Predicting crossover generation in DNA shuffling.

PubWeight™: 1.12‹?› | Rank: Top 10%

🔗 View Article (PMC 30635)

Published in Proc Natl Acad Sci U S A on March 13, 2001

Authors

G L Moore1, C D Maranas, S Lutz, S J Benkovic

Author Affiliations

1: Department of Chemical Engineering, 112A Fenske Laboratory, Pennsylvania State University, University Park, PA 16802, USA.

Articles citing this

Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res (2004) 1.46

Replacing Mn(2+) with Co(2+) in human arginase i enhances cytotoxicity toward l-arginine auxotrophic cancer cell lines. ACS Chem Biol (2010) 1.19

Creating multiple-crossover DNA libraries independent of sequence identity. Proc Natl Acad Sci U S A (2001) 1.18

Evolution of highly active enzymes by homology-independent recombination. Proc Natl Acad Sci U S A (2005) 1.08

IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J (2006) 1.02

Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers. Nucleic Acids Res (2003) 0.96

Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach. Proc Natl Acad Sci U S A (2003) 0.92

Revealing biases inherent in recombination protocols. BMC Biotechnol (2007) 0.87

eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. Nucleic Acids Res (2002) 0.86

Recombination during in vitro evolution. J Mol Evol (2005) 0.85

Computational and experimental analysis of DNA shuffling. Proc Natl Acad Sci U S A (2003) 0.83

Identification of amino acids important for substrate specificity in sucrose transporters using gene shuffling. J Biol Chem (2012) 0.81

Evolution and evolvability of proteins in the laboratory. Proc Natl Acad Sci U S A (2004) 0.75

Algorithms for optimizing cross-overs in DNA shuffling. BMC Bioinformatics (2012) 0.75

Articles cited by this

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A (1998) 24.28

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry (1999) 7.50

Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry (1997) 7.33

DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A (1994) 5.69

A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. J Biol Chem (1979) 5.32

Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res (2000) 5.11

Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci (1997) 4.86

Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry (1998) 4.85

Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry (1998) 4.75

Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res (1998) 4.62

DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature (1998) 4.21

Extracting protein alignment models from the sequence database. Nucleic Acids Res (1997) 3.17

A hierarchical approach to protein molecular evolution. Proc Natl Acad Sci U S A (1999) 1.80

A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol (1999) 1.79

Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol (1998) 1.71

Breeding of retroviruses by DNA shuffling for improved stability and processing yields. Nat Biotechnol (2000) 1.70

Designed evolution of enzymatic properties. Curr Opin Biotechnol (2000) 1.36

DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol (1999) 1.36

Enzyme engineering for nonaqueous solvents: random mutagenesis to enhance activity of subtilisin E in polar organic media. Biotechnology (N Y) (1991) 1.31

Directed evolution of industrial enzymes. Trends Biotechnol (1999) 1.29

Applications of DNA shuffling to pharmaceuticals and vaccines. Curr Opin Biotechnol (1997) 1.07

Modeling DNA mutation and recombination for directed evolution experiments. J Theor Biol (2000) 1.05

Functional and nonfunctional mutations distinguished by random recombination of homologous genes. Proc Natl Acad Sci U S A (1997) 1.03

Incremental truncation as a strategy in the engineering of novel biocatalysts. Bioorg Med Chem (1999) 1.02

Articles by these authors

Assembly of combinatorial antibody libraries on phage surfaces: the gene III site. Proc Natl Acad Sci U S A (1991) 5.94

Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. Science (1989) 5.73

Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry (1987) 4.29

Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry (1987) 3.93

Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science (1992) 3.81

Engineering the third wave of biocatalysis. Nature (2012) 3.44

A DNA fragment with an alpha-phosphorothioate nucleotide at one end is asymmetrically blocked from digestion by exonuclease III and can be replicated in vivo. Proc Natl Acad Sci U S A (1981) 3.14

Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry (1991) 3.07

At the crossroads of chemistry and immunology: catalytic antibodies. Science (1991) 3.06

Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry (1988) 2.86

Gap misrepair mutagenesis: efficient site-directed induction of transition, transversion, and frameshift mutations in vitro. Proc Natl Acad Sci U S A (1982) 2.78

Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry (2001) 2.77

Human immunodeficiency virus type 1 reverse transcriptase: spatial and temporal relationship between the polymerase and RNase H activities. Proc Natl Acad Sci U S A (1992) 2.64

Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry (1997) 2.61

Linkage of recognition and replication functions by assembling combinatorial antibody Fab libraries along phage surfaces. Proc Natl Acad Sci U S A (1991) 2.42

Production of cyclic peptides and proteins in vivo. Proc Natl Acad Sci U S A (1999) 2.42

Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry (1992) 2.41

Chemical basis for enzyme catalysis. Biochemistry (2000) 2.09

Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity. Biochemistry (1994) 2.08

Metallo-beta-lactamase: structure and mechanism. Curr Opin Chem Biol (1999) 2.06

Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis. Biochemistry (1994) 2.04

Purification and characterization of human immunodeficiency virus type 1 reverse transcriptase. Methods Enzymol (1995) 2.01

Dominance for vestibular cortical function in the non-dominant hemisphere. Cereb Cortex (2003) 1.98

Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. J Biol Chem (1992) 1.97

Cloning of the immunological repertoire in Escherichia coli for generation of monoclonal catalytic antibodies: construction of a heavy chain variable region-specific cDNA library. Proc Natl Acad Sci U S A (1989) 1.96

Update on the systematic review of palliative radiotherapy trials for bone metastases. Clin Oncol (R Coll Radiol) (2011) 1.95

On the mechanism of the metallo-beta-lactamase from Bacteroides fragilis. Biochemistry (1999) 1.94

A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity. Biochemistry (1991) 1.87

Stereochemical course of the reaction catalyzed by 5'-nucleotide phosphodiesterase from snake venom. Biochemistry (1979) 1.86

Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry (1995) 1.86

Peptide synthesis catalyzed by an antibody containing a binding site for variable amino acids. Science (1994) 1.85

Comparison of enoxaparin and warfarin for the prevention of venous thromboembolic disease after total hip arthroplasty. Evaluation during hospitalization and three months after discharge. J Bone Joint Surg Am (1999) 1.84

A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol (1999) 1.79

Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol Prog (2001) 1.75

Elementary steps in the DNA polymerase I reaction pathway. Biochemistry (1983) 1.73

The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase. Biochemistry (1995) 1.69

Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng (2001) 1.66

Solvation, reorganization energy, and biological catalysis. J Biol Chem (1998) 1.62

Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3'-->5' exonuclease activity. Proc Natl Acad Sci U S A (1993) 1.57

Characterization of the enzyme complex involving the folate-requiring enzymes of de novo purine biosynthesis. Biochemistry (1980) 1.48

Rate-limiting steps in the DNA polymerase I reaction pathway. Biochemistry (1985) 1.46

Combinatorial protein engineering by incremental truncation. Proc Natl Acad Sci U S A (1999) 1.46

Characterization of the metal-binding sites of the beta-lactamase from Bacteroides fragilis. Biochemistry (1996) 1.45

Stretching exercises--flexibility in dihydrofolate reductase catalysis. Chem Biol (1998) 1.43

DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry (1989) 1.43

IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations. Genes Immun (2008) 1.43

Protein-DNA cross-linking demonstrates stepwise ATP-dependent assembly of T4 DNA polymerase and its accessory proteins on the primer-template. Cell (1991) 1.42

Stereochemical course of the 3'----5'-exonuclease activity of DNA polymerase I. Biochemistry (1984) 1.40

Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization. Biochemistry (1992) 1.39

Interaction of Escherichia coli DNA polymerase I with azidoDNA and fluorescent DNA probes: identification of protein-DNA contacts. Biochemistry (1990) 1.38

Accessory proteins function as matchmakers in the assembly of the T4 DNA polymerase holoenzyme. Curr Biol (1995) 1.37

Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase. Biochemistry (2001) 1.36

Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. Biochemistry (1994) 1.33

A fluorescence-based assay for monitoring helicase activity. Proc Natl Acad Sci U S A (1994) 1.33

Antispasmodic effects of some medicinal plants. Planta Med (1980) 1.33

A stereospecific cyclization catalyzed by an antibody. Science (1987) 1.31

Mechanism of action of fructose 1,6-bisphosphatase. Adv Enzymol Relat Areas Mol Biol (1982) 1.30

Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides. Nucleic Acids Res (2001) 1.28

Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J Biol Chem (1989) 1.27

Metalloantibodies. Science (1990) 1.27

The carboxyl terminus of the bacteriophage T4 DNA polymerase is required for holoenzyme complex formation. Proc Natl Acad Sci U S A (1996) 1.26

