DNA Minor Groove Research Articles

Antioxidant, antibacterial, and antimutagenic activity of Piper nigrum seeds extracts.

Piper nigrum is a widely used plant in traditional remedies and known for its numerous biological properties. However, fraction-based antioxidant activity and their antimutagenic potential are not yet fully investigated. Different extracts of the seeds P. nigrum were obtained by sequential extraction in different solvents. All extracts were evaluated for antibacterial and antioxidant activities using different methods. The most active fraction was analyzed for antimutagenic activity using the Ames Salmonella test. The antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) was found to be more prominent compared to ESβL producing Klebsiella pneumoniae isolates. The MIC values were found to be lower against MRSA than K. pneumoniae. The extract showing highest antioxidant activity (methanol extract) was further tested for antimutagenic activity both against direct and indirect-acting mutagens. A varying level of antimutagenic activity was shown by methanol extract at highest tested concentration (200 µg/plate). Alkaloids, phenols, and flavonoids were detected as major class of compounds in methanol extract. Gas chromatography-mass spectrometry (GC–MS) analysis showed the presence of various phytocompounds. Based on molecular docking of two major active phytocompounds (piperine and copaene), they were found to interact at the minor groove of DNA. Molecular dynamics (MD) simulation revealed that both the ligands were quite stable with DNA under physiological conditions. The ability of phytocompounds to interact with DNA might be reducing the interaction of mutagens and could be one of the possible mechanism of anti-mutagenic activity of P. nigrum extract. This study highlights the antioxidant and antimutagenic potential of Piper nigrum. The role of phytocompounds present in the bioactive extract is needed to be explored further for herbal drug research.

Anticancer Activity of Indeno[1,2-b]-Pyridinol Derivative as a New DNA Minor Groove Binding Catalytic Inhibitor of Topoisomerase IIα

Topoisomerase IIα has been a representative anti-cancer target for decades thanks to its functional necessity in highly proliferative cancer cells. As type of topoisomerase IIα targeting drugs, topoisomerase II poisons are frequently in clinical usage. However, topoisomerase II poisons result in crucial consequences resulted from mechanistically induced DNA toxicity. For this reason, it is needed to develop catalytic inhibitors of topoisomerase IIα through the alternative mechanism of enzymatic regulation. As a catalytic inhibitor of topoisomerase IIα, AK-I-191 was previously reported for its enzyme inhibitory activity. In this study, we clarified the mechanism of AK-I-191 and conducted various types of spectroscopic and biological evaluations for deeper understanding of its mechanism of action. Conclusively, AK-I-191 represented potent topoisomerase IIα inhibitory activity through binding to minor groove of DNA double helix and showed synergistic effects with tamoxifen in antiproliferative activity.

Synthesis, characterization and DNA interaction of a novel Pt(II) macroacyclic Schiff base complex containing the piperazine moiety and its cytotoxicity and molecular docking

A new platinum Schiff base complex, [C17H28N4OPt]Cl2 (1) was prepared from the condensation of a polyamine containing piperazine moiety, (1,4-bis(3-aminopropyl)piperazine) and 2-hydroxy-benzaldehyde (H2L), in the presence of Pt2+ ion and examined by mass, FT-IR, elemental analysis 1H NMR and 13C NMR. The structure of the metal complex has been confirmed by a single-crystal X-ray structural analysis in which the Pt atom is in a square planar coordination environment. The crystal was found to be composed of two complexes that co-crystallized, the formulation being 0.973[C17H28N4OPt]Cl2, 0.014[[C17H27N4OPt]2PtCl2]Cl2. The ligand and Schiff base complex interactions with calf thymus DNA (ct-DNA) were studied using UV–Vis and fluorescence spectroscopy and molecular docking simulations. UV–Vis absorption investigations indicated hyprechromism and hypochromism effects, respectively, for the ligand and the complex. The binding constant of the Pt(II) complex with DNA (6.1 × 104 M−1) was greater than the corresponding binding value of the ligand (4 × 103 M−1). Competitive florescence results showed that molecular replacement of Hoechst in the minor groove of DNA by the ligand and Pt(II) complex resulted in the fluorescence of the DNA-Hoechst system being extinguished. Fluorescence emission spectra, using methylene blue (MB) as an intercalate probe, demonstrated only the replacement of MB by the Pt(II) complex from the MB-DNA system. Thermodynamic studies confirmed that van der Waals forces and hydrogen bonds play critical roles in the compounds-DNA binding. Based on the viscosity measurements, the effect of the ligand on DNA viscosity was less than that of the Pt(II) complex. The experimental results were supported by molecular docking studies. The results showed that the Pt(II) complex interacts with DNA via a partial intercalation mode, while the free ligand showed binding to DNA in the minor groove. In vitro cell, culture studies confirmed that the Pt(II) complex has a remarkable cytotoxic effect on human prostate carcinoma cells.

