Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with Förster Resonance Energy Transfer Technique

N. S. Gerasimova; A. N. Korovina; D. A. Afonin; K. V. Shaytan; A. V. Feofanov; V. M. Studitsky

doi:10.1134/S0006350922020063

Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with Förster Resonance Energy Transfer Technique

N. S. Gerasimova, A. N. Korovina, D. A. Afonin, K. V. Shaytan, A. V. Feofanov, V. M. Studitsky

Lomonosov Moscow State University

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Abstract: To study the structural features of elongation complexes (EC) formed during nucleosome transcription by RNA polymerase II (Pol II), it was proposed to use an approach based on the measurement of the efficiency of Förster resonance energy transfer (FRET) in polyacrylamide gel after separation of transcription intermediates by electrophoresis. Fluorescently labeled nucleosomes were obtained by introducing a pair of fluorophores (donor and acceptor) into adjacent gyres of nucleosomal DNA. Stalled ECs were formed by transcription of nucleosomes in the presence of a limited set of nucleoside triphosphates. Comparative analysis of FRET efficiency for free nucleosomes and ECs with Pol II obtained on their basis revealed changes in the structure of nucleosomes in ECs. It was found that ECs with the same RNA length can exist in different conformational states.

Original language	English
Pages (from-to)	165-170
Number of pages	6
Journal	Biophysics (Russian Federation)
Volume	67
Issue number	2
DOIs	https://doi.org/10.1134/S0006350922020063
State	Published - Apr 2022

Keywords

FRET
RNA polymerase II
chromatin
elongation complex
nucleosome
transcription

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title = "Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with F{\"o}rster Resonance Energy Transfer Technique",

abstract = "Abstract: To study the structural features of elongation complexes (EC) formed during nucleosome transcription by RNA polymerase II (Pol II), it was proposed to use an approach based on the measurement of the efficiency of F{\"o}rster resonance energy transfer (FRET) in polyacrylamide gel after separation of transcription intermediates by electrophoresis. Fluorescently labeled nucleosomes were obtained by introducing a pair of fluorophores (donor and acceptor) into adjacent gyres of nucleosomal DNA. Stalled ECs were formed by transcription of nucleosomes in the presence of a limited set of nucleoside triphosphates. Comparative analysis of FRET efficiency for free nucleosomes and ECs with Pol II obtained on their basis revealed changes in the structure of nucleosomes in ECs. It was found that ECs with the same RNA length can exist in different conformational states.",

keywords = "FRET, RNA polymerase II, chromatin, elongation complex, nucleosome, transcription",

author = "Gerasimova, {N. S.} and Korovina, {A. N.} and Afonin, {D. A.} and Shaytan, {K. V.} and Feofanov, {A. V.} and Studitsky, {V. M.}",

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year = "2022",

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doi = "10.1134/S0006350922020063",

language = "English",

volume = "67",

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T1 - Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with Förster Resonance Energy Transfer Technique

AU - Gerasimova, N. S.

AU - Korovina, A. N.

AU - Afonin, D. A.

AU - Shaytan, K. V.

AU - Feofanov, A. V.

AU - Studitsky, V. M.

PY - 2022/4

Y1 - 2022/4

N2 - Abstract: To study the structural features of elongation complexes (EC) formed during nucleosome transcription by RNA polymerase II (Pol II), it was proposed to use an approach based on the measurement of the efficiency of Förster resonance energy transfer (FRET) in polyacrylamide gel after separation of transcription intermediates by electrophoresis. Fluorescently labeled nucleosomes were obtained by introducing a pair of fluorophores (donor and acceptor) into adjacent gyres of nucleosomal DNA. Stalled ECs were formed by transcription of nucleosomes in the presence of a limited set of nucleoside triphosphates. Comparative analysis of FRET efficiency for free nucleosomes and ECs with Pol II obtained on their basis revealed changes in the structure of nucleosomes in ECs. It was found that ECs with the same RNA length can exist in different conformational states.

AB - Abstract: To study the structural features of elongation complexes (EC) formed during nucleosome transcription by RNA polymerase II (Pol II), it was proposed to use an approach based on the measurement of the efficiency of Förster resonance energy transfer (FRET) in polyacrylamide gel after separation of transcription intermediates by electrophoresis. Fluorescently labeled nucleosomes were obtained by introducing a pair of fluorophores (donor and acceptor) into adjacent gyres of nucleosomal DNA. Stalled ECs were formed by transcription of nucleosomes in the presence of a limited set of nucleoside triphosphates. Comparative analysis of FRET efficiency for free nucleosomes and ECs with Pol II obtained on their basis revealed changes in the structure of nucleosomes in ECs. It was found that ECs with the same RNA length can exist in different conformational states.

KW - FRET

KW - RNA polymerase II

KW - chromatin

KW - elongation complex

KW - nucleosome

KW - transcription

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U2 - 10.1134/S0006350922020063

DO - 10.1134/S0006350922020063

M3 - Article

AN - SCOPUS:85133141077

SN - 0006-3509

VL - 67

SP - 165

EP - 170

JO - Biophysics (Russian Federation)

JF - Biophysics (Russian Federation)

IS - 2

ER -

Analysis of Structure of Elongation Complexes in Polyacrylamide Gel with Förster Resonance Energy Transfer Technique

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Keywords

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