Predicting crossover generation in DNA shuffling.

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.

authors

Moore GL,Maranas CD,Lutz S,Benkovic SJ

doi

10.1073/pnas.051631498

keywords:

subject

Has Abstract

pub_date

2001-03-13 00:00:00

pages

3226-31

issue

6

eissn

0027-8424

issn

1091-6490

pii

98/6/3226

journal_volume

98

pub_type

杂志文章
  • Adenovirus-mediated interleukin-12 gene therapy for metastatic colon carcinoma.

    abstract::Recombinant adenoviral mediated delivery of suicide and cytokine genes has been investigated as a treatment for hepatic metastases of colon carcinoma in mice. Liver tumors were established by intrahepatic implantation of a poorly immunogenic colon carcinoma cell line (MCA-26), which is syngeneic in BALB/c mice. Intrat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.21.11302

    authors: Caruso M,Pham-Nguyen K,Kwong YL,Xu B,Kosai KI,Finegold M,Woo SL,Chen SH

    更新日期:1996-10-15 00:00:00

  • Expression of alfalfa mosaic virus coat protein in tobacco mosaic virus (TMV) deficient in the production of its native coat protein supports long-distance movement of a chimeric TMV.

    abstract::Alfalfa mosaic virus (AlMV) coat protein is involved in systemic infection of host plants, and a specific mutation in this gene prevents the virus from moving into the upper uninoculated leaves. The coat protein also is required for different viral functions during early and late infection. To study the role of the co...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.5.2549

    authors: Spitsin S,Steplewski K,Fleysh N,Belanger H,Mikheeva T,Shivprasad S,Dawson W,Koprowski H,Yusibov V

    更新日期:1999-03-02 00:00:00

  • Temporal comparisons in bacterial chemotaxis.

    abstract::Responses of tethered cells of Escherichia coli to impulse, step, exponential-ramp or exponentiated sine-wave stimuli are internally consistent, provided that allowance is made for the nonlinear effect of thresholds. This result confirms that wild-type cells exposed to stimuli in the physiological range make short-ter...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.23.8987

    authors: Segall JE,Block SM,Berg HC

    更新日期:1986-12-01 00:00:00

  • Structure of the human interleukin 2 gene.

    abstract::We have cloned two species of EcoRI-cleaved DNA segments that together cover the entire sequence for the human interleukin 2 gene and have determined the nucleotide sequence of the gene and its flanking regions. The gene contains three introns and the exon sequences can be aligned with the previously reported cDNA seq...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.24.7437

    authors: Fujita T,Takaoka C,Matsui H,Taniguchi T

    更新日期:1983-12-01 00:00:00

  • Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal.

    abstract::The structure of activated pig heart aconitase [citrate(isocitrate) hydro-lyase, EC 4.2.1.3] containing a [4Fe-4S] cluster has been refined at 2.5-A resolution to a crystallographic residual of 18.2%. Comparison of this structure to the recently determined 2.1-A resolution structure of the inactive enzyme containing a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.10.3639

    authors: Robbins AH,Stout CD

    更新日期:1989-05-01 00:00:00

  • Sequences of the joining region genes for immunoglobulin heavy chains and their role in generation of antibody diversity.

    abstract::To assess the contribution to immunoglobulin heavy chain diversity made by recombination between variable region (VH) genes and joining region (JH) genes, we have determined the sequence of about 2000 nucleotides spanning the rearranged JH gene cluster associated with the VH gene expressed in plasmacytoma HPC76. The a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.1.509

    authors: Gough NM,Bernard O

    更新日期:1981-01-01 00:00:00

  • Vibrio parahaemolyticus orchestrates a multifaceted host cell infection by induction of autophagy, cell rounding, and then cell lysis.

    abstract::The bacterial pathogen Vibrio parahaemolyticus utilizes a type III secretion system to cause death of host cells within hours of infection. We report that cell death is completely independent of apoptosis and occurs by a mechanism in which injection of multiple type III effectors causes induction of autophagy, cell ro...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0802773105

    authors: Burdette DL,Yarbrough ML,Orvedahl A,Gilpin CJ,Orth K

    更新日期:2008-08-26 00:00:00

  • Identification, purification, and molecular cloning of autonomously replicating sequence-binding protein 1 from fission yeast Schizosaccharomyces pombe.

