ITR: Information Technology for Self-Assembling Synthetic Genes

通常需要产生一个合成基因，该基因编码感兴趣的蛋白质，并针对所需的序列特性进行优化，例如在目标生物体中折叠和表达的良好翻译动力学。然而，大多数基因的长度远远超过精确DNA合成的极限。因此，定制基因的快速创造并不方便。作为初步结果，我们已经开发了一种计算优化的DNA序列，编码自己正确的自我组装的方法。许多短重叠的合成寡核苷酸被设计成在高温下以高效率正确杂交，而所有竞争的非生产性杂交事件被识别和不受欢迎。序列属性使用正式的启发式搜索进行优化。基于这些初步结果，本项目正在开发信息技术和生物技术的新方法，用于长串混合编码、调控和基因间区域的自组装。所得到的DNA构建体可以杂交到任何质粒表达载体中并转化到细胞中，或者直接用作DNA模板在体外转录-翻译耦合系统中产生蛋白质。新方法将是准确的，无酶的，在溶液中，单步，可扩展和高通量。它们将与大规模、高通量结晶和蛋白质组学研究相关，并使合成基因组的创建变得容易。

It is often desirable to produce a synthetic gene that encodes a protein of interest and is optimized for desirable sequence properties, such as good translation kinetics for folding and expression in a target organism. However, most genes are far longer than the limits of accurate DNA synthesis. Thus, the rapid creation of tailored genes has not been convenient. As preliminary results we have developed a method for the computational optimization of DNA sequences that encode their own correct self-assembly. Scores of short overlapping synthetic oligonucleotides are designed to hybridize correctly with great efficiency at a high temperature, while all competing nonproductive hybridization events are identified and disfavored. Sequence properties are optimized using a formal heuristic search. Based on these preliminary results this project is developing novel methods in information technology and biotechnology for the self-assembly of long strings of mixed coding, regulatory, and intergenic regions. The DNA constructs that result may be hybridized into any plasmid expression vector and transformed into cells, or used directly as DNA templates to produce proteins in coupled in vitro transcription-translation systems. The new methods will be accurate, enzyme-free, in solution, single step, scalable, and high-throughput. They will have relevance to large-scale, high-throughput crystallization and proteomics efforts and enable the facile creation of synthetic genomes.