Narayana N, Ginell S L, Russu I M, Berman H M
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855.
Biochemistry. 1991 May 7;30(18):4449-55. doi: 10.1021/bi00232a011.
The crystal structure of the dodecanucleotide d(CGTGAATTCACG) has been determined to a resolution of 2.7 A and refined to an R factor of 17.0% for 1532 reflections. The sequence crystallizes as a B-form double helix, with Watson-Crick base pairing. This sequence contains the EcoRI restriction endonuclease recognition site, GAATTC, and is flanked by CGT on the 5'-end and ACG on the 3'-end, in contrast to the CGC on the 5'-end and GCG on the 3'-end in the parent dodecamer d(CGCGAATTCGCG). A comparison with the isomorphous parent compound shows that any changes in the structure induced by the change in the sequence in the flanking region are highly localized. The global conformation of the duplex is conserved. The overall bend in the helix is 10 degrees. The average helical twist values for the present and the parent structures are 36.5 degrees and 36.4 degrees, respectively, corresponding to 10 base pairs per turn. The buckle at the substituted sites are significantly different from those seen at the corresponding positions in the parent dodecamer. Step 2 (GpT) is underwound with respect to the parent structure (27 degrees vs 36 degrees) and step 3 (TpG) is overwound (34 degrees vs 27 degrees). There is a spine of hydration in the narrow minor groove. The N3 atom of adenine on the substituted A10 and A22 bases are involved in the formation of hydrogen bonds with other duplexes or with water; the N3 atom of guanine on G10 and G22 bases in the parent structure does not form hydrogen bonds.
十二聚体d（CGTGAATTCACG）的晶体结构已被测定，分辨率为2.7埃，并对1532个反射进行精修，R因子为17.0%。该序列以B型双螺旋形式结晶，存在沃森-克里克碱基配对。此序列包含EcoRI限制性内切酶识别位点GAATTC，其5'端侧翼为CGT，3'端侧翼为ACG，这与亲本十二聚体d（CGCGAATTCGCG）的5'端CGC和3'端GCG不同。与同晶型亲本化合物的比较表明，侧翼区域序列变化所诱导的结构变化高度局限。双链体的整体构象得以保留。螺旋的整体弯曲度为10度。当前结构和亲本结构的平均螺旋扭转值分别为36.5度和36.4度，相当于每圈10个碱基对。取代位点处的弯曲与亲本十二聚体相应位置处的弯曲明显不同。步骤2（GpT）相对于亲本结构解旋（27度对36度），步骤3（TpG）过度缠绕（34度对27度）。在狭窄的小沟中有一条水合脊。取代的A10和A22碱基上腺嘌呤的N3原子参与与其他双链体或水形成氢键；亲本结构中G10和G22碱基上鸟嘌呤的N3原子不形成氢键。
