Magnesium effect on premelting transitions in nucleic acids: DNA duplex and RNA hairpin models

Ottová, Pavla; Espinoza-Herrera, Shirly J.; Štěpánek, Josef

doi:10.1016/j.molstruc.2010.12.025

Cited by 3 publications

(2 citation statements)

References 20 publications

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“…Secondary DNA structural prediction analysis revealed several potential hairpin sites in this template. Mg 2+ is known to increase the stability of the secondary structures of DNA and RNA [45]. It looks like polα is more sensitive to irregularities in the template than the Klenow fragment.…”

Section: Discussionmentioning

confidence: 99%

Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

et al. 2016

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DNA polymerases (pols) are sophisticated protein machines operating in the replication, repair and recombination of genetic material in the complex environment of the cell. DNA pol reactions require at least two divalent metal ions for the phosphodiester bond formation. We explore two understudied roles of metals in pol transactions with emphasis on pol α, a crucial enzyme in the initiation of DNA synthesis. We present evidence that the combination of many factors, including the structure of the template/primer, the identity of the metal, the metal turnover in the pol active site, and the influence of the concentration of nucleoside triphosphates, affect DNA pol synthesis. On the poly-dT70 template, the increase of Mg2+ concentration within the range typically used for pol reactions led to the severe loss of the ability of pol to extend DNA primers and led to a decline in DNA product sizes when extending RNA primers, simulating the effect of “counting” of the number of nucleotides in nascent primers by polα. We suggest that a high Mg2+ concentration promotes the dynamic formation of unconventional DNA structure(s), thus limiting the apparent processivity of the enzyme. Next, we found that Zn2+ supported robust polα reactions when the concentration of nucleotides was above the concentration of ions; however, there was only one nucleotide incorporation by the Klenow fragment of DNA pol I. Zn2+ drastically inhibited polα, but had no effect on Klenow, when Mg2+ was also present. It is possible that Zn2+ perturbs metal-mediated transactions in pol active site, for example affecting the step of pyrophosphate removal at the end of each pol cycle necessary for continuation of polymerization.

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Section: Discussionmentioning

confidence: 99%

Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

et al. 2016

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“…The vibrational mode of Asn was characterised by Raman scattering. Raman spectra were acquired on a modular multi-channel Raman spectrograph Jobin Yvon-Spex 270M in 90 • scattering geometry using a 532.15 nm line of a continuous-wave solid-state Nd-YAG laser for excitation, as described in references [29,30]. The power at the sample was 240 mW [supplementary figure 3 measurements were performed at room temperaturecontrolled hermetical quartz cell (2 mm).…”

Section: Characterisationmentioning

confidence: 99%

Role of pH in the synthesis and growth of gold nanoparticles using L-asparagine: a combined experimental and simulation study

Báez-Cruz

Baptista

Ntim

et al. 2021

J. Phys.: Condens. Matter

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The use of biomolecules as capping and reducing agents in the synthesis of metallic nanoparticles constitutes a promising framework to achieve desired functional properties with minimal toxicity. The system’s complexity and the large number of variables involved represent a challenge for theoretical and experimental investigations aiming at devising precise synthesis protocols. In this work, we use L-asparagine (Asn), an amino acid building block of large biomolecular systems, to synthesise gold nanoparticles (AuNPs) in aqueous solution at controlled pH. The use of Asn offers a primary system that allows us to understand the role of biomolecules in synthesising metallic nanoparticles. Our results indicate that AuNPs synthesised in acidic (pH 6) and basic (pH 9) environments exhibit somewhat different morphologies. We investigate these AuNPs via Raman scattering experiments and classical molecular dynamics simulations of zwitterionic and anionic Asn states adsorbing on (111)-, (100)-, (110)-, and (311)-oriented gold surfaces. A combined analysis suggests that the underlying mechanism controlling AuNPs geometry correlates with amine’s preferential adsorption over ammonium groups, enhanced upon increasing pH. Our simulations reveal that Asn (both zwitterionic and anionic) adsorption on gold (111) is essentially different from adsorption on more open surfaces. Water molecules strongly interact with the gold face-centred-cubic lattice and create traps, on the more open surfaces, that prevent the Asn from diffusing. These results indicate that pH is a relevant parameter in green-synthesis protocols with the capability to control the nanoparticle’s geometry, and pave the way to computational studies exploring the effect of water monolayers on the adsorption of small molecules on wet gold surfaces.

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Aminoquinolines: Fluorescent sensors to DNA – A minor groove probe. Experimental and in silico studies

Bertozo

Tutone

Pastrello

et al. 2023

Journal of Photochemistry and Photobiology A: Chemistry

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Magnesium effect on premelting transitions in nucleic acids: DNA duplex and RNA hairpin models

Cited by 3 publications

References 20 publications

Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

Role of pH in the synthesis and growth of gold nanoparticles using L-asparagine: a combined experimental and simulation study

Aminoquinolines: Fluorescent sensors to DNA – A minor groove probe. Experimental and in silico studies

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