PHD
  1. Inorganic chemistry  1.1. Coordination chemistry  1.1.1. Ligand field theory  1.1.2. Crystal field theory  1.1.3. Molecular Orbital Theory for Coordination Compounds  1.1.4. Stability of Coordination Compounds  1.1.5. Electronic spectra of coordination compounds  1.1.6. Isomerism in Coordination Compounds  1.1.7. Kinetics and mechanism of coordination reactions  1.2. Organometallic Chemistry  1.2.1. Metal Carbonyls  1.2.2. Metal alkyl and aryl  1.2.3. Fischer and Schrock carbonaceans  1.2.4. Oxidative Addition and Reductive Elimination  1.2.5. Metal Hydrides  1.2.6. Catalysis by organometallic compounds  1.2.7. Metallocenes and Sandwich Complexes  1.2.8. CH activation  1.3. Solid state chemistry  1.3.1. Crystal structures and lattices  1.3.2. Band theory and electrical properties  1.3.3. Defects in the crystal  1.3.4. Synthesis of solid state materials  1.3.5. Magnetic and optical properties of solids  1.3.6. Superconductivity  1.3.7. Solid state ionics  1.4. Bio-inorganic chemistry  1.4.1. Metalloproteins and enzymes  1.4.2. Metal ion transport and storage  1.4.3. The role of metals in medicine  1.4.4. Bioinspired catalysis  1.4.5. Metal–DNA interactions  1.4.6. Metal Complexes in Medical Science  1.5. Lanthanides and Actinides  1.5.1. Electronic configuration and oxidation states in lanthanides and actinides  1.5.2. Spectral and Magnetic Properties in Lanthanides and Actinides  1.5.3. Separation and Extraction of Lanthanides and Actinides  1.5.4. Coordination chemistry of f-block elements  1.6. Main Group Chemistry  1.6.1. Chemistry of boron compounds  1.6.2. Chemistry of Silicon and Germanium Compounds  1.6.3. Chemistry of Phosphorus and Sulfur Compounds  1.6.4. Organosilicon chemistry  1.6.5. Noble Gas Chemistry
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition and substitution reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic Reactions  2.1.7. Photochemical reactions  2.2. Stereoscopic  2.2.1. Chirality and optical activity  2.2.2. Structural analysis  2.2.3. Stereoelectronic effects  2.2.4. Asymmetric synthesis  2.2.5. Dynamic Stereochemistry  2.3. Organometallic Chemistry in Organic Synthesis  2.3.1. Organolithium and organomagnesium reagents  2.3.2. Transition metal catalyzed coupling reactions  2.3.3. Palladium-catalyzed reactions  2.3.4. Olefin Metathesis  2.3.5. Gold and silver catalysis  2.4. Natural products chemistry  2.4.1. Alkaloids and terpenoids  2.4.2. Steroids and Flavonoids  2.4.3. Total synthesis of natural products  2.4.4. Biosynthesis of natural products  2.5. Supramolecular Chemistry  2.5.1. Host-Guest Chemistry  2.5.2. Self-assembly and molecular recognition  2.5.3. Supramolecular Catalysis  2.5.4. Molecular Machines
  3. Physical Chemistry  3.1. Thermodynamics  3.1.1. Laws of Thermodynamics  3.1.2. Chemical Potential and Equilibrium  3.1.3. Statistical thermodynamics  3.1.4. Non-equilibrium thermodynamics  3.2. Quantum Chemistry  3.2.1. Schrödinger equation and its applications  3.2.2. Molecular orbital theory  3.2.3. Density functional theory  3.2.4. Post-Hartree–Fock methods  3.3. Chemical kinetics  3.3.1. Reaction rate theory  3.3.2. Mechanism and rate laws  3.3.3. Catalysis and enzyme kinetics  3.3.4. Reaction dynamics  3.4. Spectroscopy and molecular structure  3.4.1. Infrared Spectroscopy  3.4.2. UV-visible spectroscopy  3.4.3. Nuclear Magnetic Resonance Spectroscopy  3.4.4. Mass Spectrometry  3.4.5. Raman Spectroscopy  3.5. Surface and Colloid Chemistry  3.5.1. Absorption and Catalysis  3.5.2. Surfactants and micelles  3.5.3. Colloidal Stability  3.5.4. Nanomaterials and Interfaces
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.1.4. Ion Chromatography  4.2. Electroanalytical techniques  4.2.1. Voltammetry and Polarography  4.2.2. Conductometry and potentiometry  4.2.3. Colometry  4.3. Spectroscopic Methods  4.3.1. Atomic absorption spectroscopy  4.3.2. Fluorescence Spectroscopy  4.3.3. X-ray diffraction  4.3.4. Electron paramagnetic resonance spectroscopy  4.4. Chemometrics  4.4.1. Data processing and statistical methods  4.4.2. Multidisciplinary analysis  4.4.3. Machine Learning in Analytical Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.2. Quantum chemistry methods  5.3. Computational drug design  5.4. Machine Learning in Chemistry  5.5. Ab initio molecular dynamics
  6. Biophysics and Medicinal Chemistry  6.1. Drug discovery and design  6.2. Enzyme kinetics and inhibition  6.3. Chemical biology approach  6.4. Protein-ligand interactions  6.5. Bioorthogonal chemistry
  7. Materials chemistry  7.1. Polymer chemistry  7.1.1. Polymerization mechanism  7.1.2. Functional Polymers  7.1.3. Biodegradable Polymer  7.1.4. Conducting and semiconducting polymers  7.2. Nano Chemistry  7.2.1. Nanoparticles and nanostructures  7.2.2. Carbon-based nanomaterials  7.2.3. Quantum dots  7.3. Energy and Environmental Chemistry  7.3.1. Battery and Fuel Cell Chemistry  7.3.2. Green chemistry and sustainable materials  7.3.3. Photocatalysis

PHD → Inorganic chemistry → Bio-inorganic chemistry ↓


Metal–DNA interactions


Metal-DNA interactions are a fascinating area of study in the broad field of bioinorganic chemistry. These interactions involve the binding of metal ions with DNA, which can lead to important biological and chemical consequences. Understanding these interactions is important for a variety of applications, such as drug design, nanotechnology, and molecular biology.

