Detection of sequence-specific protein-DNA interactions via surface enhanced resonance Raman scattering.

We developed a new strategy to detect protein-DNA binding through surface enhanced resonance Raman scattering (SERRS). Silver-plated DNA and gold nanoparticle assemblies were used to identify sequence-specific and concentration-dependent binding of a DNA cytosine-C5-methyltransferase and the eukaryotic transcriptional regulator, TATA binding protein. Proteins were identified through specific Raman-active labels, and affinities observed correlate well with those determined by other methods. Raman-active labeling and interchangeable DNA sequences create a platform for versatile investigation of multiprotein complexes.

[1]  Keith T. Carron,et al.  Determination of the Distance Dependence and Experimental Effects for Modified SERS Substrates Based on Self-Assembled Monolayers Formed Using Alkanethiols , 1999 .

[2]  R. Young,et al.  Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays , 2004, Nature Genetics.

[3]  M. Moskovits Surface-enhanced spectroscopy , 1985 .

[4]  T. Kodadek Protein microarrays: prospects and problems. , 2001, Chemistry & biology.

[5]  D. Cahill,et al.  Protein and antibody arrays and their medical applications. , 2001, Journal of immunological methods.

[6]  R. Dasari,et al.  Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS) , 1997 .

[7]  U. Raviv,et al.  Fluidity of Bound Hydration Layers , 2002, Science.

[8]  L. Tay,et al.  SERS and the Single Molecule , 2002 .

[9]  P. Hildebrandt,et al.  Surface enhanced resonance Raman study on fluorescein dyes , 1986 .

[10]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[11]  J. Lieb,et al.  Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. , 2004, Current opinion in genetics & development.

[12]  Andreas Otto,et al.  What is observed in single molecule SERS, and why? , 2002 .

[13]  M. Majoube,et al.  Fourier transform Raman and infrared and surface-enhanced Raman spectra for rhodamine 6G , 1991 .

[14]  N. Reich,et al.  Reconciling Structure and Function in HhaI DNA Cytosine-C-5 Methyltransferase* , 2000, The Journal of Biological Chemistry.