    abstract::Autonomously replicating sequence (ARS) elements of the fission yeast Schizosaccharomyces pombe contain multiple imperfect copies of the consensus sequence reported by Maundrell et al. [Maundrell K., Hutchison, A. & Shall, S. (1988) EMBO J. 7, 2203-2209]. When cell free extracts of S. pombe were incubated with a dimer...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.1.502

    authors: Murakami Y,Huberman JA,Hurwitz J

    更新日期:1996-01-09 00:00:00

  • Absence of equilibrium cluster phase in concentrated lysozyme solutions.

    abstract::In colloidal systems, the interplay between the short range attraction and long-range repulsion can lead to a low density associated state consisting of clusters of individual particles. Recently, such an equilibrium cluster phase was also reported for concentrated solutions of lysozyme at low ionic strength and close...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0711928105

    authors: Shukla A,Mylonas E,Di Cola E,Finet S,Timmins P,Narayanan T,Svergun DI

    更新日期:2008-04-01 00:00:00

  • A simple generative model of collective online behavior.

    abstract::Human activities increasingly take place in online environments, providing novel opportunities for relating individual behaviors to population-level outcomes. In this paper, we introduce a simple generative model for the collective behavior of millions of social networking site users who are deciding between different...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1313895111

    authors: Gleeson JP,Cellai D,Onnela JP,Porter MA,Reed-Tsochas F

    更新日期:2014-07-22 00:00:00

  • Accelerated wound healing in mice by on-site production and delivery of CXCL12 by transformed lactic acid bacteria.

    abstract::Impaired wound closure is a growing medical problem associated with metabolic diseases and aging. Immune cells play important roles in wound healing by following instructions from the microenvironment. Here, we developed a technology to bioengineer the wound microenvironment and enhance healing abilities of the immune...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1716580115

    authors: Vågesjö E,Öhnstedt E,Mortier A,Lofton H,Huss F,Proost P,Roos S,Phillipson M

    更新日期:2018-02-20 00:00:00

  • Agent-based Bayesian approach to monitoring the progress of invasive species eradication programs.

    abstract::Eradication of an invasive species can provide significant environmental, economic, and social benefits, but eradication programs often fail. Constant and careful monitoring improves the chance of success, but an invasion may seem to be in decline even when it is expanding in abundance or spatial extent. Determining w...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1216146110

    authors: Keith JM,Spring D

    更新日期:2013-08-13 00:00:00

  • A two-step mechanism underlies the planar polarization of regenerating sensory hair cells.

    abstract::The restoration of planar cell polarity is an essential but poorly understood step toward physiological recovery during sensory-organ regeneration. Investigating this issue in the lateral line of the zebrafish, we found that hair cells regenerate in pairs along a single axis established by the restricted localization ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0608536103

    authors: López-Schier H,Hudspeth AJ

    更新日期:2006-12-05 00:00:00

  • Functional analysis of protein N-myristoylation: metabolic labeling studies using three oxygen-substituted analogs of myristic acid and cultured mammalian cells provide evidence for protein-sequence-specific incorporation and analog-specific redistributio

    abstract::Covalent attachment of myristic acid (C14:0) to the NH2-terminal glycine residue of a number of cellular, viral, and oncogene-encoded proteins is essential for full expression of their biological function. Substitution of oxygen for methylene groups in this fatty acid does not produce a significant change in chain len...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.21.8511

    authors: Johnson DR,Cox AD,Solski PA,Devadas B,Adams SP,Leimgruber RM,Heuckeroth RO,Buss JE,Gordon JI

    更新日期:1990-11-01 00:00:00

  • Crystal structure of fructose-1,6-bisphosphatase complexed with fructose 6-phosphate, AMP, and magnesium.

    abstract::The crystal structure of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with fructose 6-phosphate, AMP, and Mg2+ has been solved by the molecular replacement method and refined at 2.5-A resolution to a R factor of 0.215, with root-mean-square deviations of 0.013 A and 3.5 degrees for bond lengths and bond angles,...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.14.5243

    authors: Ke HM,Zhang YP,Lipscomb WN

    更新日期:1990-07-01 00:00:00

  • Calcium influx mediated by the Escherichia coli heat-stable enterotoxin B (STB).

