Quantifying the nanomachinery of the nanoparticle-biomolecule interface.

A study is presented of the nanomechanical phenomena experienced by nanoparticle-conjugated biomolecules. A thermodynamic framework is developed to describe the binding of thrombin-binding aptamer (TBA) to thrombin when the TBA is conjugated to nanorods. Binding results in nanorod aggregation (viz. directed self-assembly), which is detectable by absorption spectroscopy. The analysis introduces the energy of aggregation, separating it into TBA-thrombin recognition and surface-work contributions. Consequently, it is demonstrated that self-assembly is driven by the interplay of surface work and thrombin-TBA recognition. It is shown that the work at the surface is about -10 kJ mol(-1) and results from the accumulation of in-plane molecular forces of pN magnitude and with a lifetime of <1 s, which arises from TBA nanoscale rearrangements fuelled by thrombin-directed nanorod aggregation. The obtained surface work can map aggregation regimes as a function of different nanoparticle surface conditions. Also, the thermodynamic treatment can be used to obtain quantitative information on surface effects impacting biomolecules on nanoparticle surfaces.

[1]  V. Rotello,et al.  Nanoparticles: scaffolds and building blocks. , 2003, Accounts of chemical research.

[2]  K. Hamad-Schifferli,et al.  Ligand customization and DNA functionalization of gold nanorods via round-trip phase transfer ligand exchange. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[3]  D. Leckband,et al.  Intermolecular forces in biology , 2001, Quarterly Reviews of Biophysics.

[4]  S. Piletsky,et al.  Size matters: influence of the size of nanoparticles on their interactions with ligands immobilized on the solid surface. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[5]  Christopher E. Wilmer,et al.  Nanoscale forces and their uses in self-assembly. , 2009, Small.

[6]  Sara Linse,et al.  Understanding the nanoparticle–protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles , 2007, Proceedings of the National Academy of Sciences.

[7]  Donald Fitzmaurice,et al.  Effects of Ligand−Receptor Geometry and Stoichiometry on Protein-Induced Aggregation of Biotin-Modified Colloidal Gold , 2001 .

[8]  A. Tulinsky,et al.  The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. , 1994, The Journal of biological chemistry.

[9]  Christof M Niemeyer,et al.  Rational design of DNA nanoarchitectures. , 2006, Angewandte Chemie.

[10]  Catherine J Murphy,et al.  Seeded high yield synthesis of short Au nanorods in aqueous solution. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[11]  Kimberly Hamad-Schifferli,et al.  Gold nanoparticle-cytochrome C complexes: the effect of nanoparticle ligand charge on protein structure. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[12]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[13]  Yi Lu,et al.  MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles. , 2008, Bioconjugate chemistry.

[14]  R. Misra,et al.  Biomaterials , 2008 .

[15]  K. Hamad-Schifferli,et al.  Structure of cytochrome c at the interface with magnetic CoFe2O4nanoparticles. , 2008, Soft matter.

[16]  J. M. Oshorn.  Proc. Nat. Acad. Sei , 1978 .

[17]  J. Schlenoff,et al.  Aggregation-resistant water-soluble gold nanoparticles. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[18]  Zhiqiang Gao,et al.  Facile and controllable loading of single-stranded DNA on gold nanoparticles. , 2009, Analytical chemistry.

[19]  T. Xia,et al.  Understanding biophysicochemical interactions at the nano-bio interface. , 2009, Nature materials.

[20]  Sunho Park,et al.  Changes in Oligonucleotide Conformation on Nanoparticle Surfaces by Modification with Mercaptohexanol , 2004 .

[21]  Yuval Golan,et al.  The role of interparticle and external forces in nanoparticle assembly. , 2008, Nature materials.

[22]  C. Niemeyer.  REVIEW Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science , 2022 .

[23]  E. Vermaas,et al.  Selection of single-stranded DNA molecules that bind and inhibit human thrombin , 1992, Nature.

[24]  N. Jana,et al.  Gram-scale synthesis of soluble, near-monodisperse gold nanorods and other anisotropic nanoparticles. , 2005, Small.

[25]  Friedrich C. Simmel,et al.  A modular DNA signal translator for the controlled release of a protein by an aptamer , 2006, Nucleic acids research.

[26]  C. Mirkin,et al.  A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles. , 2000, Analytical chemistry.

[27]  Friedrich C Simmel,et al.  A DNA-based machine that can cyclically bind and release thrombin. , 2004, Angewandte Chemie.

[28]  George C. Schatz,et al.  DNA-Linked Metal Nanosphere Materials: Structural Basis for the Optical Properties , 2000 .

[29]  Jonathan S Dordick,et al.  Silica nanoparticle size influences the structure and enzymatic activity of adsorbed lysozyme. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[30]  Lei Zhang,et al.  Functionalizable and ultra stable nanoparticles coated with zwitterionic poly(carboxybetaine) in undiluted blood serum. , 2009, Biomaterials.

[31]  K. Hamad-Schifferli,et al.  Site-directed nanoparticle labeling of cytochrome c , 2009, Proceedings of the National Academy of Sciences.

[32]  P. Colombi,et al.  On the difference of equilibrium constants of DNA hybridization in bulk solution and at the solid‐solution interface , 2011, Journal of molecular recognition : JMR.

[33]  L. Depero,et al.  Thermodynamics of mechanical transduction of surface confined receptor/ligand reactions. , 2007, Journal of Colloid and Interface Science.

[34]  Chad A Mirkin,et al.  Maximizing DNA loading on a range of gold nanoparticle sizes. , 2006, Analytical chemistry.

[35]  Nancy R Forde,et al.  Mechanical processes in biochemistry. , 2004, Annual review of biochemistry.

[36]  K. Hamad-Schifferli,et al.  Protein thin film machines. , 2010, Nanoscale.

[37]  Sunho Park,et al.  Enhancement of in vitro translation by gold nanoparticle--DNA conjugates. , 2010, ACS nano.

[38]  P. Gong,et al.  DNA surface hybridization regimes , 2008, Proceedings of the National Academy of Sciences.

[39]  Catherine J. Murphy,et al.  Seed‐Mediated Growth Approach for Shape‐Controlled Synthesis of Spheroidal and Rod‐like Gold Nanoparticles Using a Surfactant Template , 2001 .

[40]  A. Adamson.  Physical chemistry of surfaces , 1960 .

[41]  Luigi Martino,et al.  Stability and binding properties of a modified thrombin binding aptamer. , 2008, Biophysical journal.

[42]  S. Manalis,et al.  Micromechanical detection of proteins using aptamer-based receptor molecules. , 2004, Analytical chemistry.

[43]  C. Glover,et al.  Gene expression profiling for hematopoietic cell culture , 2006 .

[44]  A. Chilkoti,et al.  Microcantilever sensing and actuation with end-grafted stimulus-responsive elastin-like polypeptides. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[45]  M. V. Van Dyke,et al.  Oligodeoxyribonucleotide length and sequence effects on intramolecular and intermolecular G-quartet formation. , 1997, Gene.

[46]  S. Borgne,et al.  Amidase activity and thermal stability of human thrombin , 1994, Applied biochemistry and biotechnology.

[47]  M. Gunzburg,et al.  Experimental determination of quantum dot size distributions, ligand packing densities, and bioconjugation using analytical ultracentrifugation. , 2008, Nano letters.

[48]  J. Vermant,et al.  Directed self-assembly of nanoparticles. , 2010, ACS nano.

[49]  S. Balasubramanian,et al.  DNA molecular motor driven micromechanical cantilever arrays. , 2005, Journal of the American Chemical Society.