Melting Temperature Of DNA Research Articles

Interaction of humic acids with human DNA: Proposed mechanisms and kinetics

Human DNA quantification by quantitative real-time PCR (QRT-PCR) has gained great importance in forensic DNA and ancient DNA studies. However, in such samples, DNA quantification is impaired by the frequently present humic acid (HA). We have previously shown that the addition of synthetic HA inhibits QRT-PCR. In this study we investigated the possible mechanisms of HA interaction with human DNA, and kinetics of QRT-PCR inhibition. In QRT-PCR with pure human DNA and no HA added, VMAX was 40. With DNA sample containing 4 microg/mL of HA, VMAX was 30.30 while the addition of extra Taq polymerase to the same sample changed VMAX into 38.91, amplifying between 80 and 90% of input DNA. The KM/VMAX ratio in all the samples remained constant, indicating that the mechanism of HA inhibition of QRT-PCR is uncompetitive by nature. Moreover, HA shifts the human DNA melting temperature point (Tm) from 75 to 87 degrees C and inhibits DNase I-mediated DNA cleavage, most probably affecting the enzyme's activity.

In vitro interaction between calf thymus DNA and Escherichia coli LPS in the presence of divalent cation Ca2+

With increasing addition of Escherichia coli LPS to calf thymus DNA, both dissolved in CaCl2, absorption maxima of DNA at 260 nm decreased gradually with the appearance of isosbastic points at both ends of spectra, which implied some binding between DNA and LPS. Hill plot of absorbance data showed that the binding interaction was positive cooperative in nature. For any fixed concentration of DNA and LPS, extent of interaction increased as concentration of CaCl2 was raised from 1.0 to 100 mM, signifying the electrostatic nature of the interaction, mediated through Ca2+ ion. Stepwise addition of EDTA, a chelating agent for divalent cations, to DNA-LPS bound complex gradually reversed the spectral shift with increase in absorbance at 260 nm, which implied opening up of the complex, that is, reversible nature of the interaction. Circular dichroism spectral changes of DNA by the addition of LPS indicated partial transition of DNA from B to A form. Isothermal titration calorimetric (ITC) study showed that the DNA-LPS binding was an exothermic and enthalpy-driven phenomenon. Moreover, in the presence of 100 mM CaCl2, binding constant of the interaction was found to be 2.6 x 10(4) M(-1) and 3.1 x 10(4) M(-1) from the analysis of Hill plot and ITC result, respectively. DNA-melting study showed that the LPS binding had increased the melting temperature of DNA, indicating more stabilization of DNA double helix. The binding of LPS to DNA made the complex resistant to digestion with endonucleases EcoRI and DNase I.

Compensation of DNA Stabilization and Destabilization Effects Caused by Cisplatin is Partially Disturbed in Alkaline Medium

Binding of the antitumor compound cisplatin to DNA locally distorts the double helix. These distortions correlate with a decrease in DNA melting temperature (Tm). However, the influence of cisplatin on DNA stability is more complex because it decreases the DNA charge density. In this way, cisplatin increases the melting temperature and partially compensates for the destabilizing influence of structural distortions. The stabilization is stronger at low Na+ ion concentration. Due to this compensation, the total decrease in the DNA melting temperature after cisplatin binding is much lower than the decrease caused by the distortions themselves, especially at low [Na+]. It is shown in this study that, besides Na+ concentration, pH also strongly influences the value of a change in the melting temperature caused by cisplatin. In alkaline medium (pH=10.5–10.8), a fall in the melting temperature caused by platination is enhanced several times with respect to neutral medium. Such a stronger drop in Tm is explained by a decrease in pK values of base pairs caused by lowering the charge density under platination that facilitates proton release. At neutral pH, the proton release is low for both control and platinated DNA and does not influence the melting behavior. Therefore, lowering in the charge density under platination, besides stabilization, gives additional destabilization just in alkaline medium. Destabilization caused by structural distortions due to this pH induced compensation of stabilizing effect is more pronounced. In the presence of carbonate ion, destabilization caused by high pH value is strengthened. As a decrease in DNA charge density, interstrand crosslinking caused by cisplatin also increases the DNA stability due to loss in the entropy of the melted state. However, computer modeling of DNA stability demonstrates that interstrand crosslinks formed by cisplatin do not stabilize long DNA. It is shown that the increase in Tm caused by interstrand crosslinking itself is compensated for by a local destabilization of the double helix at the sites of location of interstrand crosslinks formed by cisplatin.

