but rare cases suffering from poor yields and, traditionally, being not remotely "high-throughput"? There already exist many robust bulk ensemble average biophysical methods which illuminate several aspects of structure and function of cellular systems using well-characterized experimental apparatus [5,6], with an effect of averaging over copious molecular events, typically resulting in low measurement noise.…”

Section: The Establishment Of Single Molecule Biophysics (A) Why Both...mentioning

confidence: 99%

The physics of life: one molecule at a time

Leake

2013

Phil. Trans. R. Soc. B

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The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight. The early days of single-molecule biophysics research was centred around molecular motors and biopolymers, largely divorced from a real physiological context. The new generation of single-molecule bioscience investigations has much greater scope, involving robust methods for understanding molecular-level details of the most fundamental biological processes in far more realistic, and technically challenging, physiological contexts, emerging into a new field of ‘single-molecule cellular biophysics’. Here, I outline how this new field has evolved, discuss the key active areas of current research and speculate on where this may all lead in the near future.

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“…For example, liquid chromatography, mass spectrometry, circular dichroism, analytical ultracentrifugation, electron microscopy, Fourier transform infrared and UVvisible spectroscopies have all proved to be ''absolute musts'' in characterizing peptide-based materials [64]. However, other techniques such as light scattering, surface plasmon resonance, solid-state NMR and atomic force microscopy are being used increasingly in the field [64].…”

Section: Key Techniquesmentioning

confidence: 99%