    abstract::The heat-stable enterotoxin B (STB) of Escherichia coli is a 48-amino acid extracellular peptide that induces rapid fluid accumulation in animal intestinal models. Unlike other E. coli enterotoxins that elicit cAMP or cGMP responses in the gut [heat-labile toxin (LT) and heat-stable toxin A (STA), respectively], STB i...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.8.3202

    authors: Dreyfus LA,Harville B,Howard DE,Shaban R,Beatty DM,Morris SJ

    更新日期:1993-04-15 00:00:00

  • Isolation of the tumor-inducing RNA from oncogenic and nononcogenic Agrobacterium tumefaciens.

    abstract::Two RNA fractions have been isolated and purified from both oncogenic and nononcogenic strains of Agrobacterium tumefaciens. Both RNAs are capable of inducing the formation of transplantable tumors when introduced at wound sites in stems of Datura stramonium plants. One of these RNA fractions was found to be bound to ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.71.5.1585

    authors: Beljanski M,Aaron-da Cunha MI,Beljanski MS,Manigault P,Bourgarel P

    更新日期:1974-05-01 00:00:00

  • Coenzyme Q10 prevents peripheral neuropathy and attenuates neuron loss in the db-/db- mouse, a type 2 diabetes model.

    abstract::Diabetic peripheral neuropathy (DPN) is the most common complication in both type 1 and type 2 diabetes. Here we studied some phenotypic features of a well-established animal model of type 2 diabetes, the leptin receptor-deficient db(-)/db(-) mouse, and also the effect of long-term (6 mo) treatment with coenzyme Q10 (...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1220794110

    authors: Shi TJ,Zhang MD,Zeberg H,Nilsson J,Grünler J,Liu SX,Xiang Q,Persson J,Fried KJ,Catrina SB,Watanabe M,Arhem P,Brismar K,Hökfelt TG

    更新日期:2013-01-08 00:00:00

  • Molecular recognition of pathogen attack occurs inside of plant cells in plant disease resistance specified by the Arabidopsis genes RPS2 and RPM1.

    abstract::The Arabidopsis thaliana disease resistance genes RPS2 and RPM1 belong to a class of plant disease resistance genes that encode proteins that contain an N-terminal tripartite nucleotide binding site (NBS) and a C-terminal tandem array of leucine-rich repeats. RPS2 and RPM1 confer resistance to strains of the bacterial...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.26.15497

    authors: Leister RT,Ausubel FM,Katagiri F

    更新日期:1996-12-24 00:00:00

  • Is there a single pathway for the folding of a polypeptide chain?

    abstract::We argue that folding of the compact domains of proteins can occur with adequate rapidity in the absence of a unique directed mechanism, provided that native-like local structure dominates the folding process. We further suggest that the evolution of amino acid sequences should favor multiple paths to the folded state...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.12.4028

    authors: Harrison SC,Durbin R

    更新日期:1985-06-01 00:00:00

  • Male tolerance and male-male bonds in a multilevel primate society.

    abstract::Male relationships in most species of mammals generally are characterized by intense intrasexual competition, with little bonding among unrelated individuals. In contrast, human societies are characterized by high levels of cooperation and strong bonds among both related and unrelated males. The emergence of cooperati...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1405811111

    authors: Patzelt A,Kopp GH,Ndao I,Kalbitzer U,Zinner D,Fischer J

    更新日期:2014-10-14 00:00:00

  • Transformations, transport, and potential unintended consequences of high sulfur inputs to Napa Valley vineyards.

    abstract::Unintended anthropogenic deposition of sulfur (S) to forest ecosystems has a range of negative consequences, identified through decades of research. There has been far less study of purposeful S use in agricultural systems around the world, including the application of elemental sulfur (S(0)) as a quick-reacting fungi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1110741108

    authors: Hinckley EL,Matson PA

    更新日期:2011-08-23 00:00:00

  • Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers.

    abstract::The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the pr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1415908112

    authors: Das N,Dai J,Hung I,Rajagopalan MR,Zhou HX,Cross TA

    更新日期:2015-01-13 00:00:00

  • Composition and distribution of low density lipoprotein fractions in hyperapobetalipoproteinemia, normolipidemia, and familial hypercholesterolemia.

