Related Experiment Video
Updated: Jan 30, 2026

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide
Published on: June 23, 2016
Aminoalkoxyfluorenones and aminoalkoxybiphenyls: DNA binding modes
Svitlana O Zanoza1, Kyrylo O Klimenko2, George V Maltzev1
1A. V. Bogatsky Physico-Chemical Institute of the National Academy of Science of Ukraine, 86 Lyustdorfskaya doroga, Odessa 65080, Ukraine.
Abstract:
Many evidences suggest that DNA-drug interaction in the minor groove and the intercalation of drugs into DNA may play critical roles in antiviral, antimicrobial, and antitumor activities. As a continuous effort to develop novel antiviral agents, the series of planar fluorenone (3a-7d) were synthesized and used along with nonplanar biphenyls (11a-d) for the comparative analysis of their interaction with DNA. The chemical structure of new compounds was confirmed by 1H NMR, 13C NMR and mass spectra as well as elemental analysis. DNA affinity of 3a-7d and 11a-d was evaluated by ethidium bromide displacement assay. Affinity constant (lgKa) of 3a-7d was found to be approximately two orders of magnitude higher than constants of corresponding 11a-d. The molecular docking of aminoalkoxybiphenyls (11a-d) into minor grove of five different nucleotide sequences (d(CCIICICCII), d(CGCGTTAACGCG), d(CGCGATATCGCG), d(GGCCAATTGG), d(GGATATATCC)) demonstrated their binding capacity to the specific DNA site. The linear least squares fitting technique was successfully applied to derive an equation describing the relationship between lgKa and SF.
Related Concept Videos
Single-Strand DNA Binding Proteins
What is a Mode?
There can be more than one mode in a data set if multiple values have the same highest frequency. For instance, suppose that the Statistics exam scores of 20 students are: 50; 53; 59; 59; 63; 63; 72; 72; 72; 72; 72; 76; 78; 81; 83; 84; 84; 84; 90; 93. Here, the mode is 72, as it occurs most frequently, five times.
A data set with two modes is called bimodal. For example,...
The Equilibrium Binding Constant and Binding Strength
Ventilatory Modes
There are three ventilatory modes: full support, partial support, and spontaneous. These are described below.
Full Support Modes
Full support modes include controlled mechanical ventilation, continuous mandatory...
Ligand Binding and Linkage
Cooperative Binding of Transcription Regulators

