Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV-vis, fluorescence, circular dichroism (CD) spectroscopy, UV-rnelting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation.

Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation

The conformational transition of DNA induced by the interaction between DNA and a cationic lipid vesicle, didodecyidimethylammonium bromide (DDAB), had been investigated by circular dichroism (CD) and UV spectroscopy methods. We used singular value decomposition least squares method (SVDLS) to analyze the experimental CD spectra. Although pH value influenced the conformation of DNA in solution, the results showed that upon binding to double helical DNA, positively charged liposomes induced a conformational transition of DNA molecules from the native B-form to more compact conformations. At the same time, no obvious conformational changes occurred at single-strand DNA (ssDNA). While the cationic lipid vesicles and double-strand DNA (dsDNA) were mixed at a high molar ratio of DDAB vesicles to dsDNA, the conformation of dsDNA transformed from the B-form to the C-form resulting in an increase in duplex stability (DeltaT(m) = 8 +/- 0.4 degreesC). An increasing in T-m was also observed while the cationic lipid vesicles interacted with ssDNA.

Conformational transition of DNA in electroreduction studied by in situ UV and CD thin layer spectroelectrochemistry

Electrochemically induced three conformational transitions of calf thymus DNA from B-10.4 to Z(10.2)-DNA and from B-10.2 to B-10.4 and to C-DNA in 10 mM phosphate buffer solution (pH 7.21) at glassy carbon electrode are found and studied by in situ circular dichroism (CD) thin layer spectroelectrochemistry with singular value decomposition least square (SVDLS) analysis. It indicates that the so-called B-10.2 form and the C-form of DNA may be composed of B-10.4 and left-A DNA and of B-10.4 and right-A DNA, respectively. The irreversible electrochemical reduction of adenine and cytosine groups in the DNA molecule is studied by UV-Vis spectroelectrochemistry. Some electrochemical parameters alphan = 0.17, E-0' = -0.70 V (vs. Ag/AgCl), and the standard heterogeneous electron transfer rate constant, k(0) = 1.8 x 10(-5) cm s(-1) are obtained by double logarithmic analysis and non-linear regression. (C) 2000 Elsevier Science B.V. All rights reserved.

Electric field-induced conformational transition of bovine serum albumin from alpha-helix to beta-sheet

The irreversible conformational transition of bovine serum albumin (BSA) from alpha-helix to beta-sheet, induced by electric field near the electrode surface, was monitored by circular dichroism (CD) with a long optical path thin layer cell (LOPTLC).

The electrochemically induced conformational transition of disulfides in bovine serum albumin studied by thin layer circular dichroism spectroelectrochemistry

The conformational transition of disulfides in bovine serum albumin (BSA) induced by electrochemical redox reaction of disulfides were monitored by in-situ circular dichroism (CD) spectroelectrochemistry, with a long optical path thin layer cell and analyzed by a singular value decomposition least square (SVDLS) method. Electrochemical reduction of disulfides drives the left-handed conformation of disulfides changed into the right-handed. At open circuit, eight of the 17 disulfides were of left-handed conformation. Four of the 17 disulfides took part in the electrochemical reduction with an EC mechanism. Only one-fourth of the reduced disulfides returned to left-handed conformation in the re-oxidation process. Some parameters of the electrochemical reduction process, i.e. the number of electrons transferred and electron transfer coefficient, n=8, alphan=0.15, apparent formal potential, E-1(0') = -0.65(+/-0.01) V, standard heterogeneous electron transfer rate constant, k(1)(0) = (2.84 +/- 0.14)x 10(-5) cm s(-1) and chemical reaction equilibrium constant, K-c=(5.13 +/- 0.12) x 10(-2), were also obtained by double logarithmic analysis based on the near-UV absorption spectra with applied potentials. (C) 2001 Elsevier Science B.V. All rights reserved.

Dynamic spectroelectrochemical measurement for the conformational transition of cytochrome c induced by bromopyrogal red

The conformational transition of horse heart cytochrome c induced by bromopyrogal red (BPR) in very low concentration has been firstly investigated by dynamic spectroelectrochemical technique, both at the BPR adsorbed platinum gauze electrode and at a bare platinum gauze electrode in a solution containing BPR. The effect of BPR on the structure of cytochrome c was studied by UV-visible and Fourier transform IR spectroscopy. The unfolded cytochrome c behaves simply as an electron transfer protein with a formal potential of -142 mV vs. a normal hydrogen electrode. The difference between the formal potentials of the native and unfolded cytochrome c is coupled to a difference in conformational energy of the two states of about 40 kJ mol(-1), which agrees well with the result reported. The stability and slow refolding of the unfolded cytochrome c are discussed.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Conformation studies on sol-gel transition in triblock copolymer solutions

