PMID- 23996015
OWN - NLM
STAT- MEDLINE
DCOM- 20140423
LR  - 20130927
IS  - 2040-3372 (Electronic)
IS  - 2040-3364 (Linking)
VI  - 5
IP  - 20
DP  - 2013 Oct 21
TI  - Structural and energetic basis for hybridization limits in high-density DNA 
      monolayers.
PG  - 9988-93
LID - 10.1039/c3nr01799k [doi]
AB  - High-density monolayers (HDMs) of single-strand (ss) DNA are important nanoscale 
      platforms for the fabrication of sensors and for mechanistic studies of enzymes 
      on surfaces. Such systems can be used, for example, to monitor gene expression, 
      and for the construction of more complex nanodevices via selective hybridization 
      with the complementary oligos dissolved in solution. In this framework, 
      controlling HDM hybridization is essential to control the final properties. 
      Different studies demonstrate that at the typical density of  approximately 10(13) molecules 
      per cm(2) no more than  approximately 30-40% of the HDM ssDNA is successfully hybridized. Until 
      now, however, the origin of the HDM hybridization limit has remained unclear. In 
      this work, molecular dynamics (MD) simulations of HDM systems with variable 
      hybridization reveal that, independently of other experimental parameters, the 
      effective hybridization for a HDM of this density is intrinsically limited by 
      molecular and electrostatic crowding. A detailed structural analysis of the HDM 
      model shows good agreement with our atomic force microscopy (AFM) experiments, 
      and provides further insight into the steric hindrance behaviour and 
      time-resolved surface topography of these nanostructured systems. The explicit 
      relationship proposed between structural crowding and limited HDM hybridization 
      offers a rationale to control the final properties of HDM-based nanodevices.
FAU - Doni, Giovanni
AU  - Doni G
AD  - Department of Physics, King's College London, London WC2R 2LS, UK.
FAU - Nkoua Ngavouka, Maryse D
AU  - Nkoua Ngavouka MD
FAU - Barducci, Alessandro
AU  - Barducci A
FAU - Parisse, Pietro
AU  - Parisse P
FAU - De Vita, Alessandro
AU  - De Vita A
FAU - Scoles, Giacinto
AU  - Scoles G
FAU - Casalis, Loredana
AU  - Casalis L
FAU - Pavan, Giovanni M
AU  - Pavan GM
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Nanoscale
JT  - Nanoscale
JID - 101525249
RN  - 0 (DNA, Single-Stranded)
SB  - IM
MH  - DNA, Single-Stranded/*chemistry/metabolism
MH  - Microscopy, Atomic Force
MH  - Molecular Dynamics Simulation
MH  - Nanostructures/chemistry
MH  - Nucleic Acid Hybridization
MH  - Surface Properties
MH  - Thermodynamics
EDAT- 2013/09/03 06:00
MHDA- 2014/04/24 06:00
CRDT- 2013/09/03 06:00
PHST- 2013/09/03 06:00 [entrez]
PHST- 2013/09/03 06:00 [pubmed]
PHST- 2014/04/24 06:00 [medline]
AID - 10.1039/c3nr01799k [doi]
PST - ppublish
SO  - Nanoscale. 2013 Oct 21;5(20):9988-93. doi: 10.1039/c3nr01799k.