Structure and hydration of polycytidylic acid from the data of infrared spectroscopy, EHF dielectrometry and computer modeling

Maleev, V. Ya.; Semenov, M. A.; Kashpur, V. A.; Bolbukh, T. V.; Shestopalova, Anna V.; Anishchenko, D.

doi:10.1016/s0022-2860(01)00666-4

Cited by 14 publications

(14 citation statements)

References 13 publications

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“…Before we consider each band in detail, two spectral regions should be identified, namely, the 1700–1500 and 1100–900 cm –1 regions which correspond to the cytosine and sugar–phosphate moiety vibrations, respectively. Detailed assignments of the bands in these two regions can be found elsewhere. − The most intensive band of the first spectral region (at 1654 cm –1 ) is likely related to the stretching vibration of the CO group of cytosine. , The frequency of this band decreases compared to the corresponding band of the GO hexagon due to the presence of nitrogen in the pyrimidine ring of cytosine . It should be noted that the intensity of this band is increased due to a contribution from the band corresponding to the scissors mode of the closely located NH 2 group. , The stretching mode of the CC bond of pyrimidine ring of cytosine gives rise to the band at 1611 cm –1 (in GO this mode is responsible for the band at 1587 cm –1 ).…”

Section: Results and Discussionmentioning

confidence: 99%

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

et al. 2017

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Hybridization of nucleic acids with graphene nanomaterials is of great interest due to its potential application in genosensing and nanomedicine. In this work we study the interaction between polyribocytidylic acid (poly(rC)) and graphene oxide (GO). The study involves comparing the UV absorption spectra of the free polymer and the polymer bonded to graphene oxide and analyzing the vibrational structure of the systems and their components using FTIR spectroscopy. Spectral shifts of the electronic and vibrational bands of the poly(rC) and changes of their thermostability due to the adsorption on GO are observed. Molecular dynamics simulation of the adsorption process of the r(C)10 and r(C)30 oligomers on graphene demonstrates their disordering due to the π–π stacking of cytosines on graphene and shows that the longer oligomer adsorbs slower. The binding energies of a single cytosine stacked with graphene in water and in vacuum were determined. The calculated IR lines of the stacked cytosine with graphene are red-shifted by up to 20 cm–1 compared to free cytosine. A strong decrease of the intensities of the cytosine vibrations in the 1800–1400 cm–1 range resulting from the interaction with graphene is revealed in the spectra. When cytosine is adsorbed to graphene oxide, their complex is additionally stabilized by H-bonding. It leads to an increase of the red shifting of the cytosine lines.

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Section: Results and Discussionmentioning

confidence: 99%

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

et al. 2017

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“…[146] по 2000-е гг. [147][148][149][150][151][152]; 5) применимость инфракрасного анализа к пленкам молочной продукции [131] позволяет использовать UR-20 для промера последних, поскольку существует немало работ (последняя относится к 2012 году [155]), в которых накоплен опыт и выработаны эффективные методические подходы к измерению органических пленок [153][154][155] (впрочем, как и неорганических [156][157][158]) на нем, причем, с точки зрения эффектов инфракрасной пастеризации [105][106][107][108][109][110][111][112][113][114][115], небезынтересны работы по изучению детектирования теплового инфракрасного излучения этими пленками * [159]; 6) если рассматривать пастеризуемые сыры (в т.ч. плавленые) как гетерогенные системы, что имеет корреляцию с [134], то в пределе возможно использование UR-20 для их изучения как биокомпозитных материалов и нанобиокомпозитов, поскольку (с середины 2000-х гг.…”

Section: материалы и методыunclassified

Infrared Spectrophotometry, Infrared Spectroscopy and Infrared Spectrometry in Diary Spectral Qualimetry: Contemporary Ideas and Retro-Engineering