The gelation of physically associating triblock copolymers in a good solvent was investigated by means of the Monte Carlo simulation and a gelation process based on the conformation transition of the copolymer that was described in detail. In our simulative system, it has been found that the gelation is closely related with chain conformations, and there exist four types of chains defined as free, dangling, loop, and bridge conformations. The copolymer chains with different conformations contribute to the formation of gel in different ways. We proposed a conformational transition model, by which we evaluated the role of these four types of chains in sol-gel transition. It was concluded that the free chains keeping the conformation transition equilibrium and the dangling conformation being the hinge of conformation transition, while the chain with loop conformation enlarges the size of the congeries and the chain with bridge conformations binds the congeries consisted of the copolymer chains. In addition, the effects of temperature and concentration on the physical gelation, the association of the copolymer congeries, and the copolymer chain conformations' distribution were discussed.

Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nano-device applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 degrees C by SWNTs but no change for AT-DNA. SWNTs can induce B-A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference.

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

A DNA nanomachine induced by single-walled carbon nanotubes on gold surface

Single-walled carbon nanotubes (SWNTs) can selectively induce human telomeric i-motif DNA formation at pH 7.0. Based on this property, we design a DNA nanomachine induced by SWNTs on gold surface. The motor DNA is human telomeric G-quadruplex DNA. The reversible hybridization between the motor DNA and its complementary human telomeric i-motif DNA can be modulated by SWNTs without changing solution pH. Up to now, to our knowledge, there is no report to show that a DNA nanomachine is induced by SWNTs or a DNA nanomachine can detect i-motif formation at pH 7.0. Our work may provide a new concept for designing an SWNT-induced DNA nanomachine and for the detection of i-motif DNA structure at pH 7.0. DNA hybridization, conformational transition and i-motif formation have been characterized on surface or in solution by fluorescence confocal microscopy, circular dichroism, DNA melting and gel electrophoresis. The folding and unfolding kinetics of the DNA nanomachine on gold surface were studied by Fourier transform-surface plasmon resonance (FT-SPR). All these results indicate that SWNTs can induce the DNA nanomachine to work efficiently and reversibly.

AFM studies of DNA structures on mica in the presence of alkaline earth metal ions

As counterions of DNA on mica, Mg2+, Ca2+, Sr2+ and Ba2+ were used for,clarifying whether DNA molecules equilibrate or are trapped on mica surface. End to end distance and contour lengths were determined from statistical analysis of AFM data. It was revealed that DNA molecules can equilibrate on mica when Mg2+, Ca2+ and Sr2+ are counterions. When Ba2+ is present, significantly crossovered DNA molecules indicate that it is most difficult for DNA to equilibrate on mica and the trapping degree is different under different preparation conditions. In the presence of ethanol, using AFM we have also observed the dependence of B A conformational transition on counterion identities. The four alkaline earth metal ions cause the B-A transition in different degrees, in which Sr2+ induces the greatest structural transition.

Interactions of Safranin T with nucleic acids

The interactions of Safranin T (ST) with several nucleic acids have been investigated by electrochemical, UV-visible and CD spectroscopic techniques. The form of the nucleic acid-ST complexes is sensitive to the ratio of the two species. Two electrochemically inactive complexes such as, nucleic acid-ST and nucleic acid-2ST, were formed while ST interacts with nucleic acids. Two processes were obtained from spectral experiments: (1) at the high value of R (R is defined as the ratio of the total concentration of ST to that of nucleic acid), ST is groove-binding with stacking, (2) st the low value of R, ST is groove-binding without stacking. Intrinsic binding constants were obtained by spectral methods. The experiments also show that electrostatic binding plays an important role in the interaction of ST with nucleic acids.

Phase transition and conformational variation of N-alkylated branched poly(ethyleneimine) comblike polymer

A series of branched poly(ethyleneimine) (PEI) derived polymers with different lengths of n-alkyl side chains, denoted as PEI(n)Cs (n = 12, 14, 16, 18, 20, number of carbon atoms in alkyl side group), have been prepared by a N-alkylation method, and systematically characterized by differential scanning calorimertry (DSC) and wide-angle X-ray diffraction (WARD) as well as Fourier transform infrared spectroscopy (FTIR). The side chains grafted on these comblike polymers are long enough to form crystalline phase composed of paraffin-like crystallites. The crystallization of the side chains forces the branched poly(ethyleneimine) molecules to pack into layered structure, between which the crystallites are located. The melting temperatures of the side chain crystallites increase from -12.36 to +51.49 degreesC with increasing the length of the side chains from n. = 12 to n = 20, which are a little bit lower than the corresponding pristine n-alkanes. PEI18C was taken as an example in this work for the investigation of phase transition and conformational variation of the side chains with temperature changing.