Santiago Cuesta-Lopez

Ecole normale supérieure de Lyon | ENS Lyon · UMR 5672 - Laboratoire de Physique

There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in...

Porous silicon carbide is a promising material for ceramic receivers in next-generation concentrated solar power receivers. To investigate its tolerance to thermal shock, accelerated ageing of large coupons (50 × 50 × 5 mm) was conducted in a solar furnace to investigate the effects of thermal cycling up to 1000 °C, with gradients of up to 22 °C/mm...

The melting transition of Li‐DNA fibers immersed in ethanol‐water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard‐Bishop‐Dauxois model to determine the strengths of the intra‐ and inter‐base pair potentials. The data and analysis show that the potentials are weaker than...

The properties of single walled nanotubes and carbon fullerenes in molten alkali carbonates were studies as a function of the considered nanomaterial and the ions in the molten salt using classical molecular dynamics simulations. The adsorption and confinement in carbon nanotubes is developed by efficient adsorption of carbonate ions in inner and o...

The aim of this paper is to briefly analyze different methodologies for development of novel materials systems and coatings for use in extreme environments, with a focus on high-temperature applications in aerospace and aeronautics. The approach is based on a comparative analysis of selected major thermal stability properties of different material...

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of lp≈500Å is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed x-ray and neutron small-angle scattering on a short DNA sequence containing a...

The properties and structure of relevant interfaces involving molten alkali carbonates are studied using molecular dynamics simulations. Lithium carbonate and the Li/Na/K carbonate eutectic mixture are considered. Gas phase composed of pure CO2 or a model flue gas mixture are analysed. Likewise, the adsorption of these gas phases on graphene are st...

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA seque...

Polymeric electrospun fibers are becoming popular in microbial biotechnology due to their exceptional physicochemical characteristics, biodegradability, surface-to-volume ratio, and compatibility with biological systems, which give them a great potential as microbial supports to be used in production processes or environmental applications. In this...

Although previously developed mesoscopic DNA models have successfully reproduced thermodynamic denaturation data, recent studies show that these overestimate the rate of denaturation by orders of magnitude. Using adapted PeyrardBishop-Dauxois (PBD) models, we calculated the denaturation rates of several DNA hairpins and made comparison with experim...

The modification of carbon nanomaterials with biological molecules paves the way towards their use in biomedical and biotechnological applications, such as next generation biocatalytic processes, development of biosensors, implantable electronic devices, or drug delivery. In this study, different commercial graphene derivatives, namely, monolayer g...

The influence of molecular confinement on the melting transition of oriented Na-DNA fibers submerged in poly(ethylene glycol) (PEG) solutions has been studied. The PEG solution exerts an osmotic pressure on the fibers which, in turn, is related to the DNA intermolecular distance. Calorimetry measurements show that the melting temperature increases...

The DNA molecule can take various conformational forms. Investigations focus mainly on the so-called 'B-form', schematically drawn in the famous paper by Watson and Crick [1]. This is the usual form of DNA in a biological environment and is the only form that is stable in an aqueous environment. Other forms, however, can teach us much about DNA. Th...

Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine t...

DNA is not the static entity that structural pictures suggest. It has been longly known that it ‘breathes’ and fluctuates by local opening of the bases. Here we show that the effect of structural fluctuations, exhibited by AT-rich low stability regions present in some common transcription initiation regions, influences the properties of DNA in a di...

The melting transition of DNA, whereby the strands of the double-helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fiber DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Da...

Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting curves of short DNA sequences by allowing us to record the degree of opening in several positions along the mol...

We show that the calculated DNA denaturation curves for finite (Peyrard-Bishop-Dauxois (PBD) chains are intrinsically undefined.

The ability of the telomeric DNA-binding protein, TRF2, to stimulate t-loop formation while preventing t-loop deletion is believed to be crucial to maintain telomere integrity in mammals. However, little is known on the molecular mechanisms behind these properties of TRF2. In this report, we show that TRF2 greatly increases the rate of Holliday jun...

We show that the calculated DNA denaturation curves for finite (Peyrard-Bishop-Dauxois (PBD) chains are intrinsically undefined.

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening...

When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be used as a guide to improve them. There are nevertheless many open problems, particularly to describe DNA at the s...

Flavodoxins, noncovalent complexes between apoflavodoxins and flavin mononucleotide (FMN), are useful models to investigate the mechanism of protein/flavin recognition. In this respect, the only available crystal structure of an apoflavodoxin (that from Anabaena) showed a closed isoalloxazine pocket and the presence of a bound phosphate ion, which...

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there migh...

A Reply to the Comment by Craig J. Benham and Rajiv R. P. Singh.

Erp et al. Reply: The aim of our Letter [1] was not a criticism of earlier studies, but the introduction of a new method that is orders-of-magnitude faster than molecular dynamics (MD) for the calculation of bubble statistics in the Peyrard-Bishop-Dauxois (PBD) model of DNA. Of course, as the need for such a method had been pointed out by the study...

A Reply to the Comment by C. H. Choi et al..

Erp et al. Reply: The preceding Comment [1] to our recent Letter [2] contains an interesting discussion on the appropriate modeling of DNA local opening in vivo to allow the prediction of biologically active sites. However, it was not our aim to predict biological activity. The emphasis of our Letter was on (i) the introduction of an efficient comp...

It has been speculated that bubble formation of several base pairs due to thermal fluctuations is indicatory for biologically active sites. Recent evidence, based on experiments and molecular dynamics simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom, which m...

The theory of the liquid-glass transition is extended to describe the polymerization of RNA in a nucleotide-condensed state. In the glassy state the ribose subunits are joined by a 2'-5' or 3'-5' phosphodiester linkage to form the ribose-phosphate backbone similar to oligosaccharides and polysaccharides. The occurrence of the glass transition requi...

Proteins could be used to carry and deliver small compounds. As a tool for designing ligand binding sites in protein cores, a three-step virtual screening method is presented that has been optimised using existing data on T4 lysozyme complexes and tested in a newly engineered cavity in flavodoxin. The method can pinpoint, in large databases, ligand...

The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their contribution to protein stability is still unclear and widely debated. The best method so far devised to estimate t...