Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids
Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids
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DOI：
10.1021/bi060479t
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发表时间：
2006-08-01
期刊：
影响因子：
2.9
通讯作者：
Thompson, Katherine C.
中科院分区：
文献类型：
--
作者：
Hardman, Samantha J. O.;Thompson, Katherine C.
荧光碱基类似物被广泛用于探测核酸的结构和动力学。当碱基位于双链核酸区域时，腺嘌呤类似物2-氨基嘌呤和胞嘧啶类似物吡咯胞嘧啶的荧光被显著猝灭。为了能够从这些碱基的荧光研究中获得更详细的结构信息，我们在CIS和TDB3LYP水平上研究了氢键和碱基堆积配合物中碱基的激发态性质。结果表明，含2-氨基嘌呤和胸腺嘧啶的氢键络合物的第一激发态(荧光态)仅为2-氨基嘌呤的第一激发态。然而，对于2-氨基嘌呤与其他碱基堆积的结构就不能说同样的话了。堆积导致参与荧光转变的分子轨道分布在不止一个碱基上。降低了荧光跃迁的预测速率，从而降低了荧光量子产率。辐射率的降低随堆积排列(如A型或B型DNA)和堆积2-氨基嘌呤的碱基的相同而不同。在两个鸟嘌呤基团之间堆积2-氨基嘌呤可以显著减小第一和第二激发态之间的能隙。在所研究的任何系统中，我们都没有找到关于低能电荷转移状态的可靠证据。在吡咯胞嘧啶的情况下，发现碱基堆积降低了荧光跃迁的振子强度，但观察到分子轨道在多个碱基上的扩散很少。
Fluorescent nucleobase analogues are used extensively to probe the structure and dynamics of nucleic acids. The fluorescence of the adenine analogue 2-aminopurine and the cytosine analogue pyrrolocytosine is significantly quenched when the bases are located in regions of double-stranded nucleic acids. To allow more detailed structural information to be obtained from fluorescence studies using these bases, we have studied the excited-state properties of the bases at the CIS and TDB3LYP level in hydrogen-bonded and base-stacked complexes. The results reveal that the first excited state ( the fluorescent state) of a hydrogen-bonded complex containing 2-aminopurine and thymine is just the first excited state of 2-aminopurine alone. However, the same cannot be said for structures in which 2-aminopurine is base stacked with other nucleobases. Stacking causes the molecular orbitals involved in the fluorescence transition to spread over more than one base. The predicted rate for the fluorescence transition is reduced, thus reducing the fluorescence quantum yield. The decrease in radiative rate varies with the stacking arrangement ( e. g., A- or B- form DNA) and with the identity of the nucleobase with which 2-aminopurine is stacked. Stacking 2-aminopurine between two guanine moieties is shown to significantly decrease the energy gap between the first and second excited states. We do not find reliable evidence for a low-energy charge-transfer state in any of the systems that were studied. In the case of pyrrolocytosine, base stacking was found to reduce the oscillator strength for the fluorescence transition, but very little spreading of molecular orbitals across more than one base was observed.