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

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.


Published in:
Physical review. E, Statistical, nonlinear, and soft matter physics, 68, 1 Pt 1, 011906
Year:
2003
Publisher:
American Physical Society
ISSN:
1539-3755
Note:
Comment in: Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):063901; author reply 063902
Laboratories:




 Record created 2010-11-01, last modified 2018-09-13


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