PEPTIDE DNA HYBRIDS

我们感兴趣的是确定高分辨率的结构， 肽-DNA杂交，并利用这些结构来寻找新的 与DNA或RNA靶标结合的治疗剂。 特别是， 紧密结合单链的肽序列 寡核苷酸，从而保护它们免受核酸酶降解 正在被寻找。 根据体外筛选的结果， 实验中，选择了两个肽-DNA序列。 二维 第一个序列（KWKGSGCTTTGAC）的光谱（NOESY，TOCSY）为 尽管盐浓度、pH值和 温度，光谱没有提供足够的约束， 解决了高度柔性的三维结构 分子内复合物 第二个序列（WTG-CGCAC）已被 选自部分自互补序列，其中 氨基酸残基与单链 区域受到双链体的模板效应的青睐。 NOESY 所选混合分子在40、80、160、320和500 ms处的光谱 记录混合时间，以及TOCSY和ROESY 实验 发现这些光谱包含丰富的 很好地解决了交叉峰，使我们能够分配许多质子 在混合动力车里 初步的分子动力学工作是这样进行的， 与X-PLOR的“模拟退火”例程相比， 第一组未精炼的结构。 基于这些，我们有信心 我们将能够解决这个复杂的结构。

We are interested in determining high resolution structures of peptide-DNA hybrids and using these structures to search for new therapeutic agents that bind to DNA or RNA targets. In particular, peptide sequences that bind tightly to single-stranded oligonucleotides, and thus protect them against nuclease degradation are being sought. Based on the results of the in vitro selection experiments, two peptide-DNA sequences were selected. Two-dimensional spectra (NOESY, TOCSY) of the first sequence (KWKGSGCTTTGAC) were recorded and despite optimization of salt concentration, pH, and temperature, the spectra did not provide sufficient constraints to solve the three-dimensional structure of the highly flexible intramolecular complex. The second sequence (WTG-CGCAC) had been selected from partially self-complementary sequences, where interactions between amino acid residues and the single-stranded region are favored by the template effect of the duplex. NOESY spectra of the chosen hybrid molecule at 40, 80, 160, 320, and 500 ms mixing time were recorded, together with a TOCSY and a ROESY experiment. These spectra were found to contain a rich collection of well resolved cross peaks, allowing us to assign many of the protons in the hybrid. The preliminary molecular dynamics work performed so far with the "simulated annealing" routine of X-PLOR led to a very first set of unrefined structures. Based on these, we are confident that we will be able to solve the structure of this complex.