DNA-binding metallo-intercalators

Last updated

DNA-binding metallo-intercalators are positively charged, planar, polycyclic, aromatic compounds that unwind the DNA double helix and insert themselves between DNA base pairs. [1] Metallo-intercalators insert themselves between two intact base pairs without expelling or replacing the original nitrogenous bases; the hydrogen bonds between the nitrogenous bases at the site of intercalation remain unbroken. [1] [2] [3] In addition to π-stacking between the aromatic regions of the intercalator and the nitrogenous bases of DNA, intercalation is stabilized by van der Waals, hydrophobic, electrostatic, and entropic interactions. [2] This ability to bind to specific DNA base pairs allows for potential therapeutic applications of metallo-intercalators.

Contents

Synthesis of metallo-intercalators

Figure 1: Chemical structure of the DNA-binding metallo-intercalator complex [Ru(bpy)2(paip)]2+ with intercalative and ancillary ligands labeled. Ru(bpy)2(paip)2+.png
Figure 1: Chemical structure of the DNA-binding metallo-intercalator complex [Ru(bpy)2(paip)]2+ with intercalative and ancillary ligands labeled.

In the case of ruthenium intercalators, the general synthesis consists of preparing intercalative ligands followed by their coupling to a ruthenium metal complex coordinated by specific ancillary ligands. [6] [7] Examples of prior ruthenium complexes used as precursors for metallo-intercalators include cis-[Ru(bpy)2Cl2] and cis-[Ru(phen)2Cl2]∙2H2O, which can be synthesized into [Ru(bpy)2(maip)]2+, [Ru(bpy)2(paip)]2+, [Ru(bpy)2(bfipH)](ClO4)2, and Ru(phen)2(bfipH)](ClO4)2. [4] [5]

Mechanism of DNA-intercalation

Figure 2: Metallo-intercalators enter double stranded DNA via the major groove and p-stack between adjacent unbroken base pairs. Here, the phi ligand of a rhodium complex intercalates a DNA segment with the sequence 5'-G(5IU)TGCAAC-3' (PDB ID 454D). Metallo-intercalator DNA binding.png
Figure 2: Metallo-intercalators enter double stranded DNA via the major groove and π-stack between adjacent unbroken base pairs. Here, the phi ligand of a rhodium complex intercalates a DNA segment with the sequence 5'-G(5IU)TGCAAC-3' (PDB ID 454D).

Metallo-intercalators π-stack with unbroken DNA base pairs after entering via a groove, typically the major, (in contrast to metallo-insertors, which replace expelled base pairs after entering double stranded DNA via the minor groove). [9] [10] Intercalation of a metallo-intercalator creates less strain in the DNA duplex than insertion; metallo-insertors induce an untwist of the double helix and an opening of the phosphate backbone while metallo-intercalators marginally increase the rise and width of the major groove. [1] [9] Intercalation of metal compounds between DNA base pairs effectively stabilizes the double helix, increasing the melting temperature of the DNA duplex. [8] Binding of metallo-intercalators to DNA is reversible and depends on the properties of the intercalating molecule. Metallo-intercalators with different metal centers, oxidation states, coordination geometries, and overall sizes will exhibit varying “depths of insertion”. [3] For example, square planar complexes penetrate deeper into the DNA base pairs than octahedral or tetrahedral complexes do. [3] Also, positive charges on the metallo-intercalator strengthen DNA-binding because of electrostatic attraction to the negatively charged sugar-phosphate backbone. [6]

Therapeutic applications

Figure 3: The wide structure of metallo-intercalators containing the ligand 5,6-chrysenequinone diimine (chrysi) can be used in anticancer therapeutics to identify mismatched DNA base pairs. 5,6-chrysenequinone diimine.png
Figure 3: The wide structure of metallo-intercalators containing the ligand 5,6-chrysenequinone diimine (chrysi) can be used in anticancer therapeutics to identify mismatched DNA base pairs.

