Hierarchy of DNA immobilization and hybridization on poly-L-lysine using an atomic force microscopy study

J Nanosci Nanotechnol. 2005 Jun;5(6):951-7. doi: 10.1166/jnn.2005.125.

Abstract

The atomic force microscopy has been used to analyze the immobilization of single stranded DNA on poly-L-lysine-coated glass and subsequent hybridization with complimentary DNA with the Z-threshold parameter and fractal analysis methods. The poly-L-lysine layer, which has a thickness of approximately 7 nm, presents nano-defects that could be critical for DNA immobilization by acting as a nucleation sites for ssDNA and subsequently for dsDNA aggregates. The Z-threshold for the dsDNA aggregates is much larger than for ssDNA, but the statistical fractal dimension is very similar, suggesting a conformal increase of the dimensions of the dsDNA aggregates mainly in the Z-direction, due to an effective ssDNA-ccDNA molecular recognition. This study demonstrates the use of fractal analysis in conjunction with the distribution of heights to evaluate the efficiency of DNA-DNA molecular recognition on surfaces and the impact of nanodefects.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adsorption
  • Binding Sites
  • Coated Materials, Biocompatible / analysis
  • Coated Materials, Biocompatible / chemistry*
  • Crystallization / methods*
  • DNA / analysis
  • DNA / chemistry*
  • DNA / ultrastructure*
  • In Situ Hybridization / methods*
  • Materials Testing
  • Microscopy, Atomic Force*
  • Nucleic Acid Conformation
  • Polylysine / analysis
  • Polylysine / chemistry*
  • Protein Binding

Substances

  • Coated Materials, Biocompatible
  • Polylysine
  • DNA