[ { "id": "authors:623tf-yyz94", "collection": "authors", "collection_id": "623tf-yyz94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160308-070622092", "type": "book_section", "title": "DNA-DNA hybridization of single-copy DNA sequences", "book_title": "Molecular Evolution: Producing the Biochemical Data", "author": [ { "family_name": "Springer", "given_name": "Mark S.", "clpid": "Springer-M-S" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Zimmer", "given_name": "Elizabeth A.", "clpid": "Zimmer-E-A" } ], "abstract": "This chapter is reviews the basic principles of hybridization and the kinetics of reassociation. It provides an overview that summarizes and compares different techniques used in single-copy hybridization. The chapter then examines different estimates of distance derived from melting curves. Native DNA is isolated and purified to remove RNA and protein. Long-stranded DNA is then sheared to short fragments to permit the separation of repetitive and single-copy DNA and to reduce viscosity and gel formation. The chapter also explains the kinetics of reassociation. Rates of reassociation of DNA are influenced by several factors including genome complexity, DNA concentration, fragment size, reassociation temperature, and cation concentration. The complexity of the sheared genome is the length in base pairs (bp) of the longest nonrepeating sequence that is produced by splicing together fragments in the population. The rate of reassociation is inversely proportional to the complexity of the genome. The hybridization of tracer DNA with driver DNA is also overviewed in the chapter.", "doi": "10.1016/0076-6879(93)24018-P", "isbn": "9780121821258", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1993", "pages": "232-243" }, { "id": "authors:6k9x3-2q039", "collection": "authors", "collection_id": "6k9x3-2q039", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-185657663", "type": "book_section", "title": "In vivo competition identifies positive cis-regulatory elements required for lineage-specific gene expression in the sea urchin embryo", "book_title": "Cellular Basis of Morphogenesis", "author": [ { "family_name": "Franks", "given_name": "Roberta R.", "clpid": "Franks-R-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" } ], "contributor": [ { "family_name": "Evered", "given_name": "David", "clpid": "Evered-D" }, { "family_name": "Marsh", "given_name": "Joan", "clpid": "Marsh-J" } ], "abstract": "Several cis-regulatory elements within the 5' regulatory region of the lineage-specific CyIIIa actin gene have been identified by in vivo competition. Sea urchin eggs were coinjected with a fusion construct in which the bacterial chloramphenicol acetyltransferase (CAT) gene is controlled by the CyIIIa regulatory domain, together with molar excesses of various DNA subfragments that are derived from this region. Each subfragment studied includes one or several known sites where highly specific interactions occur in vitro with nuclear DNA-binding proteins. Coinjection of excess molecules of some of these subregions results in a decrease in the activity of the CyIIIa-CAT fusion gene, as a function of the molar subfragment: CyIIIa-CAT ratio. This result implies that these sites complete with cis sequences linked to the CAT reporter gene for limited factors that positively regulate CyIIIa transcription in the embryo, and demonstrates the functional importance of a number of the DNA-protein interactions that have been observed in vitro.", "doi": "10.1002/9780470513798.ch9", "isbn": "9780471923060", "publisher": "Wiley", "place_of_publication": "Chichester, UK", "publication_date": "1989", "pages": "156-66; discussion 166" }, { "id": "authors:07kjj-gr121", "collection": "authors", "collection_id": "07kjj-gr121", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151217-181955149", "type": "book_section", "title": "Poly(A) RNA of the Egg Cytoplasm: Structural Resemblance to the Nuclear RNA of Somatic Cells", "book_title": "Molecular Biology of Egg Maturation", "author": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Jacobs", "given_name": "Howard T.", "clpid": "Jacobs-H-T" }, { "family_name": "Thomas", "given_name": "Terry L.", "clpid": "Thomas-T-L" }, { "family_name": "Hough-Evans", "given_name": "Barbara R.", "clpid": "Hough-Evans-B-R" }, { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Porter", "given_name": "Ruth", "clpid": "Porter-R" }, { "family_name": "Whelan", "given_name": "Julie", "clpid": "Whelan-J" } ], "abstract": "This paper concerns the structural characteristics of the poly(A) RNA stored in unfertilized amphibian and echinoderm eggs. Though located in the egg cytoplasm, at least two-thirds of these maternal transcripts display an interspersed sequence organization similar to that of nuclear RNA. In Xenopus laevis interspersed poly(A) RNA molecules are synthesized and deposited in the oocyte cytoplasm throughout the main growth phase of oogenesis. Regions of the sea urchin genome that are represented by interspersed maternal transcripts have been recovered from recombinant clone libraries. In one case the same single-copy sequence is found both in an abundant message-sized 1.6 kilobase (kb) maternal transcript and in a 7.5 kb maternal transcript that structurally resembles a precursor form and is not found in embryonic polysomes. In a second example considered, a 9.5 kb transcript was identified in embryo nuclear RNA that may be identical in structure with an interspersed maternal poly(A) RNA derived from the same transcription unit. Transcription of this sequence appears to be constitutive in somatic cell nuclei, though no homologous cytoplasmic RNAs are found after early cleavage. This