Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

2008 ◽  
Vol 32 (3) ◽  
pp. 149-158 ◽  
Author(s):  
Bryan M.B. VanSchouwen ◽  
Heather L. Gordon ◽  
Stuart M. Rothstein ◽  
Yuto Komeiji ◽  
Kaori Fukuzawa ◽  
...  
1991 ◽  
Vol 11 (4) ◽  
pp. 2162-2168 ◽  
Author(s):  
E Dubois ◽  
F Messenguy

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We show here that they are also required in vitro to observe a protein-DNA complex with the promoter of the ARG5,6 gene. The specific binding of ARGR proteins in vitro is stimulated by arginine. Antibodies raised against a synthetic MCM1 polypeptide retard the migration of ARGR-DNA complex on gel mobility shift assays. This result suggests that MCM1 could be an additional regulatory element of arginine metabolism.


Nanomaterials ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 1000 ◽  
Author(s):  
Yanting Feng ◽  
Lei He ◽  
Ling Wang ◽  
Rijian Mo ◽  
Chunxia Zhou ◽  
...  

An Aflatoxin B1 (AFB1) biosensor was fabricated via an Ag nanoparticles assembly on the surface of a porous anodized aluminum (PAA) membrane. First, the Raman reporter 4-Aminothiophenol (4-ATP) and DNA (partially complementary to AFB1 aptamer) were attached to the surface of Ag nanoparticles (AgNPs) by chemical bonding to form a 4-ATP-AgNPs-DNA complex. Similarly, the surface of a PAA membrane was functionalized with an AFB1 aptamer. Then, the PAA surface was functionalized with 4-ATP-AgNPs-DNA through base complementary pairing to form AgNPs-PAA sensor with a strong Raman signal. When AFB1 was added, AgNPs would be detached from the PAA surface because of the specific binding between AFB1 and the aptamer, resulting in a reduction in Raman signals. The detection limit of the proposed biosensor is 0.009 ng/mL in actual walnut and the linear range is 0.01–10 ng/mL. The sensor has good selectivity and repeatability; it can be applied to the rapid qualitative and quantitative detection of AFB1.


2003 ◽  
Vol 47 (3) ◽  
pp. 854-862 ◽  
Author(s):  
Christian G. Noble ◽  
Faye M. Barnard ◽  
Anthony Maxwell

ABSTRACT We have investigated the interaction of quinolones with DNA by a number of methods to establish whether a particular binding mode correlates with quinolone potency. The specificities of the quinolone-mediated DNA cleavage reaction of DNA gyrase were compared for a number of quinolones. Two patterns that depended on the potency of the quinolone were identified. Binding to plasmid DNA was examined by measuring the unwinding of pBR322 by quinolones; no correlation with quinolone potency was observed. Quinolone binding to short DNA oligonucleotides was measured by surface plasmon resonance. The quinolones bound to both single- and double-stranded oligonucleotides in an Mg2+-dependent manner. Quinolones bound to single-stranded DNA with a higher affinity, and the binding exhibited sequence dependence; binding to double-stranded DNA was sequence independent. The variations in binding in the presence of metal ions showed that Mg2+ promoted tighter, more specific binding to single-stranded DNA than softer metal ions (Mn2+ and Cd2+). Single-stranded DNA binding by quinolones correlated with the in vitro quinolone potency, indicating that this mode of interaction may reflect the interaction of the quinolone with DNA in the context of the gyrase-DNA complex.


Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1420
Author(s):  
Liudmila A. Abrosimova ◽  
Nikita A. Kuznetsov ◽  
Natalia A. Astafurova ◽  
Anastasiia R. Samsonova ◽  
Andrey S. Karpov ◽  
...  

Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is ‘nicked’ rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I–DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I’s binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.


1991 ◽  
Vol 11 (4) ◽  
pp. 2162-2168
Author(s):  
E Dubois ◽  
F Messenguy

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We show here that they are also required in vitro to observe a protein-DNA complex with the promoter of the ARG5,6 gene. The specific binding of ARGR proteins in vitro is stimulated by arginine. Antibodies raised against a synthetic MCM1 polypeptide retard the migration of ARGR-DNA complex on gel mobility shift assays. This result suggests that MCM1 could be an additional regulatory element of arginine metabolism.


2006 ◽  
Vol 357 (1) ◽  
pp. 173-183 ◽  
Author(s):  
Andrew A. Napoli ◽  
Catherine L. Lawson ◽  
Richard H. Ebright ◽  
Helen M. Berman

2001 ◽  
Vol 314 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Shengfeng Chen ◽  
Angelo Gunasekera ◽  
Xiaoping Zhang ◽  
Thomas A Kunkel ◽  
Richard H Ebright ◽  
...  

2001 ◽  
Vol 314 (1) ◽  
pp. 63-74 ◽  
Author(s):  
Shengfeng Chen ◽  
Jaroslav Vojtechovsky ◽  
Gary N Parkinson ◽  
Richard H Ebright ◽  
Helen M Berman

Author(s):  
László G. Kömüves

Light microscopic immunohistochemistry based on the principle of capillary action staining is a widely used method to localize antigens. Capillary action immunostaining, however, has not been tested or applied to detect antigens at the ultrastructural level. The aim of this work was to establish a capillary action staining method for localization of intracellular antigens, using colloidal gold probes.Post-embedding capillary action immunocytochemistry was used to detect maternal IgG in the small intestine of newborn suckling piglets. Pieces of the jejunum of newborn piglets suckled for 12 h were fixed and embedded into LR White resin. Sections on nickel grids were secured on a capillary action glass slide (100 μm wide capillary gap, Bio-Tek Solutions, Santa Barbara CA, distributed by CMS, Houston, TX) by double sided adhesive tape. Immunolabeling was performed by applying reagents over the grids using capillary action and removing reagents by blotting on filter paper. Reagents for capillary action staining were from Biomeda (Foster City, CA). The following steps were performed: 1) wet the surface of the sections with automation buffer twice, 5 min each; 2) block non-specific binding sites with tissue conditioner, 10 min; 3) apply first antibody (affinity-purified rabbit anti-porcine IgG, Sigma Chem. Co., St. Louis, MO), diluted in probe diluent, 1 hour; 4) wash with automation buffer three times, 5 min each; 5) apply gold probe (goat anti-rabbit IgG conjugated to 10 nm colloidal gold, Zymed Laboratories, South San Francisco, CA) diluted in probe diluent, 30 min; 6) wash with automation buffer three times, 5 min each; 7) post-fix with 5% glutaraldehyde in PBS for 10 min; 8) wash with PBS twice, 5 min each; 9) contrast with 1% OSO4 in PBS for 15 min; 10) wash with PBS followed by distilled water for5 min each; 11) stain with 2% uranyl acetate for 10 min; 12) stain with lead citrate for 2 min; 13) wash with distilled water three times, 1 min each. The glass slides were separated, and the grids were air-dried, then removed from the adhesive tape. The following controls were used to ensure the specificity of labeling: i) omission of the first antibody; ii) normal rabbit IgG in lieu of first antibody; iii) rabbit anti-porcine IgG absorbed with porcine IgG.


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