... THE TYRANNY OF THE LATTICE ...
... THE TYRANNY OF THE LATTICE ...
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DOI：
10.1073/pnas.91.9.3579
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发表时间：
1994-04-26
影响因子：
11.1
通讯作者：
NEIDLE, S
中科院分区：
文献类型：
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作者：
DICKERSON, RE;GOODSELL, DS;NEIDLE, S
对三个不同空间群中具有和不具有 A 束的九种不同 B-DNA 十二聚体的晶体结构进行系统比较表明，晶体堆积或晶格力对于螺旋轴弯曲、小槽宽度和螺旋桨扭曲而言是次要的。虽然其他局部螺旋参数可能受到晶体堆积的影响甚至确定，但刚刚列举的属性主要由碱基序列决定。一种相同的晶体封装方案可以适应两个不同方向之一的弯曲，或者根本不弯曲。 B-DNA 的 A 区本质上是笔直且不弯曲的，碱基对倾斜度与一般序列 B-DNA 没有什么不同。当在 G.C 和 A.T 区域之间的连接处观察到弯曲时，它们总是涉及沿压缩宽主凹槽的方向绕碱基对长轴滚动，因此与 A 束弯曲连接模型正确性所需的方向成 90 度。 G.C/A.T 连接似乎是一个灵活的铰链，能够在弱晶体堆积力的局部影响下采用笔直或弯曲的构象。因此，这种力是有关 DNA 变形能力的信息来源，而不是令人遗憾的诅咒。但作为晶体堆积力弱点的一个迹象，尽管溴化和未溴化晶体是同晶的，但在主凹槽中引入单个溴原子足以消除弯曲。
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.