DNA‐binding by Functionalized Gold Nanoparticles: Mechanism and Structural Requirements

A family of nanoparticles featuring surfaces of varying hydrophobicity was synthesized. The efficiency of DNA‐binding was determined, demonstrating in a fivefold modulation in binding a 37‐mer DNA strand. Nanoparticle‐binding causes a reversible conformational change in the DNA structure, as demonstrated by circular dichroism and fluorescence experiments. Furthermore, the affinity of the nanoparticle for the DNA can be regulated by external agents, though stability of the complex is observed at relatively high ionic strengths.

[1]  V. Rotello,et al.  Reversible "irreversible" inhibition of chymotrypsin using nanoparticle receptors. , 2003, Journal of the American Chemical Society.

[2]  A. Schepartz,et al.  Highly Specific DNA Recognition by a Designed Miniature Protein , 1999 .

[3]  T. Steitz The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase. , 2004, Current opinion in structural biology.

[4]  Donald Voet,et al.  Biochemistry, 2nd ed. , 1995 .

[5]  C. Martin,et al.  Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase. , 1996, Biochemistry.

[6]  I. S. Blagbrough,et al.  Efficient calf thymus DNA condensation upon binding with novel bile acid polyamine amides. , 2002, Bioconjugate chemistry.

[7]  T. Koike,et al.  Novel Recognition of Thymine Base in Double-Stranded DNA by Zinc(II)−Macrocyclic Tetraamine Complexes Appended with Aromatic Groups , 1999 .

[8]  J. T. Welch,et al.  Sequence-selective DNA cleavage by a chimeric metallopeptide. , 2003, Journal of the American Chemical Society.

[9]  M. V. Van Dyke,et al.  Combinatorial determination of sequence specificity for nanomolar DNA-binding hairpin polyamides. , 2003, Biochemistry.

[10]  V. Rotello,et al.  Inhibition of DNA transcription using cationic mixed monolayer protected gold clusters. , 2001, Journal of the American Chemical Society.

[11]  K. Yoshikawa,et al.  Direct observation of the biphasic conformational change of DNA induced by cationic polymers , 1991, FEBS letters.

[12]  V. Rotello,et al.  Biomacromolecule Surface Recognition Using Nanoparticles , 2004 .

[13]  Vincent M Rotello,et al.  Gold nanoparticle-mediated transfection of mammalian cells. , 2002, Bioconjugate chemistry.

[14]  Jeremy M Berg,et al.  The design of functional DNA-binding proteins based on zinc finger domains. , 2004, Chemical reviews.

[15]  H. Tajmir-Riahi,et al.  The effect of HCl on the solution structure of calf thymus DNA: A comparative study of DNA denaturation by proton and metal cations using fourier transform IR difference spectroscopy , 1995, Biopolymers.

[16]  D. Lilley,et al.  Nucleic acid structure and recognition. , 1997, Biophysical chemistry.

[17]  C. Bailly,et al.  Sequence-selective targeting of long stretches of the DNA minor groove by a novel dimeric bis-benzimidazole. , 2003, Biochemistry.

[18]  D. Kahne,et al.  The Molecular Basis for Pyrimidine-Selective DNA Binding: Analysis of Calicheamicin Oligosaccharide Derivatives by Capillary Electrophoresis , 2000 .

[19]  D. Boger,et al.  A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity. , 2001, Journal of the American Chemical Society.

[20]  H. Sugiyama,et al.  Inhibition of transcription at a coding sequence by alkylating polyamide. , 2003, Journal of the American Chemical Society.

[21]  Craig T Martin,et al.  Thermodynamic and Kinetic Measurements of Promoter Binding by T 7 RNA Polymerase † , 2022 .

[22]  Peter E. Nielsen,et al.  DNA-like double helix formed by peptide nucleic acid , 1994, Nature.

[23]  Todd Emrick,et al.  Control of protein structure and function through surface recognition by tailored nanoparticle scaffolds. , 2004, Journal of the American Chemical Society.

[24]  G. S. Manning Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp? , 2003, Journal of the American Chemical Society.

[25]  I. Pelczer,et al.  Design of an Oligosaccharide Scaffold that Binds in the Minor Groove of DNA. , 2000 .

[26]  P. Dervan,et al.  Allosteric inhibition of protein--DNA complexes by polyamide--intercalator conjugates. , 2003, Journal of the American Chemical Society.

[27]  F. Nome,et al.  Effect of 1-Butanol on Micellization of Sodium Dodecyl Sulfate and on Fluorescence Quenching by Bromide Ion , 1994 .

