ArticleProceedings of the National Academy of Sciences of the United States of America2001
Creating multiple-crossover DNA libraries independent of sequence identity.
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 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 157 citations in OpenAlex.
- A primer to directed evolution: current methodologies and future directions.RSC chemical biology · 2023Review
- Tailoring Proteins to Re-Evolve Nature: A Short Review.Molecular biotechnology · 2018Review
- A highly stable laccase obtained by swapping the second cupredoxin domain.Scientific reports · 2018Article
- Biomolecular engineering for nanobio/bionanotechnology.Nano convergence · 2017Review
- Sex in a test tube: testing the benefits of in vitro recombination.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- Combinatorial engineering of 1-deoxy-D-xylulose 5-phosphate pathway using cross-lapping in vitro assembly (CLIVA) method.PloS one · 2013Article
- Restriction enzyme-free construction of random gene mutagenesis libraries in Escherichia coli.Analytical biochemistry · 2012Article
- Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis.Future medicinal chemistry · 2011Article
- Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach.The Journal of biological chemistry · 2010Article
- Exploring protein fitness landscapes by directed evolution.Nature reviews. Molecular cell biology · 2009Review
- Engineering Kinases to Phosphorylate Nucleoside Analogs for Antiviral and Cancer Therapy.Chimia · 2009Article
- The enzymatic basis for pesticide bioremediation.Indian journal of microbiology · 2008Article
- Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities.Journal of molecular biology · 2007Article
- Mutant library construction in directed molecular evolution: casting a wider net.Molecular biotechnology · 2006Review
- Laboratory-directed protein evolution.Microbiology and molecular biology reviews : MMBR · 2005Review
- Evolution of highly active enzymes by homology-independent recombination.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- On the conservative nature of intragenic recombination.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Directed evolution of protein enzymes using nonhomologous random recombination.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- FamClash: a method for ranking the activity of engineered enzymes.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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed, experimentally implemented, and modeled in silico a methodology named SCRATCHY that enables the combinatorial engineering of target proteins, independent of sequence identity. The approach combines two methods for recombining genes: incremental truncation for the creation of hybrid enzymes and DNA shuffling. First, incremental truncation for the creation of hybrid enzymes is used to create a comprehensive set of fusions between fragments of genes in a DNA homology-independent fashion. This artificial family is then subjected to a DNA-shuffling step to augment the number of crossovers. SCRATCHY libraries were created from the glycinamide-ribonucleotide formyltransferase (GART) genes from Escherichia coli (purN) and human (hGART). The developed modeling framework eSCRATCHY provides insight into the effect of sequence identity and fragmentation length on crossover statistics and draws contrast with DNA shuffling. Sequence analysis of the naive shuffled library identified members with up to three crossovers, and modeling predictions are in good agreement with the experimental findings. Subsequent in vivo selection in an auxotrophic E. coli host yielded functional hybrid enzymes containing multiple crossovers.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.