    abstract::Hyperapobetalipoproteinemia is defined as the combination of a normal low density lipoprotein (LDL) cholesterol in the face of an increased LDL apolipoprotein B (apoB) protein. To examine the physical basis for the apparent disproportion between LDL cholesterol and apoB characteristic of this syndrome, we used density...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.21.6662

    authors: Teng B,Thompson GR,Sniderman AD,Forte TM,Krauss RM,Kwiterovich PO Jr

    更新日期:1983-11-01 00:00:00

  • The Epstein-Barr virus oncogene product, latent membrane protein 1, induces the downregulation of E-cadherin gene expression via activation of DNA methyltransferases.

    abstract::The latent membrane protein (LMP1) of Epstein-Barr virus (EBV) is expressed in EBV-associated nasopharyngeal carcinoma, which is notoriously metastatic. Although it is established that LMP1 represses E-cadherin expression and enhances the invasive ability of carcinoma cells, the mechanism underlying this repression re...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.152059399

    authors: Tsai CN,Tsai CL,Tse KP,Chang HY,Chang YS

    更新日期:2002-07-23 00:00:00

  • Sterigmatocystin-DNA interactions: identification of a major adduct formed after metabolic activation in vitro.

    abstract::Sterigmatocystin (ST), a potent hepatocarcinogen, was covalently bound to calf thymus DNA by incubation in the presence of phenobarbital-induced rat liver microsomes. Acid hydrolysis of ST-modified DNA liberated a major guanine-containing adduct, present in DNA at an estimated level of 1 ST residue per 100-150 nucleot...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.1.179

    authors: Essigmann JM,Barker LJ,Fowler KW,Francisco MA,Reinhold VN,Wogan GN

    更新日期:1979-01-01 00:00:00

  • Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress.

    abstract::The mechanisms for plant growth restriction during stress conditions remains unclear. Here, we demonstrate that a phytochrome-interacting factor-like protein, OsPIL1/OsPIL13, acts as a key regulator of reduced internode elongation in rice under drought conditions. The level of OsPIL1 mRNA in rice seedlings grown under...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1207324109

    authors: Todaka D,Nakashima K,Maruyama K,Kidokoro S,Osakabe Y,Ito Y,Matsukura S,Fujita Y,Yoshiwara K,Ohme-Takagi M,Kojima M,Sakakibara H,Shinozaki K,Yamaguchi-Shinozaki K

    更新日期:2012-09-25 00:00:00

  • Carcinogenic bacterial pathogen Helicobacter pylori triggers DNA double-strand breaks and a DNA damage response in its host cells.

    abstract::The bacterial pathogen Helicobacter pylori chronically infects the human gastric mucosa and is the leading risk factor for the development of gastric cancer. The molecular mechanisms of H. pylori-associated gastric carcinogenesis remain ill defined. In this study, we examined the possibility that H. pylori directly co...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1100959108

    authors: Toller IM,Neelsen KJ,Steger M,Hartung ML,Hottiger MO,Stucki M,Kalali B,Gerhard M,Sartori AA,Lopes M,Müller A

    更新日期:2011-09-06 00:00:00

  • Bioengineered corporal tissue for structural and functional restoration of the penis.

    abstract::Various reconstructive procedures have been attempted to restore a cosmetically acceptable phallus that would allow normal reproductive, sexual, and urinary function in patients requiring penile reconstruction. However, these procedures are limited by a shortage of native penile tissue. We previously demonstrated that...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0909367106

    authors: Chen KL,Eberli D,Yoo JJ,Atala A

    更新日期:2010-02-23 00:00:00

  • Role of loop-helix interactions in stabilizing four-helix bundle proteins.

    abstract::One of the critical issues regarding proteins with a four-helix bundle motif is which interactions play the major role in stabilizing this type of folded structure: the interaction among the four alpha-helices or the interaction between the loop and helix segments. To answer this question, an energetic analysis has be...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.16.7315

    authors: Chou KC,Maggiora GM,Scheraga HA

    更新日期:1992-08-15 00:00:00