A pH responsive fluorescent probe based on dye modified i-motif nucleic acids

2018 ◽  
Vol 16 (48) ◽  
pp. 9402-9408 ◽  
Author(s):  
Pan Li ◽  
Zhe Chen ◽  
Yishun Huang ◽  
Jing Li ◽  
Fan Xiao ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Fluorescent Probe ◽  
Conformational Changes ◽  
Ph Responsive ◽  
Ph Variation

DNA-AIEgen hybrids show pH-responsive AIE effects induced by the conformational changes of DNA upon pH variation.

scholarly journals Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution

2020 ◽  
Vol 48 (9) ◽  
pp. e49-e49 ◽  
Author(s):  
Shreya Ghosh ◽  
Matthew J Lawless ◽  
Hanna J Brubaker ◽  
Kevin Singewald ◽  
Michael R Kurpiewski ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Conformational Changes ◽  
Continuous Wave ◽  
Md Simulations ◽  
Distance Measurements ◽  
Paramagnetic Resonance ◽  
Pulsed Epr ◽  
Distance Distributions ◽  
Dna Backbone ◽  
Double Electron Electron Resonance

Abstract Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2′dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules.

scholarly journals Conformational changes at the active site of creatine kinase at low concentrations of guanidinium chloride

1993 ◽  
Vol 291 (1) ◽  
pp. 103-107 ◽  
Author(s):  
H M Zhou ◽  
X H Zhang ◽  
Y Yin ◽  
C L Tsou
Keyword(s):  
Creatine Kinase ◽  
Fluorescent Probe ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Emission Intensity ◽  
Enzyme Inactivation ◽  
Amino Groups ◽  
Guanidinium Chloride ◽  
Low Concentrations

It has been previously reported that, during denaturation of creatine kinase by guanidinium chloride (GdmCl) or urea [Tsou (1986), Trends Biochem. Sci. 11, 427-429], inactivation occurs before noticeable conformational change can be detected, and it is suggested that the conformation at the active site is more easily perturbed and hence more flexible than the molecule as a whole. In this study, the thiol and amino groups at or near the active site of creatine kinase are labelled with o-phthalaldehyde to form a fluorescent probe. Both the emission intensity and anisotropy decrease during denaturation indicating exposure of this probe and increased mobility of the active site. The above conformational changes take place together with enzyme inactivation at lower GdmCl concentrations than required to bring about intrinsic fluorescence changes of the enzyme. At the same GdmCl concentration, the rate of exposure of the probe is comparable with that of inactivation and is several orders of magnitude faster than that for the unfolding of the molecule as a whole.

The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions

2001 ◽  
Vol 260 (2) ◽  
pp. 293-307 ◽  
Author(s):  
Jan Barciszewski ◽  
Janusz Jurczak ◽  
Sylwester Porowski ◽  
Thomas Specht ◽  
Volker A. Erdmann
Keyword(s):  
High Pressure ◽  
Nucleic Acids ◽  
Conformational Changes ◽  
Water Structure

PAMAM Dendrimers Undergo pH Responsive Conformational Changes without Swelling

2009 ◽  
Vol 131 (8) ◽  
pp. 2798-2799 ◽  
Author(s):  
Yi Liu ◽  
Vyacheslav S. Bryantsev ◽  
Mamadou S. Diallo ◽  
William A. Goddard III
Keyword(s):  
Conformational Changes ◽  
Pamam Dendrimers ◽  
Ph Responsive

Unusual pH-Dependent Polarity Changes in PAMAM Dendrimers:  Evidence for pH-Responsive Conformational Changes

2000 ◽  
Vol 33 (25) ◽  
pp. 9169-9172 ◽  
Author(s):  
Wei Chen ◽  
Donald A. Tomalia ◽  
James L. Thomas
Keyword(s):  
Conformational Changes ◽  
Pamam Dendrimers ◽  
Ph Responsive ◽  
Ph Dependent

Determination of Nucleic Acids Using Rivanol as the Fluorescent Probe in the Presence of SDS

2000 ◽  
Vol 33 (15) ◽  
pp. 3183-3194 ◽  
Author(s):  
Wen-You Li ◽  
Jin-Gou Xu ◽  
Xi-Wen He
Keyword(s):  
Nucleic Acids ◽  
Fluorescent Probe

Nucleic acids-protein interactions. Conformational changes induced by the binding of aromatic amines to polyadenylic acid

Biochimie ◽  
1976 ◽  
Vol 58 (4) ◽  
pp. 395-402 ◽  
Author(s):  
Maurice Durand ◽  
Hanna N. Borazan ◽  
Jean-Claude Maurizot ◽  
Jean-Luc Dimicoli ◽  
Claude Hélène
Keyword(s):  
Nucleic Acids ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Aromatic Amines ◽  
Polyadenylic Acid
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