Bhavsar Yogini P, Reilly Samantha M, Wadkins Randy M
Department of Chemistry and Biochemistry, The University of Mississippi, Coulter Hall, Room 409, MS 38677, USA.
J Nucleic Acids. 2011;2011:986820. doi: 10.4061/2011/986820. Epub 2011 Aug 15.
Topological variants of single-strand DNA (ssDNA) structures, referred to as "functional DNA," have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC) and 1,3-diaza-2-oxophenoxazine (tC(°)), can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA) to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD) spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC(°) is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.
单链DNA（ssDNA）结构的拓扑变体，被称为“功能性DNA”，已在许多基因的调控区域中被检测到，并被认为会影响基因表达。两种脱氧胞苷的荧光类似物，即吡咯并-dC（PdC）和1,3-二氮杂-2-氧代吩恶嗪（tC(°)），可以掺入DNA中。在此，我们描述了对这两种类似物的光谱研究，以确定能够报告从双链DNA（dsDNA）到ssDNA结构转变的荧光特性，这是向功能性DNA结构转变的常见途径。我们获得了DNA中荧光团的荧光检测圆二色性（FDCD）光谱、稳态荧光光谱和荧光寿命。我们的结果表明，由于配对碱基和未配对碱基之间有明显的约2纳秒变化，PdC在荧光寿命研究中具有优势。然而，tC(°)是用于报告荧光团周围DNA螺旋结构的FDCD实验的更好探针。两种荧光团都提供了互补数据来测量DNA结构转变。