Metallo-intercalators have a variety of potential therapeutic applications as a result of their structural diversity and universal photooxidative properties. One possible therapeutic application of metallo-intercalators is to combat cancerous tumor cells within the body by targeting specific mismatched DNA base pairs; the ability to modify the ligands bound to the metal center allows for a high degree of specificity in the binding interactions between the metallo-intercalator and the DNA sequence. [11] [12] [13] For example, the ligand 5,6-chrysenequinone diimine (chrysi) and its analogues are designed to be too wide to fit inside the normal span of the base pairs of B-DNA, causing it to bind instead to the wider portions of the helix at destabilized sites of mismatched bases. [11] [12] After intercalation, the sample can be photoactivated by absorbing energy during irradiation with short wavelength light. [1] This activation causes the metallo-intercalator's photooxidative properties to induce a cleavage of the sugar phosphate backbone at the site of mismatch through a radical mechanism. [1] [11] [12] Even in the absence of irradiation, the interactions between the metallo-intercalator and DNA can substantially decrease the proliferation of cells containing DNA with mismatched base pairs. [13]


Related Research Articles

Base pair Unit consisting of two nucleobases bound to each other by hydrogen bonds

A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" base pairs allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes.

Polypyridine complex

Polypyridine complexes are coordination complexes containing polypyridine ligands, such as 2,2'-bipyridine, 1,10-phenanthroline, or 2,2';6'2"-terpyridine.

Jacqueline Barton American chemist

Jacqueline K. Barton, is an American chemist. She worked as a Professor of Chemistry at Hunter College (1980–82), and at Columbia University (1983–89) before joining the California Institute of Technology. In 1997 she became the Arthur and Marian Hanisch Memorial Professor of Chemistry and from 2009 to 2019, the Norman Davidson Leadership Chair of the Division of Chemistry and Chemical Engineering at Caltech. She currently is the John G. Kirkwood and Arthur A. Noyes Professor of Chemistry.

Bridging ligand Ligand which connects two or more (usually metal) atoms in a coordination complex

In coordination chemistry, a bridging ligand is a ligand that connects two or more atoms, usually metal ions. The ligand may be atomic or polyatomic. Virtually all complex organic compounds can serve as bridging ligands, so the term is usually restricted to small ligands such as pseudohalides or to ligands that are specifically designed to link two metals.

Tris(bipyridine)ruthenium(II) chloride Chemical compound

Tris(bipyridine)ruthenium(II) chloride is the chloride salt coordination complex with the formula [Ru(bpy)3]2+ 2Cl−. This polypyridine complex is a red crystalline salt obtained as the hexahydrate, although all of the properties of interest are in the cation [Ru(bpy)3]2+, which has received much attention because of its distinctive optical properties. The chlorides can be replaced with other anions, such as PF6−.

Electrochemiluminescence Emission of light from electrochemical reactions

Electrochemiluminescence or electrogenerated chemiluminescence (ECL) is a kind of luminescence produced during electrochemical reactions in solutions. In electrogenerated chemiluminescence, electrochemically generated intermediates undergo a highly exergonic reaction to produce an electronically excited state that then emits light upon relaxation to a lower-level state. This wavelength of the emitted photon of light corresponds to the energy gap between these two states. ECL excitation can be caused by energetic electron transfer (redox) reactions of electrogenerated species. Such luminescence excitation is a form of chemiluminescence where one/all reactants are produced electrochemically on the electrodes.

Organoruthenium chemistry

Organoruthenium chemistry is the chemistry of organometallic compounds containing a carbon to ruthenium chemical bond. Several organoruthenium catalysts are of commercial interest and organoruthenium compounds have been considered for cancer therapy. The chemistry has some stoichiometric similarities with organoiron chemistry, as iron is directly above ruthenium in group 8 of the periodic table. The most important reagents for the introduction of ruthenium are ruthenium(III) chloride and triruthenium dodecacarbonyl.

Nucleic acid tertiary structure Three-dimensional shape of a nucleic acid polymer

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.

Stephen J. Lippard American chemist

Stephen James Lippard is the Arthur Amos Noyes Emeritus Professor of Chemistry at the Massachusetts Institute of Technology. He is considered one of the founders of bioinorganic chemistry, studying the interactions of nonliving substances such as metals with biological systems. He is also considered a founder of metalloneurochemistry, the study of metal ions and their effects in the brain and nervous system. He has done pioneering work in understanding protein structure and synthesis, the enzymatic functions of methane monooxygenase (MMO), and the mechanisms of cisplatin anticancer drugs. His work has applications for the treatment of cancer, for bioremediation of the environment, and for the development of synthetic methanol-based fuels.

