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Literature DB >> 3671091

Computer modelling of DNA structures involved in chromosome maintenance.

Abstract

Sequence-dependent DNA bending of synthetic and natural molecules was studied by computer analysis. Modelling of synthetic oligonucleotides and of 107 kb of natural sequences gave results which closely resembled published electrophoretic data, demonstrating the powerful predictive capacity of the procedure. The analysis was extended to the study of DNA structures involved in chromosome maintenance. Centromeric DNAs from yeast were found to have sequences in their functional elements which cause them to be unusually straight. Autonomous replicating sequences were found to have two structural domains, one consisting of unusually straight sequences surrounding the consensus and the other of bending elements in flanking DNA. In addition to a structural homology, centromeric and autonomous replicating sequences share common sequence elements. These observations show that computer modelling of natural sequences is a viable approach to the study of the biological implications of alternative DNA structures.

Entities: Chemical Species

Mesh：

Substances：
DNA

Year: 1987 PMID： 3671091 PMCID： PMC306376 DOI： 10.1093/nar/15.20.8531

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

45 in total

1. Drosophila ARSs contain the yeast ARS consensus sequence and a replication enhancer.

Authors: J S Mills; A J Kingsman; S M Kingsman
Journal: Nucleic Acids Res Date: 1986-08-26 Impact factor: 16.971

2. Analysis of DNA sequences homologous with the ARS core consensus in Saccharomyces cerevisiae.

Authors: A H Bouton; V B Stirling; M M Smith
Journal: Yeast Date: 1987-06 Impact factor: 3.239

3. Sequence-induced DNA curvature at the bacteriophage lambda origin of replication.

Authors: K Zahn; F R Blattner
Journal: Nature Date: 1985 Oct 3-9 Impact factor: 49.962

4. A common structural feature in promoter sequences of E. coli.

Authors: C S Tung; S C Harvey
Journal: Nucleic Acids Res Date: 1987-06-25 Impact factor: 16.971

5. Detection, sequence patterns and function of unusual DNA structures.

Authors: J N Anderson
Journal: Nucleic Acids Res Date: 1986-11-11 Impact factor: 16.971

6. A quantitative measure of DNA curvature enabling the comparison of predicted structures.

Authors: C S Tung; C Burks
Journal: J Biomol Struct Dyn Date: 1987-02

7. Bent DNA at a yeast autonomously replicating sequence.

Authors: M Snyder; A R Buchman; R W Davis
Journal: Nature Date: 1986 Nov 6-12 Impact factor: 49.962

8. Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae.

Authors: G B Kiss; A A Amin; R E Pearlman
Journal: Mol Cell Biol Date: 1981-06 Impact factor: 4.272

9. Isolation of a yeast centromere and construction of functional small circular chromosomes.

Authors: L Clarke; J Carbon
Journal: Nature Date: 1980-10-09 Impact factor: 49.962

10. Identification and characterization of the centromere from chromosome XIV in Saccharomyces cerevisiae.

Authors: M Neitz; J Carbon
Journal: Mol Cell Biol Date: 1985-11 Impact factor: 4.272

24 in total

1. RIP60, a mammalian origin-binding protein, enhances DNA bending near the dihydrofolate reductase origin of replication.

Authors: M S Caddle; L Dailey; N H Heintz
Journal: Mol Cell Biol Date: 1990-12 Impact factor: 4.272

2. DNA structures associated with autonomously replicating sequences from plants.

Authors: T T Eckdahl; J L Bennetzen; J N Anderson
Journal: Plant Mol Biol Date: 1989-05 Impact factor: 4.076

3. Reversion of autonomously replicating sequence mutations in Saccharomyces cerevisiae: creation of a eucaryotic replication origin within procaryotic vector DNA.

Authors: D Kipling; S E Kearsey
Journal: Mol Cell Biol Date: 1990-01 Impact factor: 4.272

Computer modelling of DNA structures involved in chromosome maintenance.

1. Drosophila ARSs contain the yeast ARS consensus sequence and a replication enhancer.

2. Analysis of DNA sequences homologous with the ARS core consensus in Saccharomyces cerevisiae.

3. Sequence-induced DNA curvature at the bacteriophage lambda origin of replication.

4. A common structural feature in promoter sequences of E. coli.

5. Detection, sequence patterns and function of unusual DNA structures.

6. A quantitative measure of DNA curvature enabling the comparison of predicted structures.

7. Bent DNA at a yeast autonomously replicating sequence.

8. Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae.

9. Isolation of a yeast centromere and construction of functional small circular chromosomes.

10. Identification and characterization of the centromere from chromosome XIV in Saccharomyces cerevisiae.

1. RIP60, a mammalian origin-binding protein, enhances DNA bending near the dihydrofolate reductase origin of replication.

2. DNA structures associated with autonomously replicating sequences from plants.

3. Reversion of autonomously replicating sequence mutations in Saccharomyces cerevisiae: creation of a eucaryotic replication origin within procaryotic vector DNA.

4. Bent DNA is a conserved structure in an adenovirus control region.

Review 5. Yeast chromosome replication and segregation.

6. Conserved DNA structures in origins of replication.

7. DNA topology of the ordered chromatin domain 5' to the human c-myc gene.

8. Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to the Adh1 gene.

9. Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain.

10. Species-specific patterns of DNA bending and sequence.