Conformational Change Detection of DNA with the Fluorogenic Reagent of o-Phthalaldehyde-β-Mercaptoethanol

Abstract

o-Phthalaldehyde-beta-mercaptoethanol (OPAME) as a fluorogenic reagent has been found wide applications in the detection of amino acids based on its reaction with primary amino groups. In this contribution, we report our new findings concerning the reactions of OPAME with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), respectively. It has been found that ssDNA can react with OPAME easily as a result of giving rise to strong fluorescence emissions, while dsDNA, prepared by hybridizing ssDNA with its complementary target prior to the reaction, displays inert chemical activity and gives out weak fluorescence emission. Mechanism investigations have shown that the reaction activity between OPAME and DNA depends on the amino groups that are related to the conformation of uncoiled and exposed extent of DNA structure, and thus the inert chemical activity of dsDNA results from screening of the dsDNA bases in the interior of the double strands. Therefore, we could design a way to detect conformation change of DNA with OPAME and further develop a novel, simple label-free sequence detection method for complementary and single-base mismatched ssDNA in the hybridization of DNA.

Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation

“…10,49 These bands are caused by the stacking interactions between the bases and the helical suprastructure of the polynucleotide that provides an asymmetric environment for the bases. 50 Gradual addition of ANS to the DNA solution does not reveal any signicant change in the CD spectrum of DNA indicating that the binding of the probe with ctDNA does not disturb the stacking of the bases. This observation emphatically rules out the possibility of intercalation of ANS in the DNA helix, and thereby implies that the uorophore binds to the host DNA through groove binding.…”

DNA binding selectivity of oligopyridine-ruthenium(ii)-lysine conjugate

“…The intensities of the characteristic bands of ct-DNA at 245 nm and 277 nm changed and additionally a new positive CD band at 320 nm appeared. The intensity of the positive band (277 nm), which reflects the stacking interactions between the DNA bases, 44 decreases progressively at low ratios (r = 0.025-0.100), but remains almost unaffected when the ratio increases from r = 0.100 to r = 0.125. These results suggest that the DNA helix is untwisted, disrupting locally the base stacking, due to the binding of complex (2).…”

“…6), where insignificant DT m changes were observed over r = 0.1. Moreover, the intensity of the DNA negative band (245 nm), which is related to the DNA helicity, 44 remains almost unaffected indicating that the ruthenated DNA adopts a B-type conformation. On the other hand, at r = 0.100 and 0.125, where no more complexes bind to DNA, the intensity of negative CD band decreases drastically as a consequence of excess of (2) in the solution, suggesting an unwinding of the helix.…”

Interaction of Two Flavonoids With Calf Thymus Dna: A Multi - Spectroscopic, Electrochemical and Molecular Modelling Approach

“…Groove binding, however, does not put so much impact on the CD signal in this report. [44][45][46][47] …”

“…The values of the binding constants K were obtained from the DNA absorption at 260 nm according to the published methods, 33,34 where the bindings of various ligands to hemoglobin were described. For weak binding affinities the data were treated using linear reciprocal plots based on the following equation.…”