Quantitative determination of size and shape of surface-bound DNA using an acoustic wave sensor

Biophysical Journal
Achilleas TsortosElectra Gizeli

Abstract

DNA bending plays a significant role in many biological processes, such as gene regulation, DNA replication, and chromosomal packing. Understanding how such processes take place and how they can, in turn, be regulated by artificial agents for individual oriented therapies is of importance to both biology and medicine. In this work, we describe the application of an acoustic wave device for characterizing the conformation of DNA molecules tethered to the device surface via a biotin-neutravidin interaction. The acoustic energy dissipation per unit mass observed upon DNA binding is directly related to DNA intrinsic viscosity, providing quantitative information on the size and shape of the tethered molecules. The validity of the above approach was verified by showing that the predesigned geometries of model double-stranded and triple-helix DNA molecules could be quantitatively distinguished: the resolution of the acoustic measurements is sufficient to allow discrimination between same size DNA carrying a bent at different positions along the chain. Furthermore, the significance of this analysis to the study of biologically relevant systems is shown during the evaluation of DNA conformational change upon protein (histone) binding.

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Citations

Oct 19, 2010·European Biophysics Journal : EBJ·Michael Saitakis, Electra Gizeli
Oct 10, 2012·ACS Applied Materials & Interfaces·Ivan E IvanovTerri A Camesano
May 1, 2009·HFSP Journal·Jonathan S Ellis, Michael Thompson
Jan 21, 2010·FEBS Letters·George PapadakisElectra Gizeli
Oct 27, 2009·Trends in Biotechnology·Guilherme N M FerreiraBrigitte Tomé
Jun 20, 2013·Scientific Reports·G PapadakisE Gizeli
Dec 18, 2009·Journal of Molecular Recognition : JMR·Rebecca L Rich, David G Myszka
May 28, 2016·Analytical Chemistry·Achilleas TsortosElectra Gizeli
Jan 18, 2012·Analytical Chemistry·George PapadakisElectra Gizeli
Jun 24, 2017·Biochimica Et Biophysica Acta. Biomembranes·Ileana F MárquezMarisela Vélez
Jun 23, 2015·Chemical Communications : Chem Comm·Achilleas TsortosElectra Gizeli
Jul 4, 2017·Chemical Communications : Chem Comm·George PapadakisElectra Gizeli
Jul 31, 2008·Physical Chemistry Chemical Physics : PCCP·Diethelm Johannsmann
Jun 4, 2011·Biopolymers·Achilleas TsortosElectra Gizeli
Apr 4, 2015·Optics Express·S LaneA Meldrum
Nov 8, 2015·Advances in Colloid and Interface Science·Qian ChenZhenghe Xu
Sep 9, 2018·Biosensors & Bioelectronics·Golam MustafaHamza Balci
Apr 29, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Edurne TellecheaIlya Reviakine
Apr 2, 2010·ACS Applied Materials & Interfaces·Dana Y GallimoreMauricio Pereira da Cunha
Jul 23, 2008·Langmuir : the ACS Journal of Surfaces and Colloids·Kathryn A MelzakElectra Gizeli
Apr 17, 2010·Langmuir : the ACS Journal of Surfaces and Colloids·Jonathan S Ellis, Michael Thompson
Sep 15, 2009·Analytical Chemistry·Diethelm JohannsmannRalf P Richter
Sep 10, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Patricia M WolnyRalf P Richter
Dec 20, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Michael AgtheLennart Bergström
Jul 9, 2020·ACS Nano·Amideddin Mataji-KojouriUtkan Demirci
May 26, 2020·Analytical Chemistry·Dimitra MilioniElectra Gizeli

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