ArticleProceedings of the National Academy of Sciences of the United States of America2001
Predicting crossover generation in DNA shuffling.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Intelligent Design of 14-3-3 Docking Proteins Utilizing Synthetic Evolution Artificial Intelligence (SYN-AI).ACS omega · 2019Article
- Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality.Molecular therapy. Methods & clinical development · 2019Article
- DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein ofBMC biophysics · 2017Article
- Identification of amino acids important for substrate specificity in sucrose transporters using gene shuffling.The Journal of biological chemistry · 2012Article
- Algorithms for optimizing cross-overs in DNA shuffling.BMC bioinformatics · 2012Article
- Replacing Mn(2+) with Co(2+) in human arginase i enhances cytotoxicity toward l-arginine auxotrophic cancer cell lines.ACS chemical biology · 2010Article
- Revealing biases inherent in recombination protocols.BMC biotechnology · 2007Article
- Mutant library construction in directed molecular evolution: casting a wider net.Molecular biotechnology · 2006Review
- IPRO: an iterative computational protein library redesign and optimization procedure.Biophysical journal · 2006Article
- Recombination during in vitro evolution.Journal of molecular evolution · 2005Article
- Evolution of highly active enzymes by homology-independent recombination.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Evolution and evolvability of proteins in the laboratory.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution.Nucleic acids research · 2004Review
- Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers.Nucleic acids research · 2003Article
- Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Computational and experimental analysis of DNA shuffling.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Growth factor engineering by degenerate homoduplex gene family recombination.Nature biotechnology · 2002Article
- Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently.Nature biotechnology · 2002Article
- eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.Nucleic acids research · 2002Article
- Creating multiple-crossover DNA libraries independent of sequence identity.Proceedings of the National Academy of Sciences of the United States of America · 2001Article
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4 authors.
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Abstract
We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model the annealing process. Statistics obtained for the annealing events then are combined with a reassembly algorithm to infer crossover allocation in the reassembled sequences. The fraction of reassembled sequences containing zero, one, two, or more crossovers and the probability that a given nucleotide position in a reassembled sequence is the site of a crossover event are estimated. Comparisons of the predictions against experimental data for five example systems demonstrate good agreement despite the fact that no adjustable parameters are used. An in silico case study of a set of 12 subtilases examines the effect of fragmentation length, annealing temperature, sequence identity and number of shuffled sequences on the number, type, and distribution of crossovers. A computational verification of crossover aggregation in regions of near-perfect sequence identity and the presence of synergistic reassembly in family DNA shuffling is obtained.
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