Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2006 34(22):6416-6424; doi:10.1093/nar/gkl738
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2006, Vol. 34, No. 22 6416-6424
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Chemistry |
Fabrication and characterization of RNA aptamer microarrays for the study of protein–aptamer interactions with SPR imaging
Department of Chemistry, University of California-Irvine Irvine, CA 92697, USA
*To whom correspondence should be addressed. Tel: +1 949 824 1746; Fax: +1 949 824 8571; Email: rcorn{at}uci.edu
Received June 20, 2006. Revised August 14, 2006. Accepted September 22, 2006.
RNA microarrays were created on chemically modified gold surfaces using a novel surface ligation methodology and employed in a series of surface plasmon resonance imaging (SPRI) measurements of DNA–RNA hybridization and RNA aptamer–protein binding. Various unmodified single-stranded RNA (ssRNA) oligonucleotides were ligated onto identical 5'-phosphate-terminated ssDNA microarray elements with a T4 RNA ligase surface reaction. A combination of ex situ polarization modulation FTIR measurements of the RNA monolayer and in situ SPRI measurements of DNA hybridization adsorption onto the surface were used to determine an ssRNA surface density of 4.0 x 1012 molecules/cm2 and a surface ligation efficiency of 85 ± 10%. The surface ligation methodology was then used to create a five-component RNA microarray of potential aptamers for the protein factor IXa (fIXa). The relative surface coverages of the different aptamers were determined through a novel enzymatic method that employed SPRI measurements of a surface RNase H hydrolysis reaction. SPRI measurements were then used to correctly identify the best aptamer to fIXa, which was previously determined from SELEX measurements. A Langmuir adsorption coefficient of 1.6 x 107 M–1 was determined for fIXa adsorption to this aptamer. Single-base variations from this sequence were shown to completely destroy the aptamer–fIXa binding interaction.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Chushak and M. O. Stone In silico selection of RNA aptamers Nucleic Acids Res., July 1, 2009; 37(12): e87 - e87. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Liu, J. Livny, M. S. Lawrence, M. D. Kimball, M. K. Waldor, and A. Camilli Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing Nucleic Acids Res., April 1, 2009; 37(6): e46 - e46. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Katilius, C. Flores, and N. W. Woodbury Exploring the sequence space of a DNA aptamer using microarrays Nucleic Acids Res., December 3, 2007; 35(22): 7626 - 7635. [Abstract] [Full Text] [PDF]
|
|