The structure-based design, synthesis and biological evaluation of DNA-binding bisintercalating bisanthrapyrazole anticancer compounds

Anticancer drugs that bind to DNA and inhibit DNA-processing enzymes represent an important class of anticancer drugs. In order to find stronger DNA binding and more potent cytotoxic compounds, a series of ester-coupled bisanthrapyrazole derivatives of 7-chloro-2-[2-[(2-hydroxyethyl)methylamino]ethyl]anthra[1,9- cd]pyrazol-6(2H)-one (AP9) were designed and evaluated by molecular docking techniques. Because the anthrapyrazoles are unable to be reductively activated like doxorubicin and other anthracyclines, they should not be cardiotoxic like the anthracyclines. Based on the docking scores of a series of bisanthrapyrazoles with different numbers of methylene linkers ( n) that were docked into an X-ray structure of double-stranded DNA, five bisanthrapyrazoles ( n = 1–5) were selected for synthesis and physical and biological evaluation. The synthesized compounds were evaluated for DNA binding and bisintercalation by measuring the DNA melting temperature increase, for growth inhibitory effects on the human erythroleukemic K562 cell line, and for DNA topoisomerase IIα-mediated cleavage of DNA and inhibition of DNA topoisomerase IIα decatenation activities. The results suggest that the bisanthrapyrazoles with n = 2–5 formed bisintercalation complexes with DNA. In conclusion, a novel group of bisintercalating anthrapyrazole compounds have been designed, synthesized and biologically evaluated as possible anticancer agents.

Synthesis, Biophysical Studies, and Antiproliferative Activity of Platinum(II) Complexes Having 1,2-Bis(aminomethyl)carbobicyclic Ligands

A selected chemical library of six platinum(II) complexes having 1,2-bis(aminomethyl)carbobicyclic ligands were synthesized after a rational design in order to evaluate their antiproliferative activity and the structure-activity relationships. The cytotoxicity studies were performed using cancer cell lines sensitive (A2780) and resistant (A2780R) to cisplatin. Excellent cytotoxicity was observed for most of complexes, which presented better resistance factors than cisplatin against the A2780R cell line. The interaction of these complexes with DNA, as the target biomolecule, was evaluated by several methods: DNA-platinum binding kinetics, changes in the DNA melting temperature, evaluation of the unwinding angle of supercoiled DNA, evaluation of the interstrand cross-links, and replication mapping. The kinetics of the interaction with glutathione was also investigated to better understand the resistant factors observed for the new complexes.

Amplified Fluorescence Turn-on Assay for Mercury(II) Based on Conjugated Polyfluorene Derivatives and Nanospheres

AbstractDetection of mercury with high sensitivity and selectivity constitutes a significant research concern. Here, we report an amplified fluorescence turn-on assay for mercury(II) with an improved performance. This sensing system takes advantage of optically amplifying fluorescent conjugated polyfluorene derivatives and DNA immobilized silica nanospheres (NSs) in addition to the specific thymine- mercury(II)-thymine(T- Hg2+-T) interaction. The employment of ion-specific T- Hg2+-T coordination increases the melting temperature (Tm) of the double-stranded DNA (dsDNA) on the hybridized NS surface. After thermal washing at 45 °C, the Hg2+ treated sample (dsDNA-NS) was effectively differentiated from that treated with nonspecific ions through monitoring fluorescence emission of fluorescein (Fl) labeled target DNA remained on the NS surface. Finally, a cationic conjugated polyfluorene derivative (CCP) was introduced to electrostatically associate with the DNA molecules on the NS surface, resulting in an amplified Fl signal via fluorescence resonance energy transfer (FRET) from the CCP to the dye molecule. In comparison with the use of Fl alone as a signal reporter, the presence of CCP significantly enhances the detection fluorescence intensity, reduces false-positive signal, and improves the detection selectivity for mercury(II). Further improvement in the probe design could yield more efficient metal ion sensors, which have the potential to be operated at room temperature and for the detection of other metal ions besides mercury(II).

