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1 Gesteland, Raymond F.; Krapcho, Karen J.; Talbot, Phil; Thulin, CraigCrystallization of the MS2 translational repressor alone and complexed to bromouridineThe coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also by binding RNA as a translational repressor. In order to study the isolated dimer in a conformation not influenced by capsid interactions, a mutant molecule was crystallized that is defective in capsid ...Crystallization; RNA Bacteriophage; RNA Hairpin; Translational Repressor1995
2 Gesteland, Raymond F.; Atkins, John F.; Tuohy, Therese M.Uninterrupted translation through putative 12-nucleotide coding gap in sequence of carA: business as usualPrevious work of others reported an untranslated stretch of 12 nucleotides in the 5' coding sequence of carA from Pseudomonas aeruginosa. However, N-terminal protein sequencing of carA-lacZ translational fusions shows that these 12 nucleotides are normally translated in a continuous triplet manner, ...Base Sequence; Protein Biosynthesis; Sequence Deletion1994
3 Gesteland, Raymond F.; Atkins, John F.; Weiss, Robert B.Slippery runs, shifty stops, backward steps and forward hops: -2, -1, +1, +2, +5 and +6 Ribosomal frameshiftingFrameshift mutations frequently express residual levels of gene activity; that is, they are often leaky. This leakiness can be used as a tool to define the functional components that affect the reading frame during gene expression. Recent technological advances in the capability to efficiently bu...Molecular Sequence Data; Mutation; RNA, Transfer; Frameshifting1987
4 Gesteland, Raymond F.; Atkins, John F.Evolutionary specialization of recoding: frameshifting in the expression of S. cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still +1An autoregulatory translational shift to the +1 frame is required for the expression of ornithine decarboxylase antizyme from fungi to mammals. In most eukaryotes, including all vertebrates and a majority of the studied fungi/yeast, the site on antizyme mRNA where the shift occurs is UCC-UGA. The me...Antizyme; ODC; Polyamines; Frameshifting2006
5 Hansen, Mark S.; Coffin, Cheryl M.; Capecchi, Mario R.Pax3:Fkhr interferes with embryonic Pax3 and Pax7 function: implications for alveolar rhabdomyosarcoma cell of origin.To investigate the role of the translocation-associated gene Pax3:Fkhr in alveolar rhabdomyosarcomas, we generated a Cre-mediated conditional knock-in of Pax3:Fkhr into the mouse Pax3 locus. Exploring embryonic tumor cell origins, we replaced a Pax3 allele with Pax3:Fkhr throughout its expression do...Neuroprogenitor; Embryogenesis2004-11-01
6 Capecchi, Mario R.Hox genes and mammalian developmentWe have examined the interactions of Hox genes in forming a cervical vertebrae, hindbrain, and limbs. In each case, it is apparent that individual Hox genes are performing individual functions but that more profound roles are apparent when they act in combination with others Hox genes. The observed ...Drosophila; Gene Expression Regulation, Developmental; Homozygote1997
7 Gesteland, Raymond F.; Atkins, John F.; Howard, Michael T.Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotidesEvidence is presented that morpholino, 2_x0001_-O-methyl, phosphorothioate, and RNA antisense oligonucleotides can direct sitespecific âˆ'1 translational frameshifting when annealed to mRNA downstream from sequences where the P- and A-site tRNAs are both capable of re-pairing with âˆ'1 frame c...Recoding; Frameshifting; Antisense; Morpholino; Phosphorothioate; 2_x0001_-O-methyl2004
8 Gesteland, Raymond F.; Atkins, John F.; Ingram, Jennifer A.; Kelly, Paul J.; Grentzmann, GuidoDual-luciferase reporter system for studying recoding signalsA new reporter system has been developed for measuring translation coupling efficiency of recoding mechanisms such as frameshifting or readthrough. A recoding test sequence is cloned in between the renilla and firefly luciferase reporter genes and the two luciferase activities are subsequently measu...Amino Acid Sequence; Genes, Reporter; HIV; Antizyme; Translation1998