Hydrogenation of carbon–nitrogen double bonds

In chemistry, the hydrogenation of carbon–nitrogen double bonds is the addition of the elements of dihydrogen (H2) across a carbon–nitrogen double bond, forming amines or amine derivatives. Although a variety of general methods have been developed for the enantioselective hydrogenation of ketones, methods for the hydrogenation of carbon–nitrogen double bonds are less general. Hydrogenation of imines is complicated by both syn/anti isomerization and tautomerization to enamines, which may be hydrogenated with low enantioselectivity in the presence of a chiral catalyst. Additionally, the substituent attached to nitrogen affects both the reactivity and spatial properties of the imine, complicating the development of a general catalyst system for imine hydrogenation. Despite these challenges, methods have been developed that address particular substrate classes, such as N-aryl, N-alkyl, and endocyclic imines.

Rhodocene Organometallic chemical compound

Rhodocene is a chemical compound with the formula [Rh(C5H5)2]. Each molecule contains an atom of rhodium bound between two planar aromatic systems of five carbon atoms known as cyclopentadienyl rings in a sandwich arrangement. It is an organometallic compound as it has (haptic) covalent rhodium–carbon bonds. The [Rh(C5H5)2] radical is found above 150 °C (302 °F) or when trapped by cooling to liquid nitrogen temperatures (−196 °C [−321 °F]). At room temperature, pairs of these radicals join via their cyclopentadienyl rings to form a dimer, a yellow solid.

Photochemical reduction of carbon dioxide harnesses solar energy to convert CO2 into higher-energy products. Environmental interest in producing artificial systems is motivated by recognition that CO2 is a greenhouse gas. The process has not been commercialized.

Tolman electronic parameter

The Tolman electronic parameter (TEP) is a measure of the electron donating or withdrawing ability of a ligand. It is determined by measuring the frequency of the A1 C-O vibrational mode (ν(CO)) of a (pseudo)-C3v symmetric complex, [LNi(CO)3] by infrared spectroscopy, where L is the ligand of interest. [LNi(CO)3] was chosen as the model compound because such complexes are readily prepared from tetracarbonylnickel(0). The shift in ν(CO) is used to infer the electronic properties of a ligand, which can aid in understanding its behavior in other complexes. The analysis was introduced by Chadwick A. Tolman.

Ruthenium anti-cancer drugs are coordination complexes of ruthenium complexes that have anticancer properties. They promise to provide alternatives to platinum-based drugs for anticancer therapy. No ruthenium anti-cancer drug has been commercialized.

Intercalation (biochemistry)

In biochemistry, intercalation is the insertion of molecules between the planar bases of deoxyribonucleic acid (DNA). This process is used as a method for analyzing DNA and it is also the basis of certain kinds of poisoning.

Transition metal nitrile complexes Class of coordination compounds containing nitrile ligands (coordinating via N)

Transition metal nitrile complexes are coordination compounds containing nitrile ligands. Because nitriles are weakly basic, the nitrile ligands in these complexes are often labile.

RAPTA is a class of experimental cancer drugs. They consist of a central ruthenium(II) atom complexed to an arene group, chlorides, and 1,3,5-triaza-7-phosphaadamantane (PTA) forming an organoruthenium half-sandwich compound. Other related ruthenium anti-cancer drugs include NAMI-A, KP1019 and BOLD-100.

A transition metal phosphido complex is a coordination complex containing a phosphido ligand (R2P, where R = H, organic substituent). With two lone pairs on phosphorus, the phosphido anion (R2P−) is comparable to an amido anion (R2N−), except that the M-P distances are longer and the phosphorus atom is more sterically accessible. For these reasons, phosphido is often a bridging ligand.

<i>cis</i>-Dichlorobis(bipyridine)ruthenium(II) Chemical compound

cis-Dichlorobis(bipyridine)ruthenium(II) is the coordination complex with the formula RuCl2(bipy)2, where bipy is 2,2'-bipyridine. It is a dark green diamagnetic solid that is a precursor to many other complexes of ruthenium, mainly by substitution of the two chloride ligands. The compound has been crystallized as diverse hydrates.

Transition metal dithiocarbamate complexes

Transition metal dithiocarbamate complexes are coordination complexes containing one or more dithiocarbamate ligand, which are typically abbreviated R2dtc−. Many complexes are known. Several homoleptic derivatives have the formula M(R2dtc)n where n = 2 and 3.