Bacteriophage T4 Dda helicase translocates in a unidirectional fashion on single-stranded DNA. J Biol Chem (1995) 1.26

A perspective on biological catalysis. Nat Struct Biol (1996) 1.26

Subcloning, characterization, and affinity labeling of Escherichia coli glycinamide ribonucleotide transformylase. Biochemistry (1990) 1.26

Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase. Biochemistry (1998) 1.25

Strength of an interloop hydrogen bond determines the kinetic pathway in catalysis by Escherichia coli dihydrofolate reductase. Biochemistry (1998) 1.24

Purification of a complex catalyzing folate cofactor synthesis and transformylation in de novo purine biosynthesis. J Biol Chem (1980) 1.23

Minimal kinetic mechanism for misincorporation by DNA polymerase I (Klenow fragment). Biochemistry (1992) 1.23

Effect of single amino acid replacements on the folding and stability of dihydrofolate reductase from Escherichia coli. Biochemistry (1987) 1.22

Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution. Biochemistry (1999) 1.22

Evaluation of the importance of hydrophobic interactions in drug binding to dihydrofolate reductase. J Med Chem (1988) 1.21

Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket. Proc Natl Acad Sci U S A (1990) 1.20

Induction of an antibody that catalyzes the hydrolysis of an amide bond. Science (1988) 1.19

NMR characterization of the metallo-beta-lactamase from Bacteroides fragilis and its interaction with a tight-binding inhibitor: role of an active-site loop. Biochemistry (1999) 1.19

Mutations in HIV reverse transcriptase which alter RNase H activity and decrease strand transfer efficiency are suppressed by HIV nucleocapsid protein. Proc Natl Acad Sci U S A (1997) 1.19

Catalytic reactions of phosphoglucose isomerase with cyclic forms of glucose 6-phosphate and fructose 6-phosphate. J Biol Chem (1973) 1.19

Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proc Natl Acad Sci U S A (2001) 1.18

Creating multiple-crossover DNA libraries independent of sequence identity. Proc Natl Acad Sci U S A (2001) 1.18

Ocular absorption of topically applied FK506 from liposomal and oil formulations in the rabbit eye. Invest Ophthalmol Vis Sci (1993) 1.17

A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase. Biochemistry (2001) 1.17

Truncating alpha-helix E' of p66 human immunodeficiency virus reverse transcriptase modulates RNase H function and impairs DNA strand transfer. J Biol Chem (1995) 1.17

Stoichiometry and DNA unwinding by the bacteriophage T4 41:59 helicase. J Biol Chem (1996) 1.17

Plasmid-related anaerobic autotrophy of the novel archaebacterium Sulfolobus ambivalens. Nature (1985) 1.16

Inactivation of DNA polymerase I (Klenow fragment) by adenosine 2',3'-epoxide 5'-triphosphate: evidence for the formation of a tight-binding inhibitor. Biochemistry (1989) 1.15

Tracking sliding clamp opening and closing during bacteriophage T4 DNA polymerase holoenzyme assembly. Biochemistry (2000) 1.15

Synthesis and application of derivatizable oligonucleotides. Nucleic Acids Res (1987) 1.14

Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase. Biochemistry (1994) 1.14

Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis. Nat Struct Biol (2001) 1.14

Purification, characterization, and kinetic studies of a soluble Bacteroides fragilis metallo-beta-lactamase that provides multiple antibiotic resistance. J Biol Chem (1998) 1.14

Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy. J Mol Biol (1992) 1.13

The function of amino acid residues contacting the nicotinamide ring of NADPH in dihydrofolate reductase from Escherichia coli. Biochemistry (1991) 1.13

Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution. J Mol Biol (1995) 1.13

A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA. Proc Natl Acad Sci U S A (1998) 1.11

Evolution of protein function by domain swapping. Adv Protein Chem (2000) 1.11

A novel combined chemical-enzymatic synthesis of cross-linked DNA using a nucleoside triphosphate analogue. Biochemistry (1991) 1.10

Probing the functional role of phenylalanine-31 of Escherichia coli dihydrofolate reductase by site-directed mutagenesis. Biochemistry (1987) 1.10

Hybrid enzymes: manipulating enzyme design. Trends Biotechnol (1998) 1.09

A rapid screen of active site mutants in glycinamide ribonucleotide transformylase. Biochemistry (1996) 1.09

Molecular basis for nonadditive mutational effects in Escherichia coli dihydrofolate reductase. Biochemistry (1995) 1.08