9 Capecchi, Mario R.; Bernstein, Kenneth E.; Thomas, Kirk R.Targeting genes for self-excision in the germ lineA procedure is described that directs the self-induced deletion of DNA sequences as they pass through the male germ line of mice. The testes-specific promoter from the angiotensin-converting enzyme gene was used to drive expression of the Cre-recombinase gene. Cre was linked to the selectable marker...Cre-recombinase; Hoxa3; Chimeric mice1999-06-15
10 Gesteland, Raymond F.; Atkins, John F.Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expressionTranslating ribosomes can shift reading frame at specific sites with high efficiency for gene expression purposes. The most common type of shift to the 1 frame involves a tandem realignment of two anticodons from pairing with mRNA sequence of the form X XXY YYZ to XXX YYY Z where the spaces indicate...1 frameshifting; 39 context effect; Codon anticodon interaction; Escherichia coli ; Recoding; tRNALys; XXXY YYZ frameshift motifs2002
11 Capecchi, Mario R.Isolation and characterization of Caenorhabditis elegans DNA sequences homologous to the v-abl oncogene.DNA sequences homologous to the v-abl oncogene were isolated from a Caenorhabditis elegans genomic library by their ability to hybridize with a v-src probe. The DNA sequence of 2465 nucleotides of one clone was determined. This region corresponds to the 5' protein kinase domain of v-abl plus approxi...Amino Acid Sequence; Animals; Base Sequence; Gene Expression Regulation; Transcription, Genetic1986-04
12 Capecchi, Mario R.Homologous recombination between coinjected DNA sequences peaks in early to mid-S phase.We have examined the effect of cell cycle position on homologous recombination between plasmid molecules coinjected into synchronized rat fibroblasts. Recombination activity was found to be low in G1 and to rise 10- to 15-fold, peaking in early to mid-S phase.Cell Line; Kinetics; Plasmids1986-06
13 Gesteland, Raymond F.; Alam, Steve L.; Nelson, Chad; Felden, Brice; Atkins, John F.Effects of 3'-terminal phosphates in RNA produced by ribozyme cleavageDuring the course of a structural investigation of a selenocysteine insertion element from rat Type 1 iodothyronine 59-deiodinase (D1 SECIS), we wished to prepare milligram quantities of an RNA that comprised the upper stem/loop of this RNA structure (41 nt; Fig+ 1A)+ This stem/loop is a stimul...In vitro runoff transcription; RNA; Trans-acting ribozymes1998
14 Capecchi, Mario R.Targeted disruption of the even-skipped gene, evx1, causes early postimplantation lethality of the mouse conceptus.Implantation within the mammalian uterus elicits dramatic changes in the growth, differentiation, and morphogenesis of the conceptus. This process is interrupted in mice carrying a targeted disruption of the murine evx1 gene, a homolog of the Drosophila even-skipped (eve) gene. Upon implantation, pr...Extraembryonic; Homozygotes; Drosophila1994-08-15
15 Gussin, Gary N.; Capecchi, Mario R.Protein synthesis directed by DNA phage messengers.Even through the amino acids corresponding to most of the 64 nucleotide triplets are now known, several important aspects of the genetic code are not yet fully understood. In particular we need more knowledge about the "punctuation marks" of the code-for example, the signals necessary for the initia...Carbon Isotopes; Escherichia coli; Genetic Code; Methionine1967-09-01
16 Gesteland, Raymond F.; Atkins, John F.; Baranov, Pavel V.P-site tRNA is a crucial initiator of ribosomal frameshiftingThe expression of some genes requires a high proportion of ribosomes to shift at a specific site into one of the two alternative frames. This utilized frameshifting provides a unique tool for studying reading frame control. Peptidyl-tRNA slippage has been invoked to explain many cases of programmed ...Translation; Recoding; Kinetic Model; Frameshifting; Ribosome2004
17 Hansen, Mark S.; Healy, Lindsey J.; Johnson, Christopher R.; Capecchi, Mario R.; Keller, Charles; Jones, Greg M.Virtual histology of transgenic mouse embryos for high-throughput phenotyping.A bold new effort to disrupt every gene in the mouse genome necessitates systematic, interdisciplinary approaches to analyzing patterning defects in the mouse embryo. We present a novel, rapid, and inexpensive method for obtaining high-resolution virtual histology for phenotypic assessment of mouse ...Forkhead Transcription Factors; Paired Box Transcription Factors2006
