Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications.
Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications.
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DOI：
10.1093/nar/gkv875
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发表时间：
2015-10-15
影响因子：
14.9
通讯作者：
Govindaraju T
中科院分区：
文献类型：
--
作者：
Narayanaswamy N;Das S;Samanta PK;Banu K;Sharma GP;Mondal N;Dhar SK;Pati SK;Govindaraju T
在分子生物学中，理解DNA的功能和结构方面需要序列特异性DNA结合探针。特别是，序列特异性荧光探针提供了实时监测活细胞中DNA的构象和结构重组的优势。基于DNA的独特的内电荷转移（ICT）过程，设计了一类新型的D2 A（one-donor-two-acceptor）近红外荧光探针QCy-DT（quinone cyanine-dithiazole）。有趣的是，QCy-DT在富含AT的DNA的存在下表现出较强的NIR荧光增强，相比于富含GC的单链DNA。结果表明，QCy-DT对含有5′-AATT-3′序列的DNA具有序列特异性的小沟识别能力，而对含有其它可变（A/T）4序列的DNA具有序列特异性的小沟识别能力。对5′-X（AATT）Y-3′识别序列周围的碱基变异的研究表明，X = A和Y = T是最优选的碱基。活细胞成像研究证实了哺乳动物细胞的渗透性、低毒性和核DNA的选择性染色能力，而不需要RNA酶处理。此外，具有富含AT基因组的恶性疟原虫显示出具有合理低的IC 50值（<4 µM）的特异性摄取。QCy-DT的合成简单、Stokes位移大、序列特异性DNA小沟识别和打开NIR荧光、光稳定性和低IC 50的寄生虫染色使得QCy-DT成为潜在的和商业上可行的DNA探针。
In molecular biology, understanding the functional and structural aspects of DNA requires sequence-specific DNA binding probes. Especially, sequence-specific fluorescence probes offer the advantage of real-time monitoring of the conformational and structural reorganization of DNA in living cells. Herein, we designed a new class of D2A (one-donor-two-acceptor) near-infrared (NIR) fluorescence switch-on probe named quinone cyanine–dithiazole (QCy–DT) based on the distinctive internal charge transfer (ICT) process for minor groove recognition of AT-rich DNA. Interestingly, QCy–DT exhibited strong NIR-fluorescence enhancement in the presence of AT-rich DNA compared to GC-rich and single-stranded DNAs. We show sequence-specific minor groove recognition of QCy–DT for DNA containing 5′-AATT-3′ sequence over other variable (A/T)4 sequences and local nucleobase variation study around the 5′-X(AATT)Y-3′ recognition sequence revealed that X = A and Y = T are the most preferable nucleobases. The live cell imaging studies confirmed mammalian cell permeability, low-toxicity and selective staining capacity of nuclear DNA without requiring RNase treatment. Further, Plasmodium falciparum with an AT-rich genome showed specific uptake with a reasonably low IC50 value (<4 µM). The ease of synthesis, large Stokes shift, sequence-specific DNA minor groove recognition with switch-on NIR-fluorescence, photostability and parasite staining with low IC50 make QCy–DT a potential and commercially viable DNA probe.