Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
Bioorg Med Chem. 2013 Oct 15;21(20):6191-7. doi: 10.1016/j.bmc.2013.04.032. Epub 2013 Apr 22.
Here, we investigated spectroscopic behaviors of tetramethylrhodamine (TMR) homo- and hetero-dimers within DNA duplex. In order to shield the chromophores from natural base pairs, we used cyclohexyl base pairs as 'insulators'; these pairs were inserted between the chromophores and nucleobases. When a single TMR moiety was sandwiched between cyclohexyl base pairs, the emission intensity increased by fivefold relative to a TMR between natural base pairs, because electron transfer from nucleobases was suppressed. Next, we inserted two TMRs between the cyclohexyl base pairs and found that they facilitated H-dimer formation of TMR; a distinct hypsochromic shift was induced only when cyclohexyl base pairs were inserted. We further examined quenching behavior of a TMR paired with a quencher dye between cyclohexyl base pairs. Interestingly, fluorescence from TMR was quenched by nitro methyl red more efficiently in the presence of cyclohexyl base pairs than in their absence. This suggests that neighboring natural base pairs disturbed electron or hole transfer between the fluorophore and the quencher. The cyclohexyl base pairs shielded the chromophore pair from the natural base pairs and allowed intrinsic electron transfer.
在这里，我们研究了四甲基罗丹明（TMR）同型和异型二聚体在 DNA 双链体中的光谱行为。为了将生色团与天然碱基对屏蔽，我们使用环己基碱基对作为“绝缘体”；这些碱基对插入在生色团和碱基之间。当单个 TMR 部分夹在环己基碱基对之间时，与在天然碱基对之间的 TMR 相比，其发射强度增加了五倍，因为来自碱基的电子转移受到了抑制。接下来，我们在环己基碱基对之间插入了两个 TMR，发现它们促进了 TMR 的 H-二聚体形成；仅当插入环己基碱基对时，才会引起明显的蓝移。我们进一步研究了在环己基碱基对之间与猝灭染料配对的 TMR 的猝灭行为。有趣的是，与不存在环己基碱基对相比，在存在环己基碱基对的情况下，硝基甲基红对 TMR 的荧光猝灭更有效。这表明相邻的天然碱基对干扰了荧光团和猝灭剂之间的电子或空穴转移。环己基碱基对将生色团对与天然碱基对屏蔽，并允许内在的电子转移。
