Site-specific mutagenesis to modify the human tumor necrosis factor gene

Prediction of mutant activity and its application in molecular design of tumor necrosis factor-alpha

Two models for prediction of the activity and stability of site-directed mutagenesis on tumor necrosis factor-alpha are established. The models are based on straightforward structural considerations, which do not require the elaboration of sitedirected mutagenesis on the protein core and the hydrophobic surface area by analyzing the pmperties of the mutated amino acid residues. The reliabilities of the models have been tested by analyzing the mutants of tumor necrosis factor-alpha (TNF-alpha) whose two leucine residues (L29, L157) were mutated. Based on these models, a TNFalpha mutant with high activity was created by molecular design.

RAMHA: a PC-based Monte-Carlo simulation of random saturation mutagenesis

Random mutagenesis is a powerful tool in protein structure-function analyses. One approach to random mutagenesis is the de novo synthesis of polypeptide-encoding oligodeoxy-nucleotides using doped nucleoside phosphoramidites. A Turbo PASCAL program, RAMHA, is described for modeling such mutagenesis. Upon entering the target sequence and the desired level of nucleotide contamination, RAMHA performs a Monte Carlo simulation of the mutagenesis, compiling statistics on the similarity of resultant mutant polypeptides to the wild-type sequence, the frequency of premature open-reading frame terminations, and other relevant outcomes. Simulated mutagenesis of two DNA targets has led to the development of two different strategies to avoid the random introduction of stop codons within mutagenized gene segments.

Insertional gene synthesis, a novel method of assembling consecutive DNA sequences within specific sites in plasmids. Construction of the HIV-1 tat gene

The construction of the HIV-1 tat gene using a novel method termed insertional gene synthesis (IGS) is described. IGS is used to assemble a gene or any DNA sequence in a stepwise manner within a plasmid containing a single stranded DNA phage origin of replication. The IGS method is based upon consecutive targeted insertions of long DNA oligonucleotides (greater than 100 bases) within the plasmid by oligonucleotide-directed mutagenesis. IGS therefore involves synthesis of only a few oligonucleotides corresponding to one strand of a gene. Furthermore, the gene is synthesized directly adjacent to bacterial gene regulatory sequences for direct expression. Using this approach, the 261 bp tat gene was assembled in three successive cycles adjacent to the lac promoter in the pEMBL-derivative, pKH125. The 15 kD tat protein was produced from this synthetic gene in E. coli upon IPTG induction. However, it was necessary to tightly control the expression of tat by including the lac I gene directly within the tat expression vector.