最新のキャピラリー電気泳動とチップ電気泳動 カルボン酸を変性剤としたインキャピラリーディネイチャリングゲル電気泳動によるＲＮＡ分離

For RNA size separation in a small sample volume (<10 nL), a strong denaturant to cleave the intramolecular hydrogen bonds that maintain the high-order structures of RNA and optimization for a small sample volume are required. We suggested, “in-capillary denaturing gel electrophoresis” as the RNA separation based on capillary gel electrophoresis, that realizes the denaturation and separation simultaneously in a capillary tube. We found that carboxylic acids were strong denaturants for in-capillary denaturing gel electrophoresis, and the performance of RNA separation was dramatically improved with a running buffer containing acetic acid. Based on the decrease of DNA melting temperature, we estimated that the denaturing ability of 2.0 M acetic acid was stronger than that of either 2.5 M formaldehyde or 7.0 M urea. The baseline separation of RNA with a size of 100−10,000 nt was achieved in only 25 min by in-capillary denaturing gel electrophoresis containing 2.0 M acetic acid. The resolution and number of plates of RNA separation were higher and larger than those obtained in a conventional capillary gel electrophoresis with sample preparation with 7.0 M urea.

Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix

Several representatives of the Crenarchaeal branch of the Archaea contain highly abundant, small, positively charged proteins exemplified by the Sso7d protein from Sulfolobus solfataricus. These proteins bind to DNA in a non-sequence-specific manner. Using publicly available genomic sequence information, we identified a second class of small Crenarchaeal DNA-binding proteins represented by the Pyrobaculum aerophilum open reading frame 3192-encoded (Pae3192) protein and its paralogs. We investigated the biochemical properties of the Pae3192 protein and an orthologous protein (Ape1322b) from Aeropyrum pernix in side-by-side experiments with the Sso7d protein. We demonstrate that the recombinant Ape1322b, Pae3192 and Sso7d proteins bind to DNA and that the DNA-protein complexes formed are slightly different for each protein. We show that like Sso7d, Pae3192 constrains negative supercoils in DNA. In addition, we show that all three proteins raise the melting temperature of duplex DNA upon binding. Finally, we present the equilibrium affinity constants and kinetic association constants of each protein for single-stranded and double-stranded DNA.

A study on the self assembly of Fe(II) and dual binding of Ni(II) porphyrazines on CT-DNA

Interaction of N , N ′, N ″, N ‴-tetramethyltetra-2,3-pyridinoporphyrazinatonickel(II), ([ Ni (2,3- tmtppa )]4+) and N , N ′, N ″, N ‴-tetramethyltetra-2,3-pyridinoporphyrazinatoiron(II), ([ Fe (2,3- tmtppa )]4+) with calf thymus DNA (CT-DNA) have been studied in 1mM phosphate buffer and low ionic strength (5 mM NaCl ) using several spectroscopic techniques: absorbance, fluorescence and circular dichroism. The 2:1 porphyrazine/DNA mole ratio, existence of moderate hypochromicity, moderate and progressive red shift and conservative ICD in the visible part of [ Fe (2,3- tmtppa )]4+ spectra suggested an outside binding with self-stacking mode. Analysis of the dramatic hypochromicity, small blue shift and bisignate ICD in the Q-band absorption region of [ Ni (2,3- tmtppa )]4+ spectra and 1:1 porphyrazine/DNA mole ratio possibly led us to the dual binding mode of this complex, i.e. at the minor and major grooves of DNA. The influence of the ionic strength on the porphyrazine-DNA binding confirmed this suggestion. The fluorescence quenching of DNA-ethidium bromide complex by porphyrazines was investigated. The values of quenching constants ( K sv ) and the rate constants of the quenching ( K q ) were determined by Stern-Volmer equation. The values of K sv have been obtained (2.07 ± 0.11) × 106 and (0.48 ± 0.01) × 106 M−1 for [ Fe (2,3- tmtppa )]4+ and [ Ni (2,3- tmtppa )]4+, respectively, at 27°C. The higher affinity of [ Fe (2,3- tmtppa )]4+ for the quenching of EB-DNA fluorescence with respect to Ni complex was attributed to self-stacking of the former along DNA helix and favorable energy transfer between EB+ and cationic porphyrazine. ΔG25 (the difference between the free energy of the native ( N ) and the denatured (D) form of DNA at 25°C), ΔHm and ΔSm (difference between enthalpy and entropy at Tm) were extracted from thermal curves. The decline in the melting temperature of DNA following the addition of porphyrazine complexes confirms that the substantial mode of Ni and Fe interaction is not intercalation. The thermodynamic results imply that both Ni and Fe complexes have a slight destabilizing effect on the DNA. A comparison between [ Ni ( tmtppa )]4+ and [ Fe ( tmtppa )]4+ indicates that the latter is more effective than the former.

