Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study

Sebastiani, Federico; Pietrini, Alberto; Longo, Marialucia; Comez, Lucia; Petrillo, C.; Sacchetti, F.; Paciaroni, Alessandro

doi:10.1021/jp411096d

Cited by 12 publications

(22 citation statements)

References 45 publications

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“…It is likely that sample quality also plays a role. A recent study on non-oriented fibers showed very similar Bragg peak behaviour in both A-and B-DNA [6], with both data sets resembling our measurements on B-DNA [8]. It is feasible that the previous study also suffered from fiber collapse, hence explaining the similarity of the two data sets.…”

Section: Neutron Diffraction Resultssupporting

confidence: 84%

“…However, the DNA often takes a combination of A and B-forms, as well as molecules with B-A interfaces, so that experimental results cannot be quantitatively interpreted. A-DNA can be prepared from randomly oriented fibers and studies of the melting process have been reported [6]. Neither DNA in solution nor in randomly oriented fibers will give unambiguous experimental information on the spatial structure.…”

Section: Introductionmentioning

confidence: 99%

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Thermal denaturation of A-DNA

et al. 2014

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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. They have the same nucleotide base pairs for 'building blocks' as B-DNA, but with different relative positions, and studying these forms gives insight into the interactions between elements under conditions far from equilibrium in the B-form. Studying the thermal denaturation is particularly interesting because it provides a direct probe of those interactions which control the growth of the fluctuations when the 'melting' temperature is approached. Here we report such a study on the 'A-form' using calorimetry and neutron scattering. We show that it can be carried further than a similar study on B-DNA, requiring the improvement of thermodynamic models for DNA.

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Section: Neutron Diffraction Resultssupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Thermal denaturation of A-DNA

et al. 2014

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“…As a direct result, we emphasized the importance of sequence length on the hysteresis phenomenon. This result is similar to previous published work [31,32], where the relevance of the sequence is key when studying DNA melting.…”

Section: Resultssupporting

confidence: 92%

“…The rise of the DNA melting temperature due to electrostatic interactions predicted in such a theoretical paper has just been proved experimentally [32].…”

Section: Temperature-driven Dna Denaturationmentioning

confidence: 80%

Stress-induced DNA damage: a case study in diffuse large B-cell lymphoma

Nicasio-Collazo

Delgado-González

Castañeda-Priego

et al. 2014

J. R. Soc. Interface.

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DNA damage is one of the mechanisms of mutagenesis. Sequence integrity may be affected by the action of thermal changes, chemical agents, both endogenous and exogenous, and other environmental issues. Abnormally high mutation rates are referred to as genomic instability: a phenomenon closely related to the onset of cancer. Mutant genotypes may be able to confer some kind of selective advantage on subclonal cell populations, leading them to multiply until dominance in a localized tissue environment that later becomes the tumour. Cellular stress, especially that of oxidative and ionic nature, is a recognized trigger for DNA-damaging processes. A physico-chemical model has shown that high hysteresis rates in DNA denaturation curves may be indicative of dissipative processes inducing DNA damage, thus potentially leading to uncontrolled mutagenesis and genome instability. We here study selectively to what extent this phenomenon may occur by analysing the sequence length and composition effects on the thermodynamic behaviour and the presence of hysteresis in pressure-driven DNA denaturation; pronounced hysteresis in the denaturation/renaturation curves may indicate thermal susceptibility to DNA damage. In particular, we consider highly mutated regions of the genome characterized in diffuse large B-cell lymphoma on a recent whole exome next-generation sequencing effort.

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“…From a broader perspective on biological matter, it is interesting to compare the protein system to the well-studied example of DNA: analogously to the observations in our protein-cation systems, cation-82 and polymer- 83 induced attraction between DNA strands can similarly stabilise and shift the melting temperature of DNA to higher values. An additional factor influencing the melting transition of DNA is its degree of hydration, 84 which provides another conceptual link between phase transitions of DNA and proteins. The crucial aspect of hydration in our protein-cation systems will be discussed in more detail in the following.…”

Section: Discussionmentioning

confidence: 99%

Tuning phase transitions of aqueous protein solutions by multivalent cations

Matsarskaia

Roosen-Runge

Lötze

et al. 2018

Phys. Chem. Chem. Phys.

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In the presence of trivalent cations, negatively charged globular proteins show a rich phase behaviour including reentrant condensation, crystallisation, clustering and lower critical solution temperature metastable liquid-liquid phase separation (LCST-LLPS). Here, we present a systematic study on how different multivalent cations can be employed to tune the interactions and the associated phase behaviour of proteins. We focus our investigations on the protein bovine serum albumin (BSA) in the presence of HoCl 3 , LaCl 3 and YCl 3 . Using UV-Vis spectroscopy and small-angle X-ray scattering (SAXS), we find that the interprotein attraction induced by Ho 3+ is very strong, while the one induced by La 3+ is comparatively weak when comparing the data to BSA-Y 3+ systems based on our previous work. Using zeta potential and isothermal titration calorimetry (ITC) measurements, we establish different binding affinities of cations to BSA with Ho 3+ having the highest one. We propose that a combination of different cation features such as radius, polarisability and in particular hydration effects determine the proteinprotein interaction induced by these cations. Our findings imply that subtle differences in cation properties can be a sensitive tool to fine-tune protein-protein interactions and phase behaviour in solution.

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Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study

Cited by 12 publications

References 45 publications

Thermal denaturation of A-DNA

Thermal denaturation of A-DNA

Stress-induced DNA damage: a case study in diffuse large B-cell lymphoma

Tuning phase transitions of aqueous protein solutions by multivalent cations

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