Molecular Basis for the DNA Sequence Specificity of the Pluramycins. A Novel Mechanism Involving Groove Interactions Transmitted through the Helix via Intercalation To Achieve Sequence Selectivity at the Covalent Bonding Step

1995 ◽  
Vol 117 (9) ◽  
pp. 2430-2440 ◽  
Author(s):  
Daekyu Sun ◽  
Mark Hansen ◽  
Laurence Hurley
Keyword(s):  
Dna Sequence ◽  
Molecular Basis ◽  
Covalent Bonding ◽  
Sequence Specificity ◽  
Dna Sequence Specificity ◽  
Sequence Selectivity

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

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.

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