A rapid method for detecting protein-nucleic acid interactions
by protein induced fluorescence enhancement

J 2016

A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement

VALUCHOVÁ, Soňa, Jaroslav FULNEČEK, Alexander PETROV, Konstantinos TRIPSIANES, Karel ŘÍHA et. al.

Basic information

Original name

A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement

Authors

VALUCHOVÁ, Soňa (703 Slovakia, belonging to the institution), Jaroslav FULNEČEK (203 Czech Republic, belonging to the institution), Alexander PETROV (124 Canada, belonging to the institution), Konstantinos TRIPSIANES (300 Greece, belonging to the institution) and Karel ŘÍHA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Scientific Reports, LONDON, NATURE PUBLISHING GROUP, 2016, 2045-2322

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.259

RIV identification code

RIV/00216224:14740/16:00088759

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/srep39653

UT WoS

000390752600001

Keywords in English

SINGLE-MOLECULE; ENDONUCLEASE XPF-ERCC1; TRANSCRIPTION FACTORS; DNA INTERACTIONS; BINDING; REPAIR; POLYMERASE; INHIBITORS; ANISOTROPY; MECHANISM

Abstract

V originále

Many fundamental biological processes depend on intricate networks of interactions between proteins and nucleic acids and a quantitative description of these interactions is important for understanding cellular mechanisms governing DNA replication, transcription, or translation. Here we present a versatile method for rapid and quantitative assessment of protein/nucleic acid (NA) interactions. This method is based on protein induced fluorescence enhancement (PIFE), a phenomenon whereby protein binding increases the fluorescence of Cy3-like dyes. PIFE has mainly been used in single molecule studies to detect protein association with DNA or RNA. Here we applied PIFE for steady state quantification of protein/NA interactions by using microwell plate fluorescence readers (mwPIFE). We demonstrate the general applicability of mwPIFE for examining various aspects of protein/DNA interactions with examples from the restriction enzyme BamHI, and the DNA repair complexes Ku and XPF/ERCC1. These include determination of sequence and structure binding specificities, dissociation constants, detection of weak interactions, and the ability of a protein to translocate along DNA. mwPIFE represents an easy and high throughput method that does not require protein labeling and can be applied to a wide range of applications involving protein/NA interactions.

Links

GA14-22346S, research and development project

Name: Funkce TDM1 proteinu v meiόze

Investor: Czech Science Foundation

GJ15-22380Y, research and development project

Name: Molekulární stavba protein-DNA komplexů zapojených v opravě nukleotidových sestřihů

Investor: Czech Science Foundation

Citovat

VALUCHOVÁ, Soňa, Jaroslav FULNEČEK, Alexander PETROV, Konstantinos TRIPSIANES and Karel ŘÍHA. A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement. Scientific Reports. LONDON: NATURE PUBLISHING GROUP, 2016, vol. 6, December, p. nestránkováno, 10 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/srep39653.

@article{1375066,
   author = {Valuchová, Soňa and Fulneček, Jaroslav and Petrov, Alexander and Tripsianes, Konstantinos and Říha, Karel},
   article_location = {LONDON},
   article_number = {December},
   doi = {http://dx.doi.org/10.1038/srep39653},
   keywords = {SINGLE-MOLECULE; ENDONUCLEASE XPF-ERCC1; TRANSCRIPTION FACTORS; DNA INTERACTIONS; BINDING; REPAIR; POLYMERASE; INHIBITORS; ANISOTROPY; MECHANISM},
   language = {eng},
   issn = {2045-2322},
   journal = {Scientific Reports},
   title = {A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement},
   url = {http://www.nature.com/articles/srep39653},
   volume = {6},
   year = {2016}
}

TY  - JOUR
ID  - 1375066
AU  - Valuchová, Soňa - Fulneček, Jaroslav - Petrov, Alexander - Tripsianes, Konstantinos - Říha, Karel
PY  - 2016
TI  - A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement
JF  - Scientific Reports
VL  - 6
IS  - December
SP  - nestránkováno
EP  - nestránkováno
PB  - NATURE PUBLISHING GROUP
SN  - 20452322
KW  - SINGLE-MOLECULE
KW  - ENDONUCLEASE XPF-ERCC1
KW  - TRANSCRIPTION FACTORS
KW  - DNA INTERACTIONS
KW  - BINDING
KW  - REPAIR
KW  - POLYMERASE
KW  - INHIBITORS
KW  - ANISOTROPY
KW  - MECHANISM
UR  - http://www.nature.com/articles/srep39653
L2  - http://www.nature.com/articles/srep39653
N2  - Many fundamental biological processes depend on intricate networks of interactions between proteins and nucleic acids and a quantitative description of these interactions is important for understanding cellular mechanisms governing DNA replication, transcription, or translation. Here we present a versatile method for rapid and quantitative assessment of protein/nucleic acid (NA) interactions. This method is based on protein induced fluorescence enhancement (PIFE), a phenomenon whereby protein binding increases the fluorescence of Cy3-like dyes. PIFE has mainly been used in single molecule studies to detect protein association with DNA or RNA. Here we applied PIFE for steady state quantification of protein/NA interactions by using microwell plate fluorescence readers (mwPIFE). We demonstrate the general applicability of mwPIFE for examining various aspects of protein/DNA interactions with examples from the restriction enzyme BamHI, and the DNA repair complexes Ku and XPF/ERCC1. These include determination of sequence and structure binding specificities, dissociation constants, detection of weak interactions, and the ability of a protein to translocate along DNA. mwPIFE represents an easy and high throughput method that does not require protein labeling and can be applied to a wide range of applications involving protein/NA interactions.
ER  -

VALUCHOVÁ, Soňa, Jaroslav FULNEČEK, Alexander PETROV, Konstantinos TRIPSIANES and Karel ŘÍHA. A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement. \textit{Scientific Reports}. LONDON: NATURE PUBLISHING GROUP, 2016, vol.~6, December, p.~nestránkováno, 10 pp. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/srep39653.

Detailed Information on Publication Record