Elongated Thrombin Binding Aptamer: A G-Quadruplex
Cation-Sensitive Conformational Switch

J 2012

Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch

RACHE, Aurore De, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ and Claudine BUESS-HERMAN

Basic information

Original name

Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch

Authors

RACHE, Aurore De, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ and Claudine BUESS-HERMAN

Edition

Chemistry - A European Journal, WEINHEIM, WILEY-VCH, 2012, 0947-6539

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.831

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/chem.201103381

UT WoS

000302073700033

Keywords in English

circular dichroism; DNA structures; G-quadruplexes; hexa-ammine ruthenium; thermal difference spectra

Abstract

V originále

Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5' end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba2+, Ca2+, K+, Mg2+, Na+, NH4+, Sr2+ and the [Ru(NH3)6]2+/3+ redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH3)6]3+, which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K+ reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.

Citovat

RACHE, Aurore De, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ and Claudine BUESS-HERMAN. Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2012, vol. 18, No 14, p. 4392-4400. ISSN 0947-6539. Available from: https://dx.doi.org/10.1002/chem.201103381.

@article{1102673,
   author = {Rache, Aurore De and Kejnovská, Iva and Vorlíčková, Michaela and BuessandHerman, Claudine},
   article_location = {WEINHEIM},
   article_number = {14},
   doi = {http://dx.doi.org/10.1002/chem.201103381},
   keywords = {circular dichroism; DNA structures; G-quadruplexes; hexa-ammine ruthenium; thermal difference spectra},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch},
   url = {http://www.sciencedirect.com/science/article/pii/S0925857415000658},
   volume = {18},
   year = {2012}
}

TY  - JOUR
ID  - 1102673
AU  - Rache, Aurore De - Kejnovská, Iva - Vorlíčková, Michaela - Buess-Herman, Claudine
PY  - 2012
TI  - Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch
JF  - Chemistry - A European Journal
VL  - 18
IS  - 14
SP  - 4392-4400
EP  - 4392-4400
PB  - WILEY-VCH
SN  - 09476539
KW  - circular dichroism
KW  - DNA structures
KW  - G-quadruplexes
KW  - hexa-ammine ruthenium
KW  - thermal difference spectra
UR  - http://www.sciencedirect.com/science/article/pii/S0925857415000658
N2  - Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5' end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba2+, Ca2+, K+, Mg2+, Na+, NH4+, Sr2+ and the [Ru(NH3)6]2+/3+ redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH3)6]3+, which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K+ reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.
ER  -

RACHE, Aurore De, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ and Claudine BUESS-HERMAN. Elongated Thrombin Binding Aptamer: A G-Quadruplex Cation-Sensitive Conformational Switch. \textit{Chemistry - A European Journal}. WEINHEIM: WILEY-VCH, 2012, vol.~18, No~14, p.~4392-4400. ISSN~0947-6539. Available from: https://dx.doi.org/10.1002/chem.201103381.

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