The role of both intercalation and groove binding at AT-rich DNA regions in the interaction process of a dinuclear Cu(I) complex probed by spectroscopic and simulation analysis

In this research paper, the synthesis process and characterization of a dinuclear Cu(I) phosphine complex, as well as spectroscopic and simulation analysis of its interaction with DNA helix, are presented. The monoclinic phase [Cu(PPh3)(L0.5)(I)]2 with a tetrahedral molecular geometry was elucidated based on X-ray single-crystal diffraction data. The significant association constant (6.88 × 105) and remarkable hyperchromism as obtained from UV–Visible spectra indicated a high binding affinity of the Cu(I) complex for DNA, which is in accordance with both intercalation and groove binding modes. The results of competitive fluorescence experiments along with molecular docking simulation proved that the planar part of the complex can insert into the core of adenine nucleobases and compete with methylene blue for the intercalative binding sites, while the bulky substituent binds in the minor groove of DNA via replacement of Hoechst molecules at A-T rich regions. According to thermodynamic parameters (the negative values of ΔH° and ΔS°), it is quite clear that the interaction process is enthalpy-favored while disfavored by entropy and van der Walls and hydrophobic forces play a major role in stabilization of right-handed B-DNA form during the interaction, as shown in the circular dichroism spectra. Based on the above findings partial intercalation mode at A-T rich region of DNA was proposed. The cytotoxicity and apoptosis results on MCF-7 cell line indicated positive effect of the Cu(I) complex in controlling growth and viability of breast cancer more than cisplatin.

Elucidation of DNA binding interaction of new Cu(II)/Zn(II) complexes derived from Schiff base and L-tryptophan amino acid: a multispectroscopic and molecular docking approach.

Herein, we describe the synthesis, structural elucidation, and DNA interaction of newly synthesized Cu(II) and Zn(II) complexes, i.e., [Cu(SB)(L-trp)(H2O)2]NO3 (1) and [Zn(SB)(L-trp)(H2O)2]NO3 (2) (SB = Schiff base obtained from the reaction between o-vanillin and 2-amino-2-methylpropane-1,3-diol; L-trp = L-tryptophan). From the analysis, a six-coordinated environment around the Cu(II) or Zn(II) center is proposed. The ability of the complexes to bind with calf thymus DNA was examined by optical spectroscopy (UV-vis titrations and steady-state fluorescence emission) and viscosity measurements. The vivid experimental results revealed that complexes 1 and 2 avidly bind to DNA through surface and groove binding modes, albeit with dissimilar intrinsic binding constants (1.54 × 104 and 1.36 × 104 M-1 for 1 and 2, respectively). Both complexes can displace ethidium bromide (EB) to some extent from the intercalated EB-DNA system, resulting in fluorescence quenching. Additional experiments such as [Fe(CN)6]4--induced quenching and thermal melting confirmed the electrostatic and groove binding mode. Furthermore, molecular docking studies verified that both complexes locate in the DNA minor groove by surface binding and were stabilized through weak intermolecular forces. The binding affinity of the lowest energy docked pose was found to be -5.37 kcal/mol for complex 1 and - 5.18 kcal/mol for complex 2. The present work is expected to pave the way for the synthesis of DNA-targeting Cu(II)/Zn(II) metal complexes for the development of chemotherapeutic agents.