Immobilization of single strand DNA on solid substrate

Abstract This Letter reports the immobilization of DNA onto a solid support by electrostatic interaction with a polycation poly(allylamine hydrochloride) (PAH). The films were analyzed by UV–vis spectroscopy. The significant observation is that single stranded DNA gets immobilized on the PAH backbone of Layer-by-Layer (LbL) films when the films are fabricated above the melting temperature of DNA. Singly stranded DNA immobilized in the LbL films is not restored into double stranded DNA at room temperature.

Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit PCR, show no preferential binding to GC rich sequences and do not influence melting temperature, Tm, even at high concentrations. In addition, SYTO-82 demonstrated a 50-fold lower detection limit in a dilution series assay. In conclusion, the properties of SYTO-82 and SYTO-13 will simplify the development of multiplex assays and increase the sensitivity of real-time PCR.

Theoretical investigation of finite size effects at DNA melting

We investigated how the finiteness of the length of a sequence affects the phase transition that takes place at the DNA melting temperature. For this purpose, we modified the transfer integral method to adapt it to the calculation of both extensive (partition function, entropy, specific heat, etc.) and nonextensive (order parameter and average separation between paired bases) thermodynamic quantities of finite sequences with open boundary conditions, and applied the modified procedure to two different dynamical models. We characterized in some detail the three effects that take place when the length of the sequence is decreased, namely, (i) the decrease of the critical temperature, (ii) the decrease of the peak values of all quantities that diverge at the thermodynamic limit but remain finite for finite sequences, like the specific heat and the correlation length, and (iii) the broadening of the temperature range over which the transition affects the dynamics of the system. We also performed a finite size scaling analysis of the two models and showed that the singular part of the free energy can indeed be expressed in terms of a homogeneous function. However, Josephson's identity is satisfied for none of the investigated models, so that the derivation of the characteristic exponents which appear, for example, in the expression of the specific heat requires some care.

Novel Bioinorganic Nanostructures Based on Mesolamellar Intercalation or Single-Molecule Wrapping of DNA Using Organoclay Building Blocks

Nanosheets or nanoclusters of aminopropyl-functionalized magnesium phyllosilicate (AMP) were prepared in water by exfoliation and used as structural building blocks for the preparation of DNA-based hybrid nanostructures in the form of ordered mesolamellar nanocomposites or highly elongated nanowires, respectively. The former consisted of alternating layers of single sheets of AMP interspaced with intercalated monolayers of intact double-stranded DNA molecules of relatively short length ( approximately 700 base pairs) that were accessible to small molecules such as ethidium bromide. In contrast, the nanowires comprised isolated micrometer-long molecules of lambda-DNA or plasmid DNA that were sheathed in an ultrathin organoclay layer and which were either protected from or remained accessible to endonuclease-mediated clipping depending on the extent of biomolecule wrapping. Both types of hybrid nanostructures showed a marked increase in the DNA melting (denaturation) temperature, indicating significant thermal stabilization of the confined biomolecules. Our results suggest that nanoscale building blocks derived from organically modified inorganic clays could be useful agents for enhancing the chemical, thermal, and mechanical stability of isolated molecules or ensembles of DNA. Such constructs should have increased potential as functional components in bionanotechnology and nonviral gene transfection.

Determination of DNA Melting Temperatures in Diffusion-Generated Chemical Gradients

For fast and reliable determination of DNA melting temperatures with single-nucleotide resolution in a microfluidic setup, stable gradients of the denaturing agent formamide were generated by means of diffusion. Formamide lowers the melting temperature of DNA, and a given formamide concentration can be mapped to a corresponding virtual temperature along the formamide gradient. We applied this concept to determine the melting temperatures of five sets of dye- and quencher-labeled oligonucleotides of different lengths. Differences in the length of complementary sequences of only one nucleotide as well as a single nucleotide mismatch can be detected with this method. Comparison with conventional melting temperature measurements based on temperature scans yields very good agreement.

