scholarly journals A 72-Base Pair AT-rich DNA Sequence Element Functions as a Bacterial Gene Silencer

2000 ◽  
Vol 276 (12) ◽  
pp. 9478-9485 ◽  
Author(s):  
Chien-Chung Chen ◽  
Ming Fang ◽  
Arundhati Majumder ◽  
Hai-Young Wu
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Sequence Element ◽  
Bacterial Gene

DNA sequence analysis of spontaneous mutations in the SUP4-o gene of Saccharomyces cerevisiae

1988 ◽  
Vol 8 (2) ◽  
pp. 978-981
Author(s):  
C N Giroux ◽  
J R Mis ◽  
M K Pierce ◽  
S E Kohalmi ◽  
B A Kunz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Transposable Elements ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Base Pair ◽  
Dna Sequence Analysis ◽  
Spontaneous Mutations ◽  
Yeast Saccharomyces Cerevisiae ◽  
Spontaneous Mutagenesis

A collection of 196 spontaneous mutations in the SUP4-o gene of the yeast Saccharomyces cerevisiae was analyzed by DNA sequencing. The classes of mutation identified included all possible types of base-pair substitution, deletions of various lengths, complex alterations involving multiple changes, and insertions of transposable elements. Our findings demonstrate that at least several different mechanisms are responsible for spontaneous mutagenesis in S. cerevisiae.

Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae

1984 ◽  
Vol 4 (4) ◽  
pp. 591-598
Author(s):  
J Cappello ◽  
C Zuker ◽  
H F Lodish
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Base Pair ◽  
Shock Treatment ◽  
Yeast Cells ◽  
Genomic Segment ◽  
Heat Shock Treatment ◽  
Shock Response

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.

scholarly journals A plant DNA-binding protein that recognizes 5-methylcytosine residues.

1989 ◽  
Vol 9 (3) ◽  
pp. 1351-1356 ◽  
Author(s):  
D L Zhang ◽  
K C Ehrlich ◽  
P C Supakar ◽  
M Ehrlich
Keyword(s):  
Dna Binding ◽  
Dna Sequence ◽  
Base Pair ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Plant Dna ◽  
Related Family ◽  
Nuclear Extracts

A novel, 5-methylcytosine-specific, DNA-binding protein, DBP-m, has been identified in nuclear extracts of peas. DBP-m specifically recognizes 5-methylcytosine residues in DNA without appreciable DNA sequence specificity, unlike a mammalian DNA-binding protein (MDBP), which recognizes 5-methylcytosine residues but only in a related family of 14-base-pair sequences.

scholarly journals Supercoiling DNA locates mismatches

2017 ◽  
Author(s):  
Andrew Dittmore ◽  
Sumitabha Brahmachari ◽  
Yasuhara Takagi ◽  
John F. Marko ◽  
Keir C. Neuman
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Dna Supercoiling ◽  
Magnetic Tweezers ◽  
Relative Probability ◽  
Base Pairs ◽  
Damage Sensing ◽  
Mismatched Base Pair ◽  
Monovalent Salt

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

scholarly journals Repetitive Dictyostelium heat-shock promotor functions in Saccharomyces cerevisiae.

1984 ◽  
Vol 4 (4) ◽  
pp. 591-598 ◽  
Author(s):  
J Cappello ◽  
C Zuker ◽  
H F Lodish
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Base Pair ◽  
Shock Treatment ◽  
Yeast Cells ◽  
Genomic Segment ◽  
Heat Shock Treatment ◽  
Shock Response

The Dictyostelium genome contains 40 copies of a 4.7-kilobase repetitive and apparently transposable DNA sequence (DIRS-1) and about 250 smaller elements that appear to be deletions or rearrangements of DIRS-1. Transcripts of these sequences are induced during differentiation and also by heat shock treatment of growing cells. We showed that one such cloned element, pB41.6 (2.5 kilobases) contains a nucleotide sequence identical to the Drosophila consensus heat shock promotor. To test whether this sequence might indeed control the expression of DIRS-1-related RNAs, we have cloned this genomic segment into yeast cells. In yeast cells, 41.6 directs synthesis of a 1.7-kilobase RNA that is induced at least 10-fold by heat shock. Transcription initiates at about 124 bases 3' of the putative promotor sequence and terminates within the 41.6 insert. A 381-base-pair subclone that contains the putative promotor sequence is sufficient to induce the heat shock response of 41.6 in yeast cells.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

1990 ◽  
Vol 10 (8) ◽  
pp. 4080-4088
Author(s):  
F Vauti ◽  
P Morandini ◽  
J Blusch ◽  
A Sachse ◽  
W Nellen
Keyword(s):  
Gene Expression ◽  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Base Pair ◽  
Regulation Of Gene Expression ◽  
Promoter Elements ◽  
Down Regulation ◽  
Heterologous Promoter ◽  
Sequence Element ◽  
Pair Sequence

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

scholarly journals Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP.

1990 ◽  
Vol 10 (8) ◽  
pp. 4080-4088 ◽  
Author(s):  
F Vauti ◽  
P Morandini ◽  
J Blusch ◽  
A Sachse ◽  
W Nellen
Keyword(s):  
Gene Expression ◽  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Base Pair ◽  
Regulation Of Gene Expression ◽  
Promoter Elements ◽  
Down Regulation ◽  
Heterologous Promoter ◽  
Sequence Element ◽  
Pair Sequence

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

Recognition and initiation site for four late promoters of phage T7 is a 22-base pair DNA sequence

Nature ◽  
1979 ◽  
Vol 280 (5717) ◽  
pp. 35-39 ◽  
Author(s):  
Nikos Panayotatos ◽  
Robert D. Wells
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Initiation Site ◽  
Phage T7

scholarly journals Site-specific DNA inversion is enhanced by a DNA sequence element in cis

1985 ◽  
Vol 82 (11) ◽  
pp. 3776-3780 ◽  
Author(s):  
H. E. Huber ◽  
S. Iida ◽  
W. Arber ◽  
T. A. Bickle
Keyword(s):  
Dna Sequence ◽  
Sequence Element ◽  
Site Specific ◽  
Dna Inversion ◽  
In Cis
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