A dual-fluorescence reporter system for high-throughput clone characterization and selection by cell sorting

Molecular biology critically depends upon the isolation of desired DNA sequences. Flow cytometry, with its capacity to interrogate and sort more than 50 000 cells/s, shows great potential to expedite clone characterization and isolation. Intrinsic heterogeneity of protein expression levels in cells limits the utility of single fluorescent reporters for cell-sorting. Here, we report a novel dual-fluorescence strategy that overcomes the inherent limitations of single reporter systems by controlling for expression variability. We demonstrate a dual-reporter system using the green fluorescent protein (GFP) gene fused to the Discosoma red fluorescent protein (DsRed) gene. The system reports the successful insertion of foreign DNA with the loss of DsRed fluorescence and the maintenance of GFP fluorescence. Single cells containing inserts are readily recognized by their altered ratios of green to red fluorescence and separated using a high-speed cell-sorter for further processing. This novel reporter system and vector were successfully validated by shotgun library construction, cloned sequence isolation, PCR amplification and DNA sequencing of cloned inserts from bacteria after cell-sorting. This simple, robust system can also be adapted for diverse biosensor assays and is amenable to miniaturization. We demonstrated that dual-fluorescence reporting coupled with high-speed cell-sorting provides a more efficient alternative to traditional methods of clone isolation

Frameshift Mutagenesis and Microsatellite Instability Induced by Human Alkyladenine DNA Glycosylase

Human alkyladenine DNA glycosylase (hAAG) excises alkylated purines, hypoxanthine, and etheno bases from DNA to form abasic (AP) sites. Surprisingly, elevated expression of hAAG increases spontaneous frameshift mutagenesis. By random mutagenesis of eight active site residues, we isolated hAAG-Y127I/H136L double mutant that induces even higher rates of frameshift mutation than does the wild-type hAAG; the Y127I mutation accounts for the majority of the hAAG-Y127I/H136L-induced mutator phenotype. The hAAG-Y127I/H136L and hAAG-Y127I mutants increased the rate of spontaneous frameshifts by up to 120-fold in S. cerevisiae and also induced high rates of microsatellite instability (MSI) in human cells. hAAG and its mutants bind DNA containing one and two base-pair loops with significant affinity, thus shielding them from mismatch repair; the strength of such binding correlates with their ability to induce the mutator phenotype. This study provides important insights into the mechanism of hAAG-induced genomic instability.National Institutes of Health (U.S.) (Grant CA055042)National Institutes of Health (U.S.) (Grant CA115802)National Institutes of Health (U.S.) (Grant ES02109

Evaluation of integrin αvβ6 cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.

Advances in precision molecular imaging promise to transform our ability to detect, diagnose and treat disease. Here, we describe the engineering and validation of a new cystine knot peptide (knottin) that selectively recognizes human integrin αvβ6 with single-digit nanomolar affinity. We solve its 3D structure by NMR and x-ray crystallography and validate leads with 3 different radiolabels in pre-clinical models of cancer. We evaluate the lead tracer's safety, biodistribution and pharmacokinetics in healthy human volunteers, and show its ability to detect multiple cancers (pancreatic, cervical and lung) in patients at two study locations. Additionally, we demonstrate that the knottin PET tracers can also detect fibrotic lung disease in idiopathic pulmonary fibrosis patients. Our results indicate that these cystine knot PET tracers may have potential utility in multiple disease states that are associated with upregulation of integrin αvβ6

Molecular Mechanism Underlying the Interaction of Typical Sac10b Family Proteins with DNA

The Sac10b protein family is regarded as a family of DNA-binding proteins that is highly conserved and widely distributed within the archaea. Sac10b family members are typically small basic dimeric proteins that bind to DNA with cooperativity and no sequence specificity and are capable of constraining DNA negative supercoils, protecting DNA from Dnase I digestion, and do not compact DNA obviously. However, a detailed understanding of the structural basis of the interaction of Sac10b family proteins with DNA is still lacking. Here, we determined the crystal structure of Mth10b, an atypical member of the Sac10b family from Methanobacterium thermoautotrophicum ΔH, at 2.2 Å. Unlike typical Sac10b family proteins, Mth10b is an acidic protein and binds to neither DNA nor RNA. The overall structure of Mth10b displays high similarity to its homologs, but three pairs of conserved positively charged residues located at the presumed DNA-binding surface are substituted by non-charged residues in Mth10b. Through amino acids interchanges, the DNA-binding ability of Mth10b was restored successfully, whereas the DNA-binding ability of Sso10b, a typical Sac10b family member, was weakened greatly. Based on these results, we propose a model describing the molecular mechanism underlying the interactions of typical Sac10b family proteins with DNA that explains all the characteristics of the interactions between typical Sac10b family members and DNA

Random mutations, protein mutability, and DNA repair: understanding protein tolerance to random amino acid changes through directed evolution

Thesis (Ph. D.)--University of Washington, 2004In nature, evolution has given rise to the astonishing and wonderful diversity of organisms on this planet. In the laboratory, directed evolution can be a powerful technique to generate variants of a given protein with novel characteristics. The end products of the selection for desired traits from large combinatorial sets of mutants can also yield insight into protein structure and function. In both laboratory and nature, new mutations may be beneficial, but are often neutral or deleterious to overall protein function. One salient question that arises is the degree of tolerance of a protein to random amino acid change.A major part of the corpus of this dissertation addresses this question of protein tolerance to random change. This basic question is quantitatively defined as calculating the probability that a random amino acid replacement will lead to a protein's functional inactivation. Using the human DNA repair enzyme 3-methyladenine DNA glycosylase (AAG), we develop a method to calculate inactivation probabilities from libraries of AAG mutants harboring random mutations throughout the gene. This analytical method is then applied to a range of diverse proteins. Remarkably, inactivation probabilities were observed to be similar among many proteins. To delineate the nature of tolerated mutations, 244 surviving AAG mutants were sequenced. Over 920 tolerated mutations were assembled into "substitutability indices" of each amino acid position across the entire AAG gene and mapped onto secondary and tertiary structures. I discuss the general factors determining the tolerability of amino acid substitutions within the same chapter.The next section of this dissertation describes the use of targeted random oligonucleotide cassette mutagenesis to study the AAG enzyme active site. Selection for altered properties yield novel human DNA glycosylases with altered active sites. This study also reveals the degree of plasticity of the human AAG substrate recognition pocket and highlights the essential residues for substrate recognition and catalysis.This dissertation demonstrates a general approach to understanding proteins' tolerance to random mutations, and to creating novel DNA glycosylases. This work can serve as a stepping stone toward new enzymes remove select altered DNA bases for potential therapeutic and biotechnological applications