Lafontaine I, Lavery R
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France.
Biopolymers. 2000;56(4):292-310. doi: 10.1002/1097-0282(2000)56:4<292::AID-BIP10028>3.0.CO;2-9.
We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA-protein or DNA-ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented.
我们描述了一种确定DNA序列-结构关系的原创方法。这种方法称为ADAPT，它将全原子分子力学与多拷贝算法相结合，以构建包含所有四种标准碱基且比例可变的核苷酸。这些核苷酸使我们能够非常快速地搜索那些在能量上有利于特定类型DNA变形或特定DNA-蛋白质或DNA-配体相互作用的碱基序列。通过能量最小化、组合序列搜索或基因组扫描，可以找到满足所选标准的序列，其方式类似于为蛋白质结构预测开发的穿线法。在后一种情况下，我们每秒能够分析大约2000个碱基对。本文展示了该方法在DNA同素异形转变、DNA变形以及特定DNA相互作用方面的应用。
