Shape readout of AT-rich DNA by carbohydrates.
Shape readout of AT-rich DNA by carbohydrates.
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DOI：
10.1002/bip.22448
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发表时间：
2014-07
期刊：
影响因子：
2.9
通讯作者：
Arya, Dev P.
中科院分区：
文献类型：
--
作者：
Kumar, Sunil;Spano, Meredith Newby;Arya, Dev P.
基因表达可以被靶向DNA的小分子改变；序列和形状选择性对于插入和沟槽结合的配体识别DNA都是极其重要的。我们已经表征了一种具有DNA“形状读出”特性的碳水化合物支架(1)。1和模型双链DNA的热力学研究表明，该分子对B*型(富含AT的连续DNA)具有很高的亲和力和选择性。用等温滴定热法(ITC)、圆二色谱(CD)滴定、紫外光热变性和差示扫描量热法(DSC)表征了1与富含AT的B*型DNA双链d[5‘-G2A6T6C2-3’]的结合。用ITC测定了不同温度、盐浓度和pH条件下的结合常数。ITC滴定符合双结合位点模型。第一个结合事件具有1：1的结合化学计量比，并且主要是由熵驱动的，结合常数约为108M−1。结合热容的变化(ΔCp)为-2 2 5±19cal/mol.K。结合常数的离子强度依赖性表明，在配体-DNA结合中有显著的电解贡献，大约有4-5个离子对参与结合。配体1与AT-链DNA的亲和力显著高于含GC插入序列，结合实验表明配体1与DNA双链的亲和力顺序为：邻接的B*型富含AT的DNA(d[5‘-G2A6T6C2-3’])>；B型交替的富含AT的DNA(d[5‘-G2(AT)6C2-3’])>；A型富含GC的DNA(d[5‘-A2G6C6T2-3’])，表明配体1优先选择B*型DNA。
Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove-binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA “shape readout” properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT-rich) DNA. Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) titration, Ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT-rich DNA duplex d[5′-G2A6T6C2-3′]. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two-binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy driven with a binding constant of approximately 108 M−1. ITC-derived binding enthalpies were used to obtain the binding-induced change in heat capacity (ΔCp) of -225±19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT-tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT-rich DNA (d[5′-G2A6T6C2-3′]) > B form alternate AT-rich DNA (d[5′-G2(AT)6C2-3′]) > A form GC-rich DNA (d[5′-A2G6C6T2-3′]), demonstrating the preference of ligand 1 for B* form DNA.
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影响因子：
14.9
作者：
Barceló F;Scotta C;Ortiz-Lombardía M;Méndez C;Salas JA;Portugal J
通讯作者：
Portugal J
影响因子：
3.9
作者：
Chaires, Jonathan B.
通讯作者：
Chaires, Jonathan B.
DOI：
10.1073/pnas.84.24.8922
发表时间：
1987-12-01
影响因子：
11.1
作者：
BRESLAUER, KJ;REMETA, DP;MARKY, LA
通讯作者：
MARKY, LA
影响因子：
64.8
作者：
ALEXEEV, DG;LIPANOV, AA;SKURATOVSKII, IY
通讯作者：
SKURATOVSKII, IY
影响因子：
14.9
作者：
Barceló, F;Capó, D;Portugal, J
通讯作者：
Portugal, J