may be a widespread form of regulation for transcription units expressed in female germ cells, and represented in the maternal poly(A) RNA pools of unfertilized eggs.", "doi": "10.1002/9780470720790.ch2", "isbn": "9780272797303", "publisher": "Wiley", "place_of_publication": "New York, NY", "publication_date": "1983", "pages": "6-24" }, { "id": "authors:edjyb-x6m18", "collection": "authors", "collection_id": "edjyb-x6m18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201001-145812635", "type": "book_section", "title": "Genomic Alterations in Evolution", "book_title": "Evolution and Development", "author": [ { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" } ], "contributor": [ { "family_name": "Bonner", "given_name": "J. T.", "clpid": "Bonner-J-T" } ], "abstract": "To understand the evolution of species it appears that we will need to know the principal sources and kinds of genomic variation and the mechanisms or systems through which genomic variation affects genes, their expression and the phenotype. In addition we will need to know the nature of the populations that give rise to new species and the way in which the selective forces act through the behavior and death of individuals. What we cannot guess at this time is how much more we will also need to learn about the genome and as yet unexpected processes.", "doi": "10.1007/978-3-642-45532-2_3", "isbn": "9783642455346", "publisher": "Springer Berlin Heidelberg", "place_of_publication": "Berlin, Heidelberg", "publication_date": "1982", "pages": "41-64" }, { "id": "authors:zwqxd-45y68", "collection": "authors", "collection_id": "zwqxd-45y68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201005-143650069", "type": "book_section", "title": "Genomic Change and Morphological Evolution Group Report", "book_title": "Evolution and Development", "author": [ { "family_name": "Dawid", "given_name": "I.", "clpid": "Dawid-I" }, { "family_name": "Britten", "given_name": "R. J.", "clpid": "Britten-R-J" }, { "family_name": "Davidson", "given_name": "E. H.", "clpid": "Davidson-E-H" }, { "family_name": "Dover", "given_name": "G. A.", "clpid": "Dover-G-A" }, { "family_name": "Gallwitz", "given_name": "D. F.", "clpid": "Gallwitz-D-F" }, { "family_name": "Garcia-Bellido", "given_name": "A.", "clpid": "Garcia-Bellido-A" }, { "family_name": "Kafatos", "given_name": "F. C.", "clpid": "Kafatos-F-C" }, { "family_name": "Kauffman", "given_name": "S. A.", "clpid": "Kauffman-S-A" }, { "family_name": "Moritz", "given_name": "K.", "clpid": "Moritz-K" }, { "family_name": "Ohno", "given_name": "S.", "clpid": "Ohno-S" }, { "family_name": "Schmidtke", "given_name": "J.", "clpid": "Schmidtke-J" }, { "family_name": "Sch\u00fctz", "given_name": "G.", "clpid": "Sch\u00fctz-G" } ], "contributor": [ { "family_name": "Bonner", "given_name": "J. T.", "clpid": "Bonner-J-T" } ], "abstract": "In our discussions, questions of gene and chromosome organization and possible functional correlates of this organization were treated, as were sequence and organizational changes observed in evolution. We further considered existing knowledge and interpretations regarding the actions of genes in development, how genes are utilized, why so many are needed, and how their arrangement may affect activity. We discussed gene famlies, repeated sequences, and in particular, transposable DNA elements and the consequences of their existence for genomic flexibility. Specifically genetic approaches to the study of gene function were addressed, leading to the discussion of gene hierarchies and the apparent existence of control genes. Finally, we considered the problems posed by the activity of many genes and the probable existence of very large numbers of interactions between them.", "doi": "10.1007/978-3-642-45532-2_2", "isbn": "9783642455346", "publisher": "Springer Berlin Heidelberg", "place_of_publication": "Berlin", "publication_date": "1982", "pages": "18-39" }, { "id": "authors:m2xsr-4ey80", "collection": "authors", "collection_id": "m2xsr-4ey80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160414-121636778", "type": "book_section", "title": "Analysis of repeating DNA sequences by reassociation", "book_title": "Nucleic Acids and Protein Synthesis Part E", "author": [ { "family_name": "Britten", "given_name": "Roy J.", "clpid": "Britten-R-J" }, { "family_name": "Graham", "given_name": "Dale E.", "clpid": "Graham-D-E" }, { "family_name": "Neufeld", "given_name": "Berney R.", "clpid": "Neufeld-B-R" } ], "contributor": [ { "family_name": "Grossman", "given_name": "Lawrence", "clpid": "Grossman-L" }, { "family_name": "Moldave", "given_name": "Kivie", "clpid": "Moldave-K" } ], "abstract": "Repetitive DNA occurs widely, if not universally, among higher organisms. A variety of procedures has been developed or adapted to examine its characteristics and a body of concepts and language has grown up to deal with its complexities. This chapter attempts to summarize this body of knowledge and technique. Owing to human frailty and the real problems of the subject, it tends to emphasize the approaches and conceptual position. The chapter describes techniques for the analysis of repeating DNA sequences by reassociation and a method for the evaluation of rate constants. The purity of the DNA's used in reassociation is critical, as the presence of contaminating proteins and metal ions can markedly alter reassociation results and reproducibility. Metal ions can be removed from DNA by passing it over Chelex 100 (Bio-Rad Labs) that has been neutralized and equilibrated with buffer.", "doi": "10.1016/0076-6879(74)29033-5", "isbn": "9780121818920", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1974", "pages": "363-418" } ]