Spielmann H P
Departments of Biochemistry and Chemistry, and the Kentucky Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536-0084, USA.
Biochemistry. 1998 Dec 1;37(48):16863-76. doi: 10.1021/bi980789e.
The dynamics of the DNA oligomer d(CGCTAGCG)2 (CTSYM) and its complex with the dye 1,1-(4,4,8,8-tetramethyl-4, 8-diazaundecamethylene)-bis-4-(3-methyl-2,3-dihydro-(benzo-1, 3-thiazole)-2-methylidene)-quinolinium tetraiodide (TOTO) (CTSYMTOTO) bis-intercalated at the 5'-CT-3' sequence steps have been determined from NMR relaxation parameters. Longitudinal and transverse 13C relaxation rates and heteronuclear NOE relaxation data were acquired and have been analyzed in the context of the Lipari and Szabo model-free formalism. The overall rotational correlation time for the CTSYM is 3.44 ns and the CTSYMTOTO is 3.48 ns. The generalized order parameters (S2) for methine carbons in the CTSYM and CTSYMTOTO are relatively high but nonuniform for the molecules and show sequence context and conformation-dependent variations. Average values of S2 = 0.79 +/- 0.02 for the CTSYM, S2 = 0.80 +/- 0.04 for the CTSYMTOTO aromatic spins, S2 = 0.76 +/- 0.02 for the CTSYM, and S2 = 0.83 +/- 0.05 for the CTSYMTOTO deoxyribose spins were found. The S2 values for the 5'-terminal deoxyribose are lower than for the other residues. The DNA backbone in CTSYMTOTO is distorted and elongated at the site of intercalation, and the C3' atom of the C3 deoxyribose residue has a very low S2 = 0.57 +/- 0.06. The low order for this spin is interpreted in terms of exchange between the C2'-endo and O1'-endo conformations of the C3 deoxyribose. Significant chemical exchange processes were found for most of the aromatic spins in CTSYM that are interpreted in terms of microsecond to millisecond time scale dynamics. The microsecond to millisecond dynamics of the bases in CTSYM are quenched upon TOTO complex formation due to unwinding of the helix and an increase in the surface area of the bases in mutual contact and the large surface area in contact with the intercalated dye. The derived order parameters combined with the solution structure provide motional models for conformational changes induced in the backbone in response to the ligand binding.
已通过核磁共振弛豫参数确定了DNA寡聚物d(CGCTAGCG)2（CTSYM）及其与染料1,1-(4,4,8,8-四甲基-4,8-二氮杂十一亚甲基)-双-4-(3-甲基-2,3-二氢-(苯并-1,3-噻唑)-2-亚甲基)-喹啉鎓四碘化物（TOTO）（CTSYMTOTO）在5'-CT-3'序列步长处双嵌入的动力学。获取了纵向和横向13C弛豫速率以及异核NOE弛豫数据，并在Lipari和Szabo无模型形式体系的背景下进行了分析。CTSYM的整体旋转相关时间为3.44纳秒，CTSYMTOTO的为3.48纳秒。CTSYM和CTSYMTOTO中次甲基碳的广义序参数（S2）相对较高，但分子中并不均匀，且显示出序列背景和构象依赖性变化。发现CTSYM的S2平均值为0.79±0.02，CTSYMTOTO芳香族自旋的S2平均值为0.80±0.04，CTSYM的S2平均值为0.76±0.02，CTSYMTOTO脱氧核糖自旋的S2平均值为0.83±0.05。5'-末端脱氧核糖的S2值低于其他残基。CTSYMTOTO中的DNA主链在嵌入位点处发生扭曲和伸长，C3脱氧核糖残基的C3'原子的S2值非常低，为0.57±0.06。这种自旋的低序性可根据C3脱氧核糖的C2'-内型和O1'-内型构象之间的交换来解释。在CTSYM中，发现大多数芳香族自旋存在显著的化学交换过程，这可根据微秒至毫秒时间尺度的动力学来解释。由于螺旋解旋以及相互接触的碱基表面积增加以及与嵌入染料接触的大表面积，CTSYM中碱基的微秒至毫秒动力学在形成TOTO复合物后被淬灭。推导得到的序参数与溶液结构相结合，为响应配体结合而在主链中诱导的构象变化提供了运动模型。