[28]  D. Graves Drug-DNA interactions. , 2001, Methods in molecular biology.

[29]  M. Vázquez,et al.  From transcription factors to designed sequence-specific DNA-binding peptides. , 2003, Chemical Society reviews.

[30]  V. Rotello,et al.  Formation and pH-controlled assembly of amphiphilic gold nanoparticles , 2000 .

[31]  J. Baker,et al.  The interaction of plasmid DNA with polyamidoamine dendrimers: mechanism of complex formation and analysis of alterations induced in nuclease sensitivity and transcriptional activity of the complexed DNA. , 1997, Biochimica et biophysica acta.

[32]  G. Barone,et al.  Interactions with Natural Polyamines and Thermal Stability of DNA. A DSC Study and a Theoretical Reconsideration , 1997 .

[33]  Peter N. Campbell,et al.  Biochemistry (2nd edn) , 1995 .

[34]  Mathias Brust,et al.  Synthesis of thiol-derivatised gold nanoparticles in a two-phase liquid-liquid system , 1994 .

[35]  F. Szoka,et al.  The influence of polymer structure on the interactions of cationic polymers with DNA and morphology of the resulting complexes , 1997, Gene Therapy.

[36]  S. P. Moulik,et al.  Thermodynamics of Micelle Formation of Ionic Surfactants: A Critical Assessment for Sodium Dodecyl Sulfate, Cetyl Pyridinium Chloride and Dioctyl Sulfosuccinate (Na Salt) by Microcalorimetric, Conductometric, and Tensiometric Measurements , 2001 .

[37]  C. L. Evans AN INTRODUCTION TO HUMAN PHYSIOLOGY , 1953, Nature.

[38]  J. Fréchet,et al.  Convergent dendrons and dendrimers: from synthesis to applications. , 2001, Chemical reviews.

[39]  P. Nielsen,et al.  Superior duplex DNA strand invasion by acridine conjugated peptide nucleic acids. , 2003, Journal of the American Chemical Society.

[40]  B. Pettitt,et al.  Stabilities of double- and triple-strand helical nucleic acids. , 1992, Progress in biophysics and molecular biology.

[41]  George M. Whitesides,et al.  Microfabrication through Electrostatic Self-Assembly , 1997 .

[42]  M. Bina,et al.  The pH-dependent structure of calf thymus DNA studied by Raman spectroscopy. , 1982, Biophysical chemistry.

[43]  J. Mackay,et al.  Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling. , 2001, Biochemistry.

[44]  C. Murphy,et al.  PREFERENTIAL ADSORPTION OF A KINKED DNA TO A NEUTRAL CURVED SURFACE : COMPARISONS TO AND IMPLICATIONS FOR NONSPECIFIC DNA : PROTEIN INTERACTIONS , 1996 .

[45]  R. Murray,et al.  Reactivity of Monolayer-Protected Gold Cluster Molecules: Steric Effects , 1998 .

[46]  Christina M. Taylor,et al.  Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands. , 2004, Biochemistry.

[47]  R. Shafer,et al.  Differential effects of spermine and its analogues on the structures of polynucleotides complexed with ethidium bromide. , 1993, The Biochemical journal.

[48]  R. Murray,et al.  DNA binding of an ethidium intercalator attached to a monolayer-protected gold cluster. , 2002, Analytical chemistry.

[49]  P. Dervan,et al.  Hydroxybenzamide/pyrrole pair distinguishes T·A from A·T base pairs in the minor groove of DNA , 2000 .

[50]  A. Lajmi,et al.  Minimalist, Alanine-Based, Helical Protein Dimers Bind to Specific DNA Sites , 2000 .

[51]  P. Nielsen,et al.  Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 Å resolution , 1997, Nature Structural Biology.

[52]  Y. Inoue,et al.  Peptide Ribonucleic Acids (PRNA). 2. A Novel Strategy for Active Control of DNA Recognition through Borate Ester Formation , 2000 .

[53]  J. Baker,et al.  DNA complexing with polyamidoamine dendrimers: implications for transfection. , 1999, Bioconjugate chemistry.

[54]  M. W. V. Dyke,et al.  Combinatorial determination of sequence specificity for nanomolar DNA-binding hairpin polyamides. , 2003 .

[55]  W. Mcallister,et al.  Exposure of T7 RNA Polymerase to the Isolated Binding Region of the Promoter Allows Transcription from a Single-stranded Template* , 2003, The Journal of Biological Chemistry.