EV20/NMS-P945, a Novel Thienoindole Based Antibody-Drug Conjugate Targeting HER-3 for Solid Tumors.

HER-3 is becoming an attractive target for antibody–drug conjugate (ADC)-based therapy. Indeed, this receptor and its ligands are found to be overexpressed in several malignancies, and re-activation of its downstream signaling axis is known to play a critical role in modulating the sensitivity of targeted therapeutics in different tumors. In this study, we generated a novel ADC named EV20/NMS-P945 by coupling the anti-HER-3 antibody EV20 with a duocarmycin-like derivative, the thienoindole (TEI) NMS-P528, a DNA minor groove alkylating agent through a peptidic cleavable linker. This ADC showed target-dependent cytotoxic activity in vitro on several tumor cell lines and therapeutic activity in mouse xenograft tumor models, including those originating from pancreatic, prostatic, head and neck, gastric and ovarian cancer cells and melanoma. Pharmacokinetics and toxicological studies in monkeys demonstrated that this ADC possesses a favorable terminal half-life and stability and it is well tolerated. These data support further EV20/NMS-P945 clinical development as a therapeutic agent against HER-3-expressing malignancies.

DNA binding site kinetics of a large antiviral polyamide

Polyamides (PAs) are powerful DNA ligands that can bind the minor groove of DNA with high affinity and specificity. While the characterization of PA-DNA behavior has focused principally on hairpin PAs 6–8 rings in size, there is increasing evidence that their behavior does not necessarily reflect the complexities that are emerging from studies of larger hairpin PAs, particularly concerning sequence mismatch tolerance and observed but unaddressed high PA-target site binding stoichiometries. To explore these complexities in more detail, kinetics studies of binding a large anti-HPV hairpin polyamide to an isolated DNA recognition site are described. Using a fluorescence assay, two distinct binding phases are observed for the first time in hairpin PA literature. PA14 concentration dependence analysis indicates that the faster binding event is diffusion-controlled; the apparent, second event is significantly slower (350–1500 fold). Both association phases are sampled in 1:1 complexes, consistent with cooperative binding of two PA molecules even under this condition. Fitting of the slow phase to a biexponential model yields two λon,app that differ by 4-5-fold, which is consistent with the high mismatch tolerance and binding site stoichiometry previously observed. A/T patterns in the recognition sequence do not affect these decay constants significantly. Dissociation decay constants are among the slowest reported for hairpin PAs (10−3 s−1), independent of A/T pattern, and may point to the efficacy of PA14 as an antiviral.

Chemical composition, antibacterial activity and study of the interaction mechanisms of the main compounds present in the Alpinia galanga rhizomes essential oil

In this research, the antibacterial activity and the interaction mechanisms of the major chemical constituent present in the Alpinia galanga rhizomes essential oil (AGREO) were investigated. Ethyl cinnamate, methyl cinnamate and n-pentadecane were the major components of AGREO. The antibacterial mechanism of AGREO on Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) was evaluated and the results proved that the potent antibacterial activity of AGREO was due to higher passive permeability of bacterial cell membrane, followed by crucial intracellular components efflux. Additionally, AGREO disrupted the intracellular physiological metabolism of EHEC O157, including inhibition of P-type ATPases activity and down-regulation expression of four virulence genes associated with EHEC infections. Notably, molecular docking studies suggested that ethyl cinnamate probably competed with the structural NAD(P)+ for the binding sites of glucose-6-phosphate dehydrogenase (G6PD), resulting in a decrease in G6PD activity with subsequent suppression of respiratory metabolism. The spectroscopic techniques and molecular docking studies proved that the AGREO major components were prone to bind to the minor groove of DNA.

Combining Multicolor FISH with Fluorescence Lifetime Imaging for Chromosomal Identification and Chromosomal Sub Structure Investigation.

