Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair

Six unnatural nucleotides featuring fluorine-substituted phenyl nucleobase analogues have been synthesized, incorporated into DNA, and characterized in terms of the structure and replication properties of the self-pairs they form. Each unnatural self-pair is accommodated in B-form DNA without detectable structural perturbation, and all are thermally stable and selective to roughly the same degree. Furthermore, the efficiency of polymerase-mediated mispair synthesis is similar for each unnatural nucleotide in the template. In contrast, the efficiency of polymerase-mediated self-pair extension is highly dependent on the specific fluorine substitution pattern. The most promising unnatural base pair candidate of this series is the 3-fluorobenzene self-pair, which is replicated with reasonable efficiency and selectivity.     

A Facile System for Encoding Unnatural Amino Acids in Mammalian Cells

A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl‐tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl‐tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal tRNA–aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins.

     

Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs

Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

Anomalous scaling in epitaxial growth on vicinal surfaces: meandering and mounding instabilities in a linear growth equation with spatiotemporally correlated noise

We have undertaken an extensive analytical and kinetic Monte Carlo study of the (2+1) dimensional discrete growth model on a vicinal surface. A non-local, phenomenological continuum equation describing surface growth in unstable systems with anomalous scaling is presented. The roughness produced by unstable growth is first studied considering various effects in surface diffusion processes (corresponding to temperature, flux, diffusion anisotropy). We found that the thermally activated roughness is well-described by a generalized Lai–Das Sarma–Villain model with non linear growth continuum equation and uncorrelated noise. The corresponding critical exponents are computed analytically for the first time and show a continuous variation in agreement with simulation results of a solid-on-solid model. However, the roughness related to the meandering instability is found, unexpectedly, to be well described by a linear continuum equation with spatiotemporally correlated noise.     

高效液相色谱法测定水体中的氯虫酰胺残留量

采用Kromasil C18不锈钢柱(250mm×4.6mm i.d..5μm),以甲醇-水混合溶剂(65:35,V/V)为流动相,流速1.0mL/min,光电二极管阵列检测器,检测波长236nm和柱温35C,建立了不同水体中氯虫酰胺残留的高效液相色谱分析方法.氯虫酰胺水样直接用二氯甲烷进行液-液分配萃取.在0.10-10mg/L的浓度范围内,氯虫酰胺峰面积(y)与质量浓度(x)呈现良好的相关性,其线性回归方程为y=2170.4x 2641.7,r2=0.9991.井水和池塘水中添加质量浓度为0.01-1.00mg/L时,其平均回收率分别为94.70%-100.37%和89.14%-100.22%,变异系数分别为0.81%-5.11%和1.81%-5.30%,水样中的氯虫酰胺最低检测质量浓度(LOQ)为7.5×10-3mg/L,方法快速、灵敏度高、重现性好,具有较好的准确度和精密度,可用于环境中水样和土壤样中氯虫酰胺的残留检测分析.