Real-time study of a DNA strand displacement reaction using dual polarization interferometry.

A DNA strand displacement reaction on a solid-liquid interface was investigated using dual polarization interferometry. This effective analytical technique allows the real-time, simultaneous determination of the thickness, density, and mass of a biological layer. The displacement process was examined, and the changes in thickness, density, and mass were determined. Injection of the displacement DNA resulted in an increase in density and a decrease in mass and thickness, which indicated that a portion of the target DNA was displaced from the double-stranded DNA (dsDNA). The effects of the displacement DNA concentration and toehold length on the displacement efficiency were also examined. Increasing the displacement DNA concentration and the toehold length increased the changes in mass and the displacement efficiency. At the concentration of 0.2 μM, the toeholds with 4, 5, 6, and 7 bases had displacement percentages of 24.54%, 25.99%, 30.16%, and 70.41%, respectively. At displacement DNA concentrations exceeding that of the dsDNA, the displacement percentage was not concentration-dependent. Above a certain concentration, the percentage remained stable with increasing concentration. Comparison using different toehold sequences showed that the displacement efficiency increases with increasing bonding force between the base pairs.

[1]  Erik Winfree,et al.  Catalyzed relaxation of a metastable DNA fuel. , 2006, Journal of the American Chemical Society.

[2]  Hjalmar Brismar,et al.  Adsorption and activity of Thermomyces lanuginosus lipase on hydrophobic and hydrophilic surfaces measured with dual polarization interferometry (DPI) and confocal microscopy. , 2008, Colloids and surfaces. B, Biointerfaces.

[3]  Helen Berney,et al.  Dual polarization interferometry size and density characterisation of DNA immobilisation and hybridisation. , 2005, Biosensors & bioelectronics.

[4]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[5]  S J Tendler,et al.  Surface plasmon resonance analysis of dynamic biological interactions with biomaterials. , 2000, Biomaterials.

[6]  Chih-Kung Lee,et al.  Homopolyvalent antibody-antigen interaction kinetic studies with use of a dual-polarization interferometric biosensor. , 2006, Biosensors & bioelectronics.

[7]  P. J. Dobson,et al.  Ellipsometric and Interferometric Characterization of DNA Probes Immobilized on a Combinatorial Array , 1997 .

[8]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[9]  Darko Stefanovic,et al.  Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. , 2006, Biochemistry.

[10]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[11]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[12]  R. Georgiadis,et al.  Sequence-dependent DNA immobilization: specific versus nonspecific contributions. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[13]  S. Grant,et al.  Coagulation and Stabilization of Colloidal Particles by Adsorbed DNA Block Copolymers: The Role of Polymer Conformation , 1996 .

[14]  Joseph F. Clark,et al.  Apolipoprotein E isoprotein-specific interactions with tissue plasminogen activator. , 2004, Biochimica et biophysica acta.

[15]  Pamela E. Constantinou,et al.  From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal , 2009, Nature.

[16]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[17]  Andrew D. Ellington,et al.  Exponential growth by cross-catalytic cleavage of deoxyribozymogens , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  G Gauglitz,et al.  Characterization of biomembranes by spectral ellipsometry, surface plasmon resonance and interferometry with regard to biosensor application. , 1994, Biosensors & bioelectronics.

[19]  N. Seeman,et al.  An immobile nucleic acid junction constructed from oligonucleotides , 1983, Nature.

[20]  W. Han,et al.  アルミニウム単結晶中の変形が誘起したマイクロツインと積層欠陥 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター , 2008 .

[21]  Selim Elhadj,et al.  Optical properties of an immobilized DNA monolayer from 255 to 700 nm. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[22]  Chih-Kung Lee,et al.  Measurement of dimensions of pentagonal doughnut-shaped C-reactive protein using an atomic force microscope and a dual polarisation interferometric biosensor. , 2006, Biosensors & bioelectronics.

[23]  S. Satija,et al.  Using Self-Assembly To Control the Structure of DNA Monolayers on Gold: A Neutron Reflectivity Study , 1998 .

[24]  L. Stols,et al.  Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. , 1993, Biochemistry.

[25]  P. Hsieh,et al.  Formation of a single base mismatch impedes spontaneous DNA branch migration. , 1993, Journal of molecular biology.

[26]  Erik Winfree,et al.  Dynamic allosteric control of noncovalent DNA catalysis reactions. , 2008, Journal of the American Chemical Society.

[27]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[28]  A. Turberfield,et al.  Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. , 2008, Physical review letters.

[29]  P. Claesson,et al.  Buildup of polyelectrolyte multilayers of polyethyleneimine and microfibrillated cellulose studied by in situ dual-polarization interferometry and quartz crystal microbalance with dissipation. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[30]  C. Green,et al.  Reassociation rate limited displacement of DNA strands by branch migration. , 1981, Nucleic acids research.

[31]  Darko Stefanovic,et al.  Behavior of polycatalytic assemblies in a substrate-displaying matrix. , 2006, Journal of the American Chemical Society.

[32]  P. Hsieh,et al.  The kinetics of spontaneous DNA branch migration. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[33]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[34]  G. Bijelic,et al.  Adsorption characteristics of stoichiometric and nonstoichiometric molecular polyelectrolyte complexes on silicon oxynitride surfaces. , 2011, Langmuir : the ACS journal of surfaces and colloids.

[35]  Fan Yang,et al.  Real-time study of genomic DNA structural changes upon interaction with small molecules using dual-polarization interferometry. , 2009, Analytical Chemistry.

[36]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[37]  Michael V. Gormally,et al.  Dual-beam polarization interferometry resolves mechanistic aspects of polyelectrolyte adsorption. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[38]  T. M. Herne,et al.  Observation of Hybridization and Dehybridization of Thiol-Tethered DNA Using Two-Color Surface Plasmon Resonance Spectroscopy , 1997 .

[39]  A Mathewson,et al.  Dual polarisation interferometry characterisation of DNA immobilisation and hybridisation detection on a silanised support. , 2006, Biosensors & bioelectronics.

[40]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[41]  J. Lu,et al.  Cationic copolymer-mediated DNA immobilization: interfacial structure and composition as determined by ellipsometry, dual polarization interferometry, and neutron reflection. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[42]  Y. Okahata,et al.  Kinetic measurements of DNA hybridization on an oligonucleotide-immobilized 27-MHz quartz crystal microbalance. , 1998, Analytical chemistry.

[43]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.