scholarly journals Determining DNA Sequence Specificity of Natural and Artificial Transcription Factors by Cognate Site Identifier Analysis

2009 ◽  
pp. 637-653 ◽  
Author(s):  
Mary S. Ozers ◽  
Christopher L. Warren ◽  
Aseem Z. Ansari
Keyword(s):  
Transcription Factors ◽  
Dna Sequence ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Artificial Transcription Factors

scholarly journals The DNA sequence specificity of stimulation of DNA polymerases by factor D.

1987 ◽  
Vol 262 (18) ◽  
pp. 8868-8874 ◽  
Author(s):  
M Fry ◽  
R Sharf ◽  
P Weisman-Shomer ◽  
P C Evers ◽  
L A Loeb
Keyword(s):  
Dna Sequence ◽  
Dna Polymerases ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Stimulation Of

scholarly journals Multicomponent differentiation-regulated transcription factors in F9 embryonal carcinoma stem cells.

1991 ◽  
Vol 11 (3) ◽  
pp. 1686-1695 ◽  
Author(s):  
M K Shivji ◽  
N B La Thangue
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Dna Binding ◽  
Embryonal Carcinoma ◽  
Regulatory Sequence ◽  
Dependent Manner ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Cell Extracts

Murine F9 embryonal carcinoma (F9 EC) stem cells have an E1a-like transcription activity that is down-regulated as these cells differentiate to parietal endoderm. For the adenovirus E2A promoter, this activity requires at least two sequence-specific transcription factors, one that binds the cyclic AMP-responsive element (CRE) and the other, DRTF1, the DNA-binding activity of which is down-regulated as F9 EC cells differentiate. Here we report the characterization of several binding activities in F9 EC cell extracts, referred to as DRTF 1a, 1b and 1c, that recognize the DRTF1 cis-regulatory sequence (-70 to -50 region). These activities can be chromatographically separated but are not distinguishable by DNA sequence specificity. Activity 1a is a detergent-sensitive complex in which DNA binding is regulated by phosphorylation. In contrast, activities 1b and 1c are unaffected by these treatments but exist as multicomponent protein complexes even before DNA binding. Two sets of DNA-binding polypeptides, p50DR and p30DR, affinity purified from F9 EC cell extracts produce complexes 1b and 1c. Both polypeptides appear to be present in the same DNA-bound protein complex and both directly contact DNA. These affinity-purified polypeptides activate transcription in vitro in a binding-site-dependent manner. These data indicate the in F9 EC stem cells, multicomponent differentiation-regulated transcription factors contribute to the cellular E1a-like activity.

Thermodynamic and Kinetic Basis for the Relaxed DNA Sequence Specificity of “Promiscuous” Mutant EcoRI Endonucleases

2005 ◽  
Vol 348 (2) ◽  
pp. 307-324 ◽  
Author(s):  
Paul J. Sapienza ◽  
Crystal A. dela Torre ◽  
William H. McCoy ◽  
Samyukta V. Jana ◽  
Linda Jen-Jacobson
Keyword(s):  
Dna Sequence ◽  
Sequence Specificity ◽  
Dna Sequence Specificity

Reaction of the antitumor antibiotic CC-1065 with DNA: structure of a DNA adduct with DNA sequence specificity

Science ◽  
1984 ◽  
Vol 226 (4676) ◽  
pp. 843-844 ◽  
Author(s):  
L. Hurley ◽  
V. Reynolds ◽  
D. Swenson ◽  
G. Petzold ◽  
T. Scahill
Keyword(s):  
Dna Sequence ◽  
Dna Structure ◽  
Dna Adduct ◽  
Antitumor Antibiotic ◽  
Sequence Specificity ◽  
Dna Sequence Specificity

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 Evolution of DNA replication origin specification and gene silencing mechanisms

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Y. Hu ◽  
A. Tareen ◽  
Y-J. Sheu ◽  
W. T. Ireland ◽  
C. Speck ◽  
...  
Keyword(s):  
Dna Replication ◽  
Gene Silencing ◽  
Dna Sequence ◽  
Origin Recognition Complex ◽  
Separate Analysis ◽  
Sequence Specificity ◽  
Replication Origins ◽  
Origin Firing ◽  
Dna Sequence Specificity ◽  
Α Helix

Abstract DNA replication in eukaryotic cells initiates from replication origins that bind the Origin Recognition Complex (ORC). Origin establishment requires well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove. Using a massively parallel origin selection assay coupled with a custom mutual-information-based modeling approach, and a separate analysis of whole-genome replication profiling, here we show that the Orc4 α-helix contributes to the DNA sequence-specificity of origins in S. cerevisiae and Orc4 α-helix mutations change genome-wide origin firing patterns. The DNA sequence specificity of replication origins, mediated by the Orc4 α-helix, has co-evolved with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference.

scholarly journals Role for first zinc finger of WT1 in DNA sequence specificity: Denys–Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites

2017 ◽  
Vol 46 (8) ◽  
pp. 3864-3877 ◽  
Author(s):  
Dongxue Wang ◽  
John R Horton ◽  
Yu Zheng ◽  
Robert M Blumenthal ◽  
Xing Zhang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Zinc Finger ◽  
Binding Sites ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Drash Syndrome

Dna Sequence Specificity of Antitumor Agents: Oncogenes as possible targets for cancer therapy

1988 ◽  
Vol 27 (5) ◽  
pp. 503-510 ◽  
Author(s):  
J. A. Hartley ◽  
J. W. Lown ◽  
W. B. Mattes ◽  
K. W. Kohn
Keyword(s):  
Cancer Therapy ◽  
Dna Sequence ◽  
Antitumor Agents ◽  
Sequence Specificity ◽  
Dna Sequence Specificity
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