Understanding the structure of chromatin in chromosomes during normal and diseased state of cells is still one of the key challenges in structural biology. Using DAPI staining alone together with Fluorescence lifetime imaging (FLIM), the environment of chromatin in chromosomes can be explored. Fluorescence lifetime can be used to probe the environment of a fluorophore such as energy transfer, pH and viscosity. Multicolor FISH (M-FISH) is a technique that allows individual chromosome identification, classification as well as assessment of the entire genome. Here we describe a combined approach using DAPI as a DNA environment sensor together with FLIM and M-FISH to understand the nanometer structure of all 46 chromosomes in the nucleus covering the entire human genome at the single cell level. Upon DAPI binding to DNA minor groove followed by fluorescence lifetime measurement and imaging by multiphoton excitation, structural differences in the chromosomes can be studied and observed. This manuscript provides a blow by blow account of the protocol required to perform M-FISH-FLIM of whole chromosomes.

N-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking studies

Benzenesulfonamide-based imine compounds 5–8 were prepared and screened for their binding properties to the FSdsDNA. The structures of synthesized compounds were elucidated by the spectroscopic and analytical methods. Compounds 5–8 were screened for their interactions with the FSdsDNA. Compound 8 showed the highest binding affinity to the FSdsDNA with intrinsic binding constant of 3.10 × 104 M−1. The compounds caused the quenching of the DNA–EB emission indicating displacement of EB (ethidium bromide) from the FSdsDNA. Finally, the binding interactions between the DNA and binder molecules 5–8 were examined by the molecular docking studies. The compounds locate approximately same region of the minor groove of DNA via hydrogen bonding contacts between the sulfonamide oxygen atoms and the DG10/DG16 nucleotides of DNA. Communicated by Ramaswamy H. Sarma

Protective effect of baicalein on DNA oxidative damage and its binding mechanism with DNA: An in vitro and molecular docking study

In this work, the protective effect of baicalein on DNA oxidative damage and its possible protection mechanisms were investigated. 2-thiobarbituric acid (TBA) colorimetry and agarose gel electrophoresis study found that baicalein protected the deoxyribose residue and double-stranded backbone of DNA from the damage of hydroxyl radicals. Antioxidant analysis results showed that baicalein has excellent radicals scavenging effects and Fe2+ chelating ability, which might be the mechanism of baicalein protecting DNA. DNA binding studies indicated that baicalein bound to the minor groove of DNA with moderate binding affinity (K = (7.35 ± 0.91) × 103 M−1). Hydrogen bonding and van der Waals forces played a major role in driving the binding process. Molecular docking further confirmed the experimental results. This binding could stabilize DNA double helix structure, thereby protecting DNA from oxidative damage. This study may provide theoretical basis for designing new functional foods of baicalein for DNA damage protection.

Examining the Effects of Netropsin on the Mobility of DNA using Capillary Electrophoresis

Netropsin binds the minor groove of DNA, particularly at AT-rich sequences. The presence of DNA A-tracts, contiguous repeated adenine base sequences, causes a natural curve of the helix axis. Orienting multiple A-tracts on a 98-base pair DNA fragment either in-phase or out-of-phase creates different shapes in the DNA. These molecular shape differences alter DNA mobility. Capillary electrophoresis (CE) has been widely used to examine the free solution mobility of negatively charged analytes. Here we attempt to better understand how netropsin binding affects the mobility in free solution of double-stranded DNA fragments with different A-tract arrangements. Results to date are presented.

Novel polyamide amidine anthraquinone platinum(II) complexes: cytotoxicity, cellular accumulation, and fluorescence distributions in 2D and 3D cell culture models.