Introduction

DNA or deoxyribonucleic acid is the molecular blueprint for life. It carries the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses. DNA is composed of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups linked by ester bonds. These strands run in opposite directions to each other and are, therefore, anti-parallel. The nucleotides on each strand are linked via hydrogen bonds.

Metals can interact with DNA in a variety of ways because of the negatively charged phosphate groups in the DNA backbone, the nitrogenous bases, and the unique three-dimensional structure of DNA. Metal ions, especially transition metals, can coordinate to these sites, altering the structural and biochemical properties of DNA.

Let us take a deeper look at the types and mechanisms of metal-DNA interactions and explore some of their visual representations.

Types of metal–DNA interactions

Direct contact

In direct interactions, the metal ions bind directly to DNA. These interactions can be classified into several types, including:

  • Covalent bonding: In covalent bonding, metal ions form covalent bonds with DNA. This is often seen with transition metals, which can form stable complexes with nucleobases. For example, cisplatin, a platinum-based anticancer drug, forms covalent bonds with the nitrogen atoms of the guanine base.
  • Electrostatic interactions: Electrostatic interactions occur when metal ions bind to DNA phosphate groups via ionic bonds. These interactions are typically weaker than covalent bonds but can still significantly affect DNA structure and function.

Indirect interaction

Indirect interactions involve the binding of metal ions to a ligand or molecule that, in turn, interacts with DNA. This type of interaction often results in a change in the chemical environment or structure of DNA, affecting its biological activity.

Mechanism of metal-DNA interaction

Covalent bond mechanism

Covalent binding of metal ions to DNA often involves coordination of nucleobases. Transition metals such as platinum can displace other ligands to form coordination complexes with bases. The nitrogen atoms in the purines (adenine and guanine) and pyrimidines (cytosine and thymine) are common sites for coordination.

Pt(NH₃)₂Cl₂ + DNA → [Pt(NH₃)₂(DNA)] + 2 Cl⁻

This reaction binds cisplatin to DNA, inhibiting its replication and transcription process, which is the principle used in cancer treatment.

Electrostatic interaction mechanism

Positively charged metal ions can bind to negatively charged phosphate groups on the DNA backbone. This bond can be represented by the general equation:

M²⁺ + DNA(PO₄)⁻² → M-DNA

The energies involved in electrostatic interactions are often lower than those of covalent interactions, making them reversible and able to play a role in transient processes such as DNA condensation and regulation.

Visual representation of interactions

Phosphate Backbone Metal ions

The visualization above shows the binding of a metal ion to the negatively charged phosphate backbone of DNA. The blue line represents the DNA backbone, while the yellow circle shows the position of the metal ion.

Importance of metal–DNA interactions

Metal-DNA interactions can alter the structural and biochemical properties of DNA. These effects result in:

  • DNA strand breakage: The binding of certain metal ions can cause the breaking of phosphodiester bonds, resulting in DNA strand breaks.
  • Changes in DNA structure: Metal ions can induce transitions between DNA structures, such as from B-DNA to Z-DNA, or stabilize unusual structures such as DNA quadruplexes.
  • Modulation of gene expression: By altering DNA structure, metal ions can affect the interaction of DNA with proteins such as transcription factors, thereby affecting gene expression.

Applications of metal-DNA interactions

Biological applications

Metal–DNA interactions are used in a variety of biological applications, such as:

  • Cancer therapy: Metal-based drugs such as cisplatin are used to treat cancer by interfering with DNA replication.
  • Antibiotic development: Certain metal complexes can target bacterial DNA, acting as potential antibiotics.

Technical applications

In technology, metal–DNA interactions have the following possibilities:

  • Nanoelectronics: DNA can serve as a framework for assembling metal nanoparticles, allowing the creation of nanoscale electronic devices.
  • Biosensors: Metal ions can be used to create DNA-based sensors to detect specific biological molecules or environmental pollutants.

Challenges in studying metal-DNA interactions

Despite the promising applications, studying metal-DNA interactions involves many challenges, including:

  • Complexity of DNA: The varied structures and dynamics of DNA make it difficult to predict how metal ions will interact under different circumstances.
  • Metal ion speciation: Metal ions can have different chemical forms, which affects their reactivity and interaction with DNA.
  • Experimental limitations: Many of the techniques used to study these interactions in vitro may not accurately reflect in vivo conditions.

Outlook

As research into metal-DNA interactions continues to progress, we anticipate the development of new therapeutic, diagnostic, and technological applications. The continued exploration of these interactions will deepen our understanding of DNA's role in biology and open new avenues for leveraging metal ions in scientific and industrial innovation.

Metal-DNA interactions provide a rich avenue of scientific investigation, bridging inorganic chemistry with biology. With ongoing research and discovery, the potential for technological breakthroughs, biological insights, and therapeutic advances is enormous.


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Metal–DNA interactions

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