18 Thomas, Kirk R.; Capecchi, Mario R.Nonreciprocal exchanges of information between DNA duplexes coinjected into mammalian. cell nucleiWe have examined the mechanism of homologous recombination between plasmid molecules coinjected into cultured mammalian cells. Cell lines containing recombinant DNA molecules were obtained by selecting for the reconstruction of a functional Neor gene from two plasmids that bear different amber mutat...Animals; Cells, Cultured; DNA Restriction Enzymes; Kinetics1985-01
19 Gesteland, Raymond F.; Baranov, Pavel V.; Atkins, John F.Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coliABSTRACT: The rare codons AGG and AGA comprise 2% and 4%, respectively, of the arginine codons of Escherichia coli K-12, and their cognate tRNAs are sparse. At tandem occurrences of either rare codon, the paucity of cognate aminoacyl tRNAs for the second codon of the pair facilitates peptidyl-tRNA...Gene expression; Frameshifting; E. coli; Arginine codons2005
20 Gesteland, Raymond F.; Atkins, John F.; Wills, Norma M.rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshiftBase pairing between the 3' end of 16S rRNA and mRNA is shown to be important for the programmed -1 frameshifting utilized in decoding the Escherichia coli dnaX gene. This pairing is the same as the Shine-Dalgarno pairing used by prokaryotic ribosomes in selection of translation initiators, but for ...Frameshifting; Escherichia coli; Binding Sites; Base Composition1994
21 Capecchi, Mario R.Illegitimate cre-dependent chromosome rearrangements in transgenic mouse spermatids.The bacteriophage P1 Cre/loxP system has become a powerful tool for in vivo manipulation of the genomes of transgenic mice. Although in vitro studies have shown that Cre can catalyze recombination between cryptic "pseudo-loxP" sites in mammalian genomes, to date there have been no reports of loxP-si...Chromatin; Female; Mice, Inbred C57BL; Phenotype2000-12-05
22 Gesteland, Raymond F.; Ivanov, Ivaylo P.; Atkins, John F.Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast but "2 in budding yeastThe coding sequence for mammalian ornithine decarboxylase antizyme is in two different partially overlapping reading frames with no independent ribosome entry to the second ORF. Immediately before the stop codon of the first ORF, a proportion of ribosomes undergo a quadruplet translocation event t...Antizyme; Frameshifting; Ornithine decarboxylase antizyme; Recoding; S. pombe1998
23 Capecchi, Mario R.Housekeeping gene xanthine oxidoreductase is necessary for milk fat droplet enveloping and secretion: gene sharing in the lactating mammary gland.Xanthine oxidoreductase (XOR) is the rate-limiting enzyme in purine catabolism occurring in most cell types. However, this housekeeping gene is expressed at very high levels in a number of mammalian tissues including the lactating mammary epithelium, suggesting additional roles for XOR in these tiss...Body Weight; Cell Differentiation; Cell Membrane; Epithelium2002-12-15
24 Capecchi, Mario R.Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function together to control development of the mammary gland in response to pregnancy.Although the role of Hox genes in patterning the mammalian body plan has been studied extensively during embryonic and fetal development, relatively little is known concerning Hox gene function in adult animals. Analysis of mice with mutant Hoxa9, Hoxb9, and Hoxd9 genes shows that these paralogous g...Embryonic and Fetal Development; Gene Expression Regulation, Developmental; Genotype; Mice, Knockout1999-01
25 Capecchi, Mario R.Selective degradation of abnormal proteins in mammalian tissue culture cells.The degradation rates of several missense mutants of hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) in mouse L cells are compared to those of the wild-type enzyme. Although the rates of total protein breakdown in the mutant cell lines are identical to that of the parental L cell line, ...Gene Expression Regulation; Mice, Transgenic; Microscopy, Fluorescence1974-12-01
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