Photodynamic Properties of Dipeptide-Modified Hypocrellin B Derivatives: The Role of Tyrosine and Tryptophan Groups

Three long-wavelength absorbing dipeptide-modified hypocrellin B (HB) derivatives, Gly-HB, Tyr-HB, and Trp-HB, were prepared for application in photodynamic therapy (PDT). Their abilities to produce free radicals and singlet oxygen were compared in detail with EPR technique, and their binding interactions with calf thymus DNA (CT DNA) were studied by absorption spectra and DNA melting temperature measurements. Tyr-HB and Trp-HB distinguish themselves from Gly-HB and HB remarkably by their significantly improved efficiencies to generate semiquinone anion radicals, superoxide anion radicals, and hydroxyl radicals, as well as their affinity to CT DNA, as the result of the electron-donating properties and intercalating abilities of tyrosine and tryptophan groups. Tyr-HB and Trp-HB show remarkably enhanced photodamage capabilities on CT DNA than their parent HB in aerobic conditions. Moreover, they possess moderate photodamage abilities on CT DNA even in anaerobic conditions, indicating the role of Type I mechanism in their photodynamic behaviors.

The interaction of native DNA with Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine

The interaction of native calf thymus DNA with the Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine (ZnL 2+ and CuL 2+), in 1 mM Tris–HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results support for an intercalative interaction of both ZnL 2+ and CuL 2+ with DNA, showing CuL 2+ an affinity of approximately 10 times higher than ZnL 2+. In particular, the values of the binding constant, determined by UV spectrophotometric titration, equal to 7.3 × 10 4 and 1.3 × 10 6 M −1, for ZnL 2+ and CuL 2+, respectively, indicate the occurrence of a marked interaction with a binding size of about 0.7 in base pairs. The temperature dependence of the absorbance at 258 nm suggests that both complexes strongly increase the DNA melting temperature (Tm) already at metal complex-DNA molar ratios equal to 0.1. As evidenced by the quenching of the fluorescence of ethidium bromide-DNA solutions in the presence of increasing amounts of metal complex, ZnL 2+ and CuL 2+ are able to displace the ethidium cation intercalated into DNA. A tight ZnL 2+–DNA and CuL 2+–DNA binding has been also proven by the appearance, in both metal complex-DNA solutions, of a broad induced CD band in the range 350–450 nm. In the case of the CuL 2+–DNA system, the shape of the CD spectrum, at high CuL 2+ content, is similar to that observed for ψ-DNA solutions. Such result allowed us to hypothesize that CuL 2+ induces the formation of supramolecular aggregates of DNA in aqueous solutions.

DNA Binding and Cytotoxicity of Ruthenium(II) and Rhenium(I) Complexes of 2-Amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine

[Ru(tBu2bpy)2(2-appt)](PF6)2 [1.(PF6)2, tBu2bpy = 4,4'-di-tert-butyl-2,2'-bipyridine, 2-appt = 2-amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine] and [Re(CO)3(2-appt)Cl] (2) were prepared and characterized by X-ray crystal analysis. The binding of 1.(PF6)2 and 2 to calf thymus DNA (ct DNA) led to increases in the DNA melting temperature (Delta Tm = +12 degrees C), modest hypochromism (29% and 5% of the absorption bands at lambda max = 450 and 376 nm, respectively), and insignificant shifts in the absorption maxima. The binding constants of 1.(PF6)2 and 2 with ct DNA, as determined by absorption titration, are (8.9 +/- 0.5) x 104 and (3.6 +/- 0.1) x 104 dm3 mol-1, respectively. UV-vis absorption titration, DNA melting studies, and competition dialysis using synthetic oligonucleotides [poly(dA-dT)2 and poly(dG-dC)2] revealed that 1.(PF6)2 and 2 exhibit a binding preference for AT sequences. A modeling study on the interaction between 1 or 2 and B-DNA revealed that the minor groove is the most favored binding site and an extensive hydrogen-bonding network is formed. As determined by MTT assays, 1.(PF6)2 and 2 exhibited moderate cytotoxicities toward several human cancer cell lines (KB-3-1, HepG2, and HeLa), as well as a multi-drug-resistant cancer cell line (KB-V-1). According to confocal microscopic and flow cytometric studies, 1.(PF6)2 and 2 induced apoptosis (50-60%) in cancer cells with <5% necrosis detected.