1- and 1,5-Aminoalkylamine substituted anthraquinones (AAQs, 1C3 and 1,5C3) were peptide coupled to 1-, 2-, and 3-pyrrole lexitropsins to generate compounds that incorporated both DNA minor groove and intercalating moieties. The corresponding platinum(II) amidine complexes were synthesized through a synthetically facile amine-to-platinum mediated nitrile 'Click' reaction. The precursors as well as the corresponding platinum(II) complexes were biologically evaluated in 2D monolayer cells and 3D tumour cell models. Despite having cellular accumulation levels that were up to five-fold lower than that of cisplatin, the platinum complexes had cytotoxicities that were only three-fold lower. Accumulation was lowest for the complexes with two or three pyrrole groups, but the latter was the most active of the complexes exceeding the activity of cisplatin in the MDA-MB-231 cell line. All compounds showed moderate to good penetration into spheroids of DLD-1 cells with the distributions being consistent with active uptake of the pyrrole containing complexes in regions of the spheroids starved of nutrients.

Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition.

Thymine DNA glycosylase (TDG), as a repair enzyme, plays essential roles in maintaining the genome integrity by correcting several mismatched/damaged nucleobases. TDG acquires an efficient strategy to search for the lesions among a vast number of cognate base pairs. Currently, atomic-level details of how TDG translocates along DNA as it approaches the lesion site and the molecular mechanisms of the interplay between TDG and DNA are still elusive. Here, by constructing the Markov state model based on hundreds of molecular dynamics simulations with an integrated simulation time of ∼25 μs, we reveal the rotation-coupled sliding dynamics of TDG along a 9 bp DNA segment containing one G·T mispair. We find that TDG translocates along DNA at a relatively faster rate when distant from the lesion site, but slows down as it approaches the target, accompanied by deeply penetrating into the minor-groove, opening up the mismatched base pair and significantly sculpturing the DNA shape. Moreover, the electrostatic interactions between TDG and DNA are found to be critical for mediating the TDG translocation. Notably, several uncharacterized TDG residues are identified to take part in regulating the conformational switches of TDG occurred in the site-transfer process, which warrants further experimental validations.

Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies.

Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.

Mesenchymal stromal cells expressing a dominant-negative high mobility group A1 transgene exhibit improved function during sepsis.

High mobility group (HMG)A proteins are nonhistone chromatin proteins that bind to the minor groove of DNA, interact with transcriptional machinery, and facilitate DNA‐directed nuclear processes. HMGA1 has been shown to regulate genes involved with systemic inflammatory processes. We hypothesized that HMGA1 is important in the function of mesenchymal stromal cells (MSCs), which are known to modulate inflammatory responses due to sepsis. To study this process, we harvested MSCs from transgenic (Tg) mice expressing a dominant‐negative (dn) form of HMGA1 in mesenchymal cells. MSCs harvested from Tg mice contained the dnHMGA1 transgene, and transgene expression did not change endogenous HMGA1 levels. Immunophenotyping of the cells, along with trilineage differentiation revealed no striking differences between Tg and wild‐type (WT) MSCs. However, Tg MSCs growth was decreased compared with WT MSCs, although Tg MSCs were more resistant to oxidative stress‐induced death and expressed less IL‐6. Tg MSCs administered after the onset of Escherichia coli‐induced sepsis maintained their ability to improve survival when given in a single dose, in contrast with WT MSCs. This survival benefit of Tg MSCs was associated with less tissue cell death, and also a reduction in tissue neutrophil infiltration and expression of neutrophil chemokines. Finally, Tg MSCs promoted bacterial clearance and enhanced neutrophil phagocytosis, in part through their increased expression of stromal cell‐derived factor‐1 compared with WT MSCs. Taken together, these data demonstrate that expression of dnHMGA1 in MSCs provides a functional advantage of the cells when administered during bacterial sepsis.

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel.

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using 1H and 13C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). CT-DNA quenches the fluorescence of these probes via a static quenching mechanism. In the case of R1 and R4, the observed ΔHo < 0 and ΔSo > 0suggest that these probes interact with CT-DNA through H-bonding and hydrophobic interactions, while in the interaction of R2 and R3, van der Walls and H-boding forces are found to be dominant (ΔHo < 0 and ΔSo < 0). Results of molecular docking investigations corroborate well with that of spectral studies, and these probes bind in the minor groove of DNA. These probes are found to be effective fluorescent staining agents for DNA in agarose gel in gel electrophoresis experiment with sensitivity comparable to that of EB, and DNA amounts as low as 37.5ng are visually detectable in the gel.

Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove.

This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔTm, biosensor SPR with a KD of 4 nM, a similar KD from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central –CH of the benzodiimidazole is close to the –C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.

Synthesis, characterization, crystal structures, DFT, TD-DFT, molecular docking and DNA binding studies of novel copper(II) and zinc(II) complexes bearing halogenated bidentate N,O-donor Schiff base ligands

A novel series of transition metal complexes of Cu(II) and Zn(II), including: [Cu(L1)2]: C1, [Cu(L2)2]: C2, [Cu(L3)2]: C3, [Cu(L4)2]: C4, [Zn(L1)2]: Z1, [Zn (L2)2]: Z2, [Zn (L3)2]: Z3, and [Zn (L4)2]: Z4, with four halogenated bis-N,O-bidentate Schiff base ligands (HL1: 2-ethoxy-6-[(4-fluorophenyl)iminomethyl]phenol; HL2: 2-ethoxy-6-[(4-chlorophenylimino)methyl]phenol; HL3: 2-ethoxy-6-[(4-bromophenyl)iminomethyl]phenol; HL4: 2-ethoxy-6-[(4-iodophenylimino)methyl]phenol have been synthesized and characterized by elemental analyses, FT-IR, UV–Vis and 1H NMR spectroscopic techniques. Furthermore, the crystal structures of HL2, HL4, Z1 and Z2 were determined by single crystal X-ray analysis. These bidentate ligands coordinated to the metal(II) ions through the deprotonated phenolic oxygens and the azomethine nitrogens. The X-ray diffraction analysis revealed that Z1 and Z2 adapted distorted tetrahedral geometries. Theoretical calculation of the synthesized compounds, carried out by DFT as well as TD-DFT using B3LYP method with employing the Def2-TZVP basis set, indicated that the calculated results are in accordance with the experimental findings. NBO analysis has been used to elucidate charge transfer information of the HL2, HL4, Z1 and Z2. Moreover, binding ability of the Schiff base ligands and their metal complexes with FS-DNA was studied by spectroscopic and computational methods. The results of both methods showed that the ligands bound in minor grooves of DNA. The oxygen of the ethoxy group has played an important role in DNA binding investigations.

Ancillary Ligand in Ternary CuII Complexes Guides Binding Selectivity toward Minor-Groove DNA.

Copper-containing compounds known as Casiopeínas are biologically active molecules which show promising antineoplastic effects against several cancer types. Two possible hypotheses regarding the mode of action of the Casiopeínas have emerged from the experimental evidence: the generation of reactive oxygen species or the ability of the compounds to bind and interact with nucleic acids. Using robust molecular dynamics simulations, we investigate the interaction of four different Casiopeínas with the DNA duplex d(GCACGAACGAACGAACGC). The studied copper complexes contain either 4–7- or 5–6-substituted dimethyl phenanthroline as the primary ligand and either glycinate or acetylacetonate as the secondary ligand. For statistical significance and to reduce bias in the simulations, four molecules of each copper compound were manually placed at a distance of 10 Å away from the DNA and 20 independent molecular dynamics simulations were performed, each reaching at least 30 μs. This time scale allows us to reproduce expected DNA terminal base-pair fraying and also to observe intercalation/base-pair eversion events generated by the compounds interacting with DNA. The results reveal that the secondary ligand is the guide toward the mode of binding between the copper complex and DNA in which glycinate prefers minor-groove binding and acetylacetonate produces base-pair eversion and intercalation. The CuII complexes containing glycinate interact within the DNA minor groove which are stabilized principally by the hydrogen bonds formed between the amino group of the aminoacidate moiety, whereas the compounds with the acetylacetonate do not present a stable network of hydrogen bonds and the ligand interactions enhance DNA breathing dynamics that result in base-pair eversion.