2016

Food Engineering Theory and Practice

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Infrared spectrophotometry, infrared spectroscopy and infrared spectrometry are basic quality testing techniques for different diary industry aims. Vibrartional spectroscopy, as well as rotational spectroscopy, is a power instrument for the structural analysis of different biological media and, consequently, for structural analysis for food qualimetry. This article presents a precision review of qualimetry of diary samples and their components based on infrared techniques. Author also present some retrophysical / retrotechnical investigations for adaptation of retro-spectral devices for diary qualimetry.Keywords: NIR, MIR, infrared spectrophotometry, infrared spectroscopy, infrared spectrometry, spectral qualimetry, structural analysis, diary industry, vibrational spectra. ВведениеМетоды инфракрасной спектроскопии являются мощным многопрофильным средством анализа молока, молочных продуктов и производных субстанций, имеющим достаточно длительную (много десятилетий -первый коммерческий инфракрасный анализатор молока близкой к современной конструкции был продемонстрирован в начале 1970-х [1]) историю применимости в молочном хозяйстве. Для промышленного применения немаловажно, что, в отличие от ряда других, альтернативных современных способов, он является методом неразрушающего контроля [2], не влияющим на параметры пробы при поточном анализе. Новые автоматизированные подходы категорически изменили бытовавшее ещё недавно мнение об ограниченной применимости инфракрасной спектроскопии в массовой практике ферм и производственных предприятий; в особенности -учитывая распространение DIY подхода и модернизации оборудования с устаревающим интерфейсом, но работоспособной схемой оптической регистрации [3]. Поэтому имеет смысл рассмотрение последних трендов развития методов ИК спектроскопии, используемых в молочной отрасли, с целью распространения аналогичных подходов в условиях России. Если для 1970-1980-х гг. немногочисленные комплексные исследования, включавшие в себя инфракрасную спектроскопию молока, были внове и представляли собой высокодифференцированные коллаборационные работы -продукты взаимодействия лабораторий разного профиля [4,5], то в настоящее время во многих местах они являются стандартными процедурами определения качества на потоке и не вызывают затруднений даже для одного лаборанта -пользователя автоматизированного оборудования. Поэтому

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“…In the IR spectroscopy the main difficulties are associated with the strong OH vibration of water molecules. This problem may be resolved by applying this method with respect to DNA-water systems prepared in wet films with changing water content [51][52][53][54]. Analyzing the changes in IR spectra which occur in several frequency modes (e.g.…”

Section: Hydrationmentioning

confidence: 99%

“…Monte Carlo simulations enable to evaluate the low energy conformations of various complexes of DNA fragments, including their complexes with ligands, and to determine the hydration properties of the complexes being formed [54,55,83,84].…”

Section: Computer Modelingmentioning

confidence: 99%

Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment

Evstigneev

Shestopalova

2014

Challenges and Advances in Computational Chemistry and Physics

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In this chapter we demonstrate the large usefulness of using complex approach for understanding the mechanism of binding of biologically active compounds (antitumour antibiotics, mutagens etc.) with nucleic acids (NA). The applications of various biophysical methods and computer modeling to determination of structural (Infra-red and Raman vibrational spectroscopies, computer modeling by means of Monte-Carlo, molecular docking and molecular dynamics methods) and thermodynamic (UV-VIS spectrophotometry, microcalorimetry, molecular dynamics simulation) parameters of NA-ligand complexation with estimation of the role of water environment in this process, are discussed. The strategy of energy analysis of the NA-ligand binding reactions in solution is described, which is based on decomposition of experimentally measured net Gibbs free energy of binding in terms of separate energetic contributions from particular physical factors. The main outcome of such analysis is to answer the questions "What physical factors and to what extent stabilize/destabilize NA-ligand complexes?" and "What physical factors most strongly affect the bioreceptor binding affinity?"

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Structure and hydration of polycytidylic acid from the data of infrared spectroscopy, EHF dielectrometry and computer modeling

Cited by 14 publications

References 13 publications

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

Infrared Spectrophotometry, Infrared Spectroscopy and Infrared Spectrometry in Diary Spectral Qualimetry: Contemporary Ideas and Retro-Engineering

Structure, Thermodynamics and Energetics of Drug-DNA Interactions: Computer Modeling and Experiment

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