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首页> 外文期刊>Chemistry: A European journal >Reversed assembly of dyes in an RNA duplex compared with those in DNA
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Reversed assembly of dyes in an RNA duplex compared with those in DNA

机译：与DNA相比，RNA双链体中染料的反向组装

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We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4'-methylthioazobenzene, and thiazole orange) on D-threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3'-side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5'-side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H-aggregates) even on an A-type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA-thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA-dye conjugates are potentially useful probes for real-time monitoring of RNA interference (RNAi) mechanisms.
机译：我们通过杂交两个RNA低聚物来制备反向染料簇，每个寡核苷酸在链中心的D-苏氨酸（苏氨酸核苷酸）上束缚了染料（甲基红，4'-甲基硫代偶氮苯和噻唑橙）。 NMR光谱分析表明，来自每条链的两种染料在双链体中彼此以反平行的方式轴向堆叠，并位于天然核碱基的3'侧。有趣的是，染料的这种位置关系与我们先前报道的在DNA中组装的位置关系完全相反：DNA中的染料位于天然核碱基的5'侧。该观察结果也与二聚化染料的圆二色性相一致，在二色化染料中，相对于DNA，染料的棉效应（即两种染料的缠绕特性）在RNA中是相反的。进一步的光谱分析表明，染料在RNA双链体上的聚集引起明显的七色性和谱带的变窄，从而表明即使在A型螺旋上，染料也被轴向堆叠（即，H-聚集）。基于这些结果，我们还制备了RNA双链体中的荧光团（噻唑橙）和淬灭剂（甲基红）的异二聚体。噻唑橙的荧光因激子相互作用而被甲基红强烈淬灭，因此带有和不带有互补链的带有淬灭剂的RNA-噻唑橙缀合物的荧光强度比高达27。我们相信这些RNA染料偶联物可能是实时监测RNA干扰（RNAi）机制的潜在探针。

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