Application of Polarization Modulation Infrared Reflection Absorption Spectrosocpy Under Electrochemical Control for Structural Studies of Biomimetic Assemblies

Brand, Izabella

doi:10.1515/zpch-2014-0657

Cited by 16 publications

(9 citation statements)

References 150 publications

(399 reference statements)

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“…Here, infrared spectroscopy (IRS) is of particular importance as it is one of the most relevant analytical techniques used to probe the composition and structure of organic molecules, including biomolecules such as DNA and proteins. , Since different functional groups absorb the IR light at different frequencies, different molecular fragments of a complex supramolecular assembly may be analyzed simultaneously. Reflection-based IRS techniques allow in situ and ex situ studies of the structure and conformation of biomolecules adsorbed on metallic surfaces. ,− In addition, the structure of short dsDNA fragments adsorbed on a gold surface has been investigated by means of polarization modulation infrared reflection absorption spectroscopy (PM IRRAS). , …”

Section: Introductionmentioning

confidence: 99%

What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute–Biopolymer Interactions

et al. 2020

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Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and doublestranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar−phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.

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Section: Introductionmentioning

confidence: 99%

What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute–Biopolymer Interactions

et al. 2020

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“…Infrared spectroscopy (IRS), one of the most important analytical techniques for identification of the molecular structure, can contribute to this task accomplishment. Absorption of the IR light by various molecular groups at different frequencies allows a simultaneous, label-free measurement of absorption modes originating from these groups, , and reflection based IR spectroscopy allows in situ analysis of the composition and structure of organic molecules adsorbed at the liquid|solid interface. , Moreover, due to the excellent signal-to-noise ratio, polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) is particularly attractive for simultaneous in situ studies of changes in the structure, orientation, and hydration of biomolecules adsorbed at solid surfaces. , …”

Section: Introductionmentioning

confidence: 99%

“…37,38 Moreover, due to the excellent signal-to-noise ratio, polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) is particularly attractive for simultaneous in situ studies of changes in the structure, orientation, and hydration of biomolecules adsorbed at solid surfaces. 36,39 In this article, in situ PM IRRAS under electrochemical control was for the first time used to study the electrodepotential induced changes in the structure and orientation of DNA duplexes tethered to polycrystalline gold electrodes via an alkanethiol linker. Here, DNA duplexes composed of either cytosine-guanine (dGdC) 20 or adenine-thymine (dAdT) 25 were studied.…”

Section: ■ Introductionmentioning

confidence: 99%

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Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials

2017

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Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT) or cytosine-guanine (dGdC) base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT) molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC) helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.

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“…The liquid layer thickness for this experiment (Figure A) scales to that of the gold substrate in pure ethanol (with no adsorbed SAM film), indicating that approximating the four-layer system (air/ethanol/SAM/gold) as a three-layer system (air/ethanol/gold) in the C–O stretch region is in good agreement. Previous studies have estimated the liquid layer thickness ranges between 10 and 30 nm for AP-XPS ,, and 0.5–5 μm for electrochemical studies using various FTIR techniques. ,− In our system, the meniscus is only produced in a finite thickness of up to 12 nm. It is possible to achieve a thickness of several micrometers, as observed with previous PM-IRRAS and infrared spectroscopy setups. ,,,− However, the limitation in our setup is the wettability of the surface and finite volume in the beaker needed to produce the meniscus, before overflow occurs.…”

Section: Resultsmentioning

confidence: 95%

New Approach to Simultaneous In Situ Measurements of the Air/Liquid/Solid Interface Using PM-IRRAS

2020

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Vibrational spectroscopy techniques have evolved to measure gases, liquids, and solids at surfaces and interfaces. In the field of surface-sensitive vibrational spectroscopy, infrared spectroscopy measures the adsorption on surfaces and changes from reactions. Previous polarized modulated-infrared reflection− absorption spectroscopy (PM-IRRAS) measurements at the gas/ solid interface were developed to observe catalytic reactions near reaction conditions. Other PM-IRRAS measurements use liquid cells where the sample is submerged and compressed against a prism that has traditionally been used for electrochemical reactions. This article presents a new method that is used to observe in situ adsorption of molecules using PM-IRRAS at the gas/liquid/solid interface. We demonstrate the meniscus method by measuring the adsorption of octadecanethiol on gold surfaces. Characterization of self-assembled monolayers (SAMs), the "gold standard" for PM-IRRAS calibration measurements, was measured in ethanol solutions. The condensed-phase (air/liquid) interface in addition to the liquid/solid interface was measured simultaneously in solution. These are compared with liquid attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy measurements to confirm the presence of the SAM and liquid ethanol. A model of the three-phase system is used to approximate the thickness of the liquid ethanol layer and correlate these values to signal attenuation using PM-IRRAS. This proof-of-concept study enables the measurement of reactions at the gas/liquid/solid interface that could be adapted for other reactions at the electrode and electrolyte interfaces with applications in environmental science and heterogeneous catalysis.

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Application of Polarization Modulation Infrared Reflection Absorption Spectrosocpy Under Electrochemical Control for Structural Studies of Biomimetic Assemblies

Cited by 16 publications

References 150 publications

What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute–Biopolymer Interactions

What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute–Biopolymer Interactions

Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials

New Approach to Simultaneous In Situ Measurements of the Air/Liquid/Solid Interface Using PM-IRRAS

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