References

  1. 1 2 3 4 5 Zeglis, Brian M.; Pierre, Valerie C.; Barton, Jacqueline K. (2007). "Metallo-intercalators and Metallo-insertors" (PDF). Chemical Communications. 44 (44): 4565–79. doi:10.1039/b710949k. PMC   2790054 . PMID   17989802.
  2. 1 2 Gill, Martin R., and Jim A. Thomas. "Ruthenium(ii) Polypyridyl Complexes and DNA-from Structural Probes to Cellular Imaging and Therapeutics - (RSC Publishing)." Chem Soc Rev, n.d. Web. 26 Jan. 2015. <http://pubs.rsc.org/en/Content/ArticlePDF/2012/CS/c2cs15299a>.
  3. 1 2 3 Pages, Benjamin J., Dale L. Ang, Elise P. Wright, and Janice R. Aldrich-Wright. "Metal Complex Interactions with DNA." Royal Society of Chemistry, n.d. Web. 26 Jan. 2015. <http://pubs.rsc.org/en/content/articlehtml/2014/dt/c4dt02700k>.
  4. 1 2 Vargiu, Attilio V., and Alessandra Magistrato. "Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study." Inorganic Chemistry. Inorganic Chemistry, n.d. Web. 26 Jan. 2015. <http://pubs.acs.org/doi/pdfplus/10.1021/ic201659v>.
  5. 1 2 Raman, Natarajan; Rajakumar, Ramasubbu (2014). "Bis-amide Transition Metal Complexes: Isomerism and DNA Interaction Study". Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 120: 428–436. doi:10.1016/j.saa.2013.10.037. PMID   24211801.
  6. 1 2 Liu, Yun-Jun; Liang, Zhen-Hua; Li, Zheng-Zheng; Yao, Jun-Hua; Huang, Hong-Liang (2011). "Ruthenium(II) Polypyridyl Complexes: Synthesis and Studies of DNA Binding, Photocleavage, Cytotoxicity, Apoptosis, Cellular Uptake, and Antioxidant Activity". DNA and Cell Biology. 30 (2): 829–38. doi:10.1016/j.ejmech.2009.10.043. PMID   19932529.
  7. ↑ Du, Ke-Jie, Jin-Quan Wang, Jun-Feng Kou, Guan-Ying Li, Li-Li Wang, Hui Chao, and Liang-
  8. 1 2 Kielkopf, C. L., K. E. Erkkila, B. P. Hudson, J. K. Barton, and D. C. Rees. "INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3'" RCSB Protein Data Bank. N.p., n.d. Web. 26 Jan. 2015. <http://www.rcsb.org/pdb/explore/explore.do?structureId=454D>.
  9. 1 2 Lauria, Antonino, Riccardo Bonsignore, and Alessio Terenzi. "Nickel(ii), Copper(ii) and Zinc(ii) Metallo-intercalators: Structural Details of the DNA-binding by a Combined Experimental and Computational Investigation - (RSC Publishing)." Royal Society of Chemistry, n.d. Web. 26 Jan. 2015. <http://pubs.rsc.org/EN/content/articlehtml/2014/dt/c3dt53066c>.
  10. ↑ Alessandro Biancardi, Azzurra Burgalassi, Alessio Terenzi, Angelo Spinello, Giampaolo Barone, Tarita Biver, and Benedetta Mennucci. |title="A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA‐Intercalator Salphen‐Type ZnII Complex" |journal=Chemistry–A European Journal, |date=2015 |volume=20 |issue=24 |pages=7439-7447. |doi=10.1002/chem.201304876
  11. 1 2 3 4 Pierre, VC; Kaiser, JT; Barton, JK (2007). "Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator". Proc. Natl. Acad. Sci. U.S.A. 104 (2): 429–34. doi: 10.1073/pnas.0610170104 . PMC   1766401 . PMID   17194756.
  12. 1 2 3 4 Junicke, H.; Hart, J. R.; Kisko, J.; Glebov, O.; Kirsch, I. R.; Barton, J. K. (2003). "Bioinorganic Chemistry Special Feature: A Rhodium(III) Complex for High-affinity DNA Base-pair Mismatch Recognition". Proceedings of the National Academy of Sciences. 100 (7): 3737–42. doi: 10.1073/pnas.0537194100 . PMC   152991 . PMID   12610209.
  13. 1 2 Hart, J. R.; Glebov, O.; Ernst, R. J.; Kirsch, I. R.; Barton, J. K. (2006). "DNA Mismatch-specific Targeting and Hypersensitivity of Mismatch-repair-deficient Cells to Bulky Rhodium(III) Intercalators". Proceedings of the National Academy of Sciences. 103 (42): 15359–5363. doi: 10.1073/pnas.0607576103 . PMC   1622828 . PMID   17030786.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.