A Mutate-and-Map Strategy for Inferring Base Pairs in Structured Nucleic Acids: Proof of Concept on a DNA/RNA Helix
A Mutate-and-Map Strategy for Inferring Base Pairs in Structured Nucleic Acids: Proof of Concept on a DNA/RNA Helix
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DOI：
10.1021/bi101123g
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发表时间：
2010-09-07
期刊：
影响因子：
2.9
通讯作者：
Das, Rhiju
中科院分区：
文献类型：
--
作者：
Kladwang, Wipapat;Das, Rhiju
我们提出了一种快速的化学策略，用于识别结构化核酸系统中的碱基对。该方法超越了传统的化学作图方法，通过监测每个残基的化学可及性的扰动，以响应在序列上遥远但在三维空间上邻近的残基的系统诱变。作为一个概念的证明，我们提出了高通量的硫酸二甲酯的可及性数据的嵌合DNA/RNA系统中，每一个可能的序列变异和删除在一个20 bp的区域已经合成和测试。数据表明，该系统的88%的碱基对可以被稳健地推断，其中A/A和T/C DNA/RNA错配给出了最强的信号。这些结果指出了在更大更复杂的未知结构的核酸系统中进行快速碱基对推断的可行性。
We propose a rapid chemical strategy for identifying base pairs in structured nucleic acid systems. The approach goes beyond traditional chemical mapping approaches by monitoring perturbations of each residue's chemical accessibility in response to systematic mutagenesis of residues that are distant in sequence but nearby in three dimensions. As a proof of concept, we present high-throughput dimethyl sulfate accessibility data for a chimeric DNA/RNA system in which every possible sequence variation and deletion in a 20 bp region has been synthesized and tested. The data demonstrate that 88% of the system's base pairs can be robustly inferred, with A/A and T/C DNA/RNA mismatches giving the strongest signals. These results point to the feasibility of rapid base pair inference in larger and more complex nucleic acid systems with unknown structure.