Thermal unwinding of Polyadenylic·Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions

M. Ivanov, V. Sizov, A. Kudrev

Результат исследований: Научные публикации в периодических изданияхстатья

Выдержка

The molecular mechanism of Poly(A)•Poly(U) (Polyadenylic•Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV–Vis-melting experiments. UV–Vis absorption spectra of Poly(A)•Poly(U) were measured at different temperatures (20–70 °C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)•Poly(U) altered by formation of the ternary [Poly(A)•Poly(U)]*(TMPyP4)n complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 °C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)•Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)12•(rU)12 oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)12•(rU)12 oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.

Язык оригиналаанглийский
Номер статьи127365
ЖурналJournal of Molecular Structure
Том1202
Ранняя дата в режиме онлайн8 ноя 2019
DOI
СостояниеОпубликовано - 15 фев 2020

Отпечаток

Poly U
Poly A
Porphyrins
Polyribonucleotides
Acids
Molecular dynamics
Oligonucleotides
Computer simulation
Melting
Denaturation
Melting point
Absorption spectra
Stabilization
Hot Temperature
tetra(4-N-methylpyridyl)porphine
Ligands
Temperature
Experiments

Предметные области Scopus

  • Аналитическая химия
  • Спектроскопия
  • Органическая химия
  • Неорганическая химия

Цитировать

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abstract = "The molecular mechanism of Poly(A)•Poly(U) (Polyadenylic•Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV–Vis-melting experiments. UV–Vis absorption spectra of Poly(A)•Poly(U) were measured at different temperatures (20–70 °C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)•Poly(U) altered by formation of the ternary [Poly(A)•Poly(U)]*(TMPyP4)n complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 °C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)•Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)12•(rU)12 oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)12•(rU)12 oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.",
keywords = "Chemometric analysis, Melting, Molecular dynamics simulations, Poly(A)•Poly(U), TMPyP4",
author = "M. Ivanov and V. Sizov and A. Kudrev",
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doi = "10.1016/j.molstruc.2019.127365",
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Thermal unwinding of Polyadenylic·Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions. / Ivanov, M.; Sizov, V.; Kudrev, A.

В: Journal of Molecular Structure, Том 1202, 127365, 15.02.2020.

Результат исследований: Научные публикации в периодических изданияхстатья

TY - JOUR

T1 - Thermal unwinding of Polyadenylic·Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions

AU - Ivanov, M.

AU - Sizov, V.

AU - Kudrev, A.

PY - 2020/2/15

Y1 - 2020/2/15

N2 - The molecular mechanism of Poly(A)•Poly(U) (Polyadenylic•Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV–Vis-melting experiments. UV–Vis absorption spectra of Poly(A)•Poly(U) were measured at different temperatures (20–70 °C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)•Poly(U) altered by formation of the ternary [Poly(A)•Poly(U)]*(TMPyP4)n complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 °C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)•Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)12•(rU)12 oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)12•(rU)12 oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.

AB - The molecular mechanism of Poly(A)•Poly(U) (Polyadenylic•Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV–Vis-melting experiments. UV–Vis absorption spectra of Poly(A)•Poly(U) were measured at different temperatures (20–70 °C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)•Poly(U) altered by formation of the ternary [Poly(A)•Poly(U)]*(TMPyP4)n complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 °C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)•Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)12•(rU)12 oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)12•(rU)12 oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.

KW - Chemometric analysis

KW - Melting

KW - Molecular dynamics simulations

KW - Poly(A)•Poly(U)

KW - TMPyP4

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U2 - 10.1016/j.molstruc.2019.127365

DO - 10.1016/j.molstruc.2019.127365

M3 - Article

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VL - 1202

JO - Journal of Molecular Structure

JF - Journal of Molecular Structure

SN - 0022-2860

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