Singh Isha, Kim Myong-Jung, Molt Robert W, Hoshika Shuichi, Benner Steven A, Georgiadis Millie M
Department of Biochemistry & Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States.
Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States.
ACS Synth Biol. 2017 Nov 17;6(11):2118-2129. doi: 10.1021/acssynbio.7b00150. Epub 2017 Aug 15.
A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXK DNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.
合成生物学的一个目标是开发新的核碱基，使其在扩展遗传字母表的同时，保留天然核碱基的理想特性。咪唑并[1,2-a]-1,3,5-三嗪-2(8H)-4(3H)-二酮（X）与2,4-二氨基嘧啶（K）之间的非标准沃森-克里克碱基对正是如此，这两个核碱基通过互补的氢键排列配对，且不与任何天然核碱基互补。在此，我们报道了一种B型双链DNA寡核苷酸的晶体结构，该结构包含GATCXK DNA中的两个连续X:K碱基对，其作为主客体复合物在1.75 Å分辨率下测定。X:K碱基对具有显著的螺旋桨扭转角，类似于A:T碱基对所观察到的扭转角，并且计算得出的氢键配对能量比A:T碱基对的弱。因此，尽管包含X:K碱基对会导致双链DNA结构在整体上与类似的G:C结构相似，但X:K碱基对在局部和能量上更类似于A:T碱基对。
