Naef Felix, Magnasco Marcelo O
Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906. doi: 10.1103/PhysRevE.68.011906. Epub 2003 Jul 16.
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.
RNA与高密度寡核苷酸阵列的结合与溶液实验显示出诱人的差异。我们在此分析其序列特异性，将结合亲和力与大型数据集中的序列组成进行拟合。我们的结果表明，荧光标记会干扰结合，导致一种两难困境。为了被检测到，RNA必须既能发光又能结合：没有标记时，即使结合了也看不见，而标记过多时则不会结合。一个标记寡核苷酸结合的简单模型揭示了结合能与标记概率之间的相互作用。
