Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes.
Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes.
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DOI：
10.1021/ja108118v
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发表时间：
2011-05-18
影响因子：
15
通讯作者：
Arya DP
中科院分区：
文献类型：
--
作者：
Kumar S;Xue L;Arya DP
合成并表征了具有柔性连接体2，2 ′-（亚乙二氧基）双（乙胺）的二聚体新霉素-新霉素缀合物3。二聚体3可以以高亲和力选择性地结合富含AT的DNA双链体。通过使用ITC（等温量热法）、CD（圆二色性）、FID（荧光嵌入剂置换）和UV（紫外线）热变性实验，在具有不同碱基组成和构象的3种不同核酸之间进行生物物理研究。从这项研究中可以得出几个结论：（1）用3和多核苷酸进行的FID测定表明3对富含AT的序列的偏好超过富含GC的序列。(2)氢火焰离子化检测和紫外热变性实验表明3对poly（dA）.poly（dT）DNA双链体的亲和力高于poly（dA）. 2 poly（dT）DNA三链体。与新霉素相反，3使poly（dA）. 2 poly（dT）三链体不稳定，但使poly（dA）.poly（dT）双链体稳定，表明大沟为结合位点。(3)UV热变性研究和ITC实验表明，3稳定连续AT-道DNA比DNA双链体交替AT基地。(4)CD和FID滴定研究显示，对于富含AT的DNA双链体，DNA结合位点大小为10~12个碱基对/药物，这取决于双链体的结构/序列。(5)3和分子内DNA双链体[d（5 '-A12-x-T12 - 3'），X =六乙二醇接头]之间的FID和ITC滴定导致结合化学计量为1：1，在100 mM KCl下结合常数约为108 M-1。(6)使用AT碱基含量和位置不同的3和512发夹DNA序列的FID测定也显示出对连续AT丰富的结合选择性3比对具有交替AT碱基对的DNA双链体更高。(7)盐依赖性研究表明，在DNA双链体d[5 ′-A12-x-T12 - 3 ′]和3. (8)3和DNA双链体之间的ITC衍生的结合常数遵循以下顺序：AT连续，d[5 '-G3 A5 T5 C3 - 3']> AT交替，d[5 '-G3（AT）5C 3 - 3']> GC富集d[5 '-A3 G5 C5 T3 - 3']。(9)3以比具有交替AT碱基对的DNA双链体（B DNA，d[5 ′-G3（AT）5C 3 - 3 ′]）高一个数量级的亲和力结合含有DNA双链体（B* DNA，d[5 ′-G3 A5 T5 C3 - 3 ′]）的AT段，并且以比富含GC的DNA（A形式，d[5 ′-A3 G5 C5 T3 - 3 ′]）高几乎三个数量级的亲和力结合含有DNA双链体（D）的AT段。
A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2’-(Ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (Isothermal Calorimetry), CD (Circular Dichroism), FID (Fluorescent Intercalator Displacement), and UV (Ultra-Violet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 towards AT rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA).poly(dT) DNA duplex than the poly(dA).2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA).2poly(dT) triplex but stabilizes poly(dA).poly(dT) duplex, suggesting major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10~12 base pairs/drug, depending upon the structure/sequence of the duplex for AT rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5’-A12-x -T12-3’), × = hexaethylene glycol linker] result in a binding stoichiometry of 1:1 with a binding constant ~ 108 M-1 at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT rich than towards DNA duplexes with alternate AT base pairs. (7) Salt dependent studies indicate the formation of 3 ion pairs during binding of the DNA duplex d[5’-A12-x -T12-3’] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes follow the order, AT continuous, d[5’-G3A5T5C3-3’] > AT alternate, d[5’-G3(AT)5C3-3’] > GC rich d[5’-A3G5C5T3-3’]. (9) 3 binds to AT tract containing DNA duplex (B* DNA, d[5’-G3A5T5C3-3’]) with an order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5’-G3(AT)5C3-3’]) and with almost three orders of magnitude higher affinity than a GC rich DNA (A form, d[5’-A3G5C5T3-3’]).
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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：
15
作者：
Boger, DL;Fink, BE;Hedrick, MP
通讯作者：
Hedrick, MP
影响因子：
15
作者：
Bifulco, G;Galeone, A;Gomez-Paloma, L
通讯作者：
Gomez-Paloma, L
影响因子：
4.7
作者：
Charles, Irudayasamy;Xi, Hongjuan;Arya, Dev P.
通讯作者：
Arya, Dev P.
影响因子：
2.9
作者：
Hud, NV;Plavec, J
通讯作者：
Plavec, J