Mechanistic Differences in DNA Nanoparticle Formation in the Presence of Oligolysines and Poly-l-lysine

We studied the effectiveness of trilysine (Lys3), tetralysine (Lys4), pentalysine (Lys5), and poly-l-lysine (PLL) (MW 50000) on lambda-DNA nanoparticle formation and characterized the size, shape, and stability of nanoparticles. Light scattering experiments showed EC50 (lysine concentration at 50% DNA compaction) values of approximately 0.0036, 2, and 20 micromol/L, respectively, for PLL, Lys5, and Lys4 at 10 mM [Na+]. Plots of log EC50 versus log [Na+] showed positive slopes of 1.09 and 1.7, respectively, for Lys4 and Lys5 and a negative slope of -0.1 for PLL. Hydrodynamic radii of oligolysine condensed particles increased (48-173 nm) with increasing [Na+], whereas no significant change occurred to nanoparticles formed with PLL. There was an increase in the size of nanoparticles formed with Lys5 at >40 degrees C, whereas no such change occurred with PLL. The DNA melting temperature increased with oligolysine concentration. These results indicate distinct differences in the mechanism(s) by which oligolysines and PLL provoke DNA condensation to nanoparticles.

Single Molecule Force Spectroscopy of Salt-dependent Bacteriophage T7 Gene 2.5 Protein Binding to Single-stranded DNA

The gene 2.5 protein (gp2.5) encoded by bacteriophage T7 binds preferentially to single-stranded DNA. This property is essential for its role in DNA replication and recombination in the phage-infected cell. gp2.5 lowers the phage lambda DNA melting force as measured by single molecule force spectroscopy. T7 gp2.5-Delta26C, lacking 26 acidic C-terminal residues, also reduces the melting force but at considerably lower concentrations. The equilibrium binding constants of these proteins to single-stranded DNA (ssDNA) as a function of salt concentration have been determined, and we found for example that gp2.5 binds with an affinity of (3.5 +/- 0.6) x 10(5) m(-1) in a 50 mm Na(+) solution, whereas the truncated protein binds to ssDNA with a much higher affinity of (7.8 +/- 0.9) x 10(7) m(-1) under the same solution conditions. T7 gp2.5-Delta26C binding to single-stranded DNA also exhibits a stronger salt dependence than the full-length protein. The data are consistent with a model in which a dimeric gp2.5 must dissociate prior to binding to ssDNA, a dissociation that consists of a weak non-electrostatic and a strong electrostatic component.

Unprecedented dual binding behaviour of acridine group of dye: A combined experimental and theoretical investigation for the development of anticancer chemotherapeutic agents

Acridine group of dyes are well known in the field of development of probes for nucleic acid structure and conformational determination because of their relevance in the development of novel chemotherapeutic agents, footprinting agents and for gene manipulation in biotechnology and medicine. Here, we report the interaction of 9- N,N-dimethylaniline decahydroacridinedione (DMAADD), a new class of dye molecule with calf thymus DNA (CT-DNA) which has been studied extensively by means of traditional experimental and theoretical techniques. The changes in the base stacking of CT-DNA upon the binding of DMAADD are reflected in the circular dichroic (CD) spectral studies. Competitive binding study shows that the enhanced emission intensity of ethidium bromide (EB) in presence of DNA was quenched by the addition of DMAADD indicating that it displaces EB from its binding site in DNA and the apparent binding constant has been estimated to be (3.3 ± 0.2) × 10 5 M − 1 . This competitive binding study and further fluorescence experiments reveal that DMAADD is a moderate binder of CT-DNA, while viscosity measurements show that the mode of binding is partial intercalation. Generally, one would expect increase in the melting temperature ( T m) of DNA in presence of intercalators. Interestingly, an unusual decrease in melting temperature (Δ T m of − 4 ± 0.2 °C) of DNA by the addition of DMAADD was observed. From our knowledge such a decreasing trend in melting point was not reported before for all the possible modes of binding. Molecular modeling gave the pictorial view of the binding model which clearly shows that of the various mode of binding, the dye prefers the major groove binding to the sites rich in GC residues and to the sites rich in AT residues it prefers intercalation mode of binding either through major or minor groove with the inclusion of the N,N-dimethylaniline (DMA) group inside the double helix which has been stacked in between the bases, under physiological relevant pH of 7.5.