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research article

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

Naef, Felix  
•
Magnasco, Marcelo O.
2003
Physical Review E

RNA binding to high-density oligonucleotide arrays has shown tantalizing differences with solution experiments. We analyze here its sequence specificity, fitting binding affinities to sequence composition in large datasets. Our results suggest that the fluorescent labels interfere with binding, causing a catch-22. To be detected, the RNA must both glow and bind: without labels it cannot be seen even if bound, while with too many it will not bind. A simple model for the binding of labeled oligonucleotides sheds light on the interplay between binding energies and labeling probability.

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Type
research article
DOI
10.1103/PhysRevE.68.011906
Author(s)
Naef, Felix  
Magnasco, Marcelo O.
Date Issued

2003

Publisher

American Physical Society

Published in
Physical Review E
Volume

68

Issue

1 Pt 1

Article Number

011906

Note

Comment in: Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):063901; author reply 063902

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
UPNAE  
Available on Infoscience
November 1, 2010
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/56507
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