Site-Specific Cross-Linking of Nucleic Acids Using the Abasic Site

1999 ◽  
Vol 1 (2) ◽  
pp. 311-314 ◽  
Author(s):  
Muthiah Manoharan ◽  
Laura K. Andrade ◽  
P. Dan Cook
Keyword(s):  
Nucleic Acids ◽  
Cross Linking ◽  
Abasic Site ◽  
Site Specific

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

Photochemical Cross-Linking Between Proteins and Nucleic Acids as a Probe of Nucleoprotein Interactions

1980 ◽  
Vol 346 (1 Applications) ◽  
pp. 386-388 ◽  
Author(s):  
Ruth Sperling ◽  
Abraham Havron ◽  
Joseph Sperling
Keyword(s):  
Nucleic Acids ◽  
Cross Linking

Site-Specific Cross-Linking of Human and Bovine Hemoglobins Differentially Alters Oxygen Binding and Redox Side Reactions Producing Rhombic Heme and Heme Degradation†

Biochemistry ◽  
2002 ◽  
Vol 41 (23) ◽  
pp. 7407-7415 ◽  
Author(s):  
Enika Nagababu ◽  
Somasundaram Ramasamy ◽  
Joseph Moses Rifkind ◽  
Yiping Jia ◽  
Abdu I. Alayash
Keyword(s):  
Cross Linking ◽  
Side Reactions ◽  
Oxygen Binding ◽  
Site Specific ◽  
Heme Degradation

scholarly journals Alteration of the substrate specificity of human lysozyme by site-specific intermolecular cross-linking

FEBS Letters ◽  
1994 ◽  
Vol 355 (3) ◽  
pp. 271-274 ◽  
Author(s):  
Michiro Muraki ◽  
Yoshifumi Jigami ◽  
Kazuaki Harata
Keyword(s):  
Substrate Specificity ◽  
Cross Linking ◽  
Human Lysozyme ◽  
Site Specific

scholarly journals Site-specific cross-linking of proteins to DNA via a new bioorthogonal approach employing oxime ligation

2018 ◽  
Vol 54 (49) ◽  
pp. 6296-6299 ◽  
Author(s):  
Suresh S. Pujari ◽  
Yi Zhang ◽  
Shaofei Ji ◽  
Mark D. Distefano ◽  
Natalia Y. Tretyakova
Keyword(s):  
Cross Linking ◽  
Cross Link ◽  
Site Specific ◽  
Link Formation

Model site-specific DNA–protein cross-link formation by bioorthogonal oxime ligation.

Furan warheads for covalent trapping of weak protein-protein interactions: cross-linking of thymosin β4 to actin

2021 ◽  
Author(s):  
Laia Miret Casals ◽  
Willem Vannecke ◽  
Kurt Hoogewijs ◽  
Gianluca Arauz ◽  
Marina Gay ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
3D Structure ◽  
Cross Linking ◽  
Thymosin Β4 ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Protein Protein Interaction ◽  
Covalent Trapping

We describe furan as a triggerable ‘warhead’ for site-specific cross-linking using the actin and thymosin β4 (Tβ4)-complex as model of a weak and dynamic protein-protein interaction with known 3D structure...

scholarly journals High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label

2019 ◽  
Vol 48 (2) ◽  
pp. 924-933 ◽  
Author(s):  
Marcel Heinz ◽  
Nicole Erlenbach ◽  
Lukas S Stelzl ◽  
Grace Thierolf ◽  
Nilesh R Kamble ◽  
...  
Keyword(s):  
High Resolution ◽  
Nucleic Acids ◽  
Spin Label ◽  
Double Resonance ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Spin Labels ◽  
Abasic Site ◽  
Abasic Sites ◽  
Rna And Dna

Abstract Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.

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