Dickerson R E, Goodsell D S, Neidle S
Molecular Biology Institute, University of California, Los Angeles 90024.
Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3579-83. doi: 10.1073/pnas.91.9.3579.
A systematic comparison of crystal structures of nine different B-DNA dodecamers, in three different space groups, with and without A-tracts, shows that crystal packing or lattice forces are of secondary importance for helix axis bending, minor-groove width, and propeller twist. While other local helix parameters may be influenced or even established by crystal packing, the properties just enumerated are determined primarily by base sequence. One and the same crystal packing scheme can accommodate a bend in one of two different directions, or no bend at all. A-tract regions of B-DNA are inherently straight and unbent, with base-pair inclination no different from that of general-sequence B-DNA. Where bends are observed at junctions between G.C and A.T regions, they always involve a roll about base-pair long axes in a direction that compresses the wide major groove and, hence, are 90 degrees away from that necessary for the correctness of the junction model of A-tract bending. The G.C/A.T junction appears to be a flexible hinge, capable of adopting either a straight or a bent conformation under the local influence of weak crystal packing forces. Such forces therefore are a source of information about DNA deformability and not a curse to be deplored. But as an indication of the weakness of crystal packing forces, introduction of a single bromine atom in the major groove is sufficient to eliminate a bend, although brominated and unbrominated crystals are isomorphous.
对九个不同的B-DNA十二聚体在三种不同空间群中的晶体结构进行系统比较，有A序列和无A序列的情况均包含在内，结果表明，晶体堆积或晶格力对于螺旋轴弯曲、小沟宽度和螺旋桨扭转来说是次要的。虽然其他局部螺旋参数可能会受到晶体堆积的影响甚至由其决定，但上述列举的性质主要由碱基序列决定。同一种晶体堆积方案可以容纳两个不同方向之一的弯曲，或者根本没有弯曲。B-DNA的A序列区域本质上是直的且未弯曲，碱基对倾斜度与一般序列的B-DNA无异。在G.C和A.T区域之间的连接处观察到弯曲时，它们总是涉及围绕碱基对长轴的滚动，其方向会压缩较宽的大沟，因此与A序列弯曲的连接模型正确所需的方向相差90度。G.C/A.T连接处似乎是一个灵活的铰链，在弱晶体堆积力的局部影响下能够采取直的或弯曲的构象。因此，这些力是有关DNA可变形性的信息来源，而不是令人遗憾的祸根。但是，作为晶体堆积力较弱的一个迹象，在大沟中引入单个溴原子就足以消除弯曲，尽管溴化和未溴化的晶体是同晶型的。
