Novel Recognition of Thymine Base in Double-Stranded DNA by Zinc(II)−Macrocyclic Tetraamine Complexes Appended with Aromatic Groups

Kinoshita–Kikuta, Emiko; Murata, Mariko; Katsube, Naomi; Koike, Takao; Kimura, Eiichi

doi:10.1021/ja983884j

Cited by 125 publications

(64 citation statements)

References 45 publications

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“…The base moieties of certain nucleotides (uridine, deoxythymidine, and guanosine) do exhibit some acidic character and can be deprotonated in alkaline solution (pKa ϭ 9.5, 10.0, and 9.6, respectively) [50]. Furthermore, certain metal complexes are known to bind N3-deprotonated thymine and uridine at physiological pH [51][52][53]. In the gas phase, internal Coulombic repulsion in highly charged oligonucleotide anions could encourage deprotonation of guanine and/or thymine residues.…”

Section: Methodsmentioning

confidence: 99%

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Keller

Brodbelt

2005

J. Am. Soc. Mass Spectrom.

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Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca ϩ2 , Sr ϩ2 , or Ba ϩ2 altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5=-and 3=-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/ Ba ϩ2 complexes produced abundant fragment ions corresponding to metallated a n Ϫm species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba ϩ2 and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a n Ϫm ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba ϩ2 ion may direct formation of the metallated a n Ϫm species. and function of DNA and RNA. Mono-and divalent cations are thought to induce bending in DNA duplexes [1,2], and are also known to stabilize triplex [3,4], and quadruplex [5,6] structures. Metal cations are also required for the proper folding and function of many forms of RNA, including most ribozymes [7,8]. The interactions of DNA with several natural products [9] and synthetic drugs and drug candidates [10,11] are known to be metal-mediated.Mass spectrometry (MS) is well-established as a useful tool for the structural characterization and sequencing of nucleic acids [12][13][14], and has also been employed to characterize a number of nucleic acid/metal ion interactions [15]. Several previous studies have focused on the interactions of the anticancer therapeutic cisplatin or its derivatives with DNA [16 -22]. Relatively few studies have addressed binary interactions of nucleic acids and metal cations [23][24][25][26][27]. Most of these studies have focused primarily on complexes with the smaller alkali and alkaline earth metals (e.g., Na ϩ , Mg ϩ2 ), although a few complexes with transition metals [25,26] or f-block elements [23,25] have also been investigated. The fragmentation behavior of these complexes has been characterized using parent species in relatively low charge states (often Ϫ2), but intermediate and high charge state precursors have not been studied. A more complete characterization of the entire charge state envelope produced by electrospray ionization would not only enhance our theoretical underst...

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Section: Methodsmentioning

confidence: 99%

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Keller

Brodbelt

2005

J. Am. Soc. Mass Spectrom.

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“…The enhanced cooperativity of the heterodinuclear Zn 2 -Ni 2 complex over the homonuclear ones, when the 5'-linked nucleoside is uridine, suggests another mode of bimetallic acceleration. It has been well established that azacrown chelates of Zn 2 exhibit high affinity to uracil base: the central ion is coordinated to deprotonated N(3), and the secondary amino groups of the azacrown are H-bonded to the carbonyl O-atoms of the uracil base [24]. Accordingly, one may tentatively assume that the Zn 2 ion of [Zn,Ni-1] 4 binds to deprotonated N(3) of the 5'-linked uridine, while the Ni 2 ion interacts with the phosphate group and provides the aqua ligand that serves as an intracomplex general acid protonating the departing 5'-oxy anion concerted with the bond cleavage (Scheme 2).…”

mentioning

confidence: 99%

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

Wang

Mikkola²,

Lönnberg³

2004

Chemistry & Biodiversity

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The ability of bimetallic homo- and heteronuclear complexes of two spiro-linked ligands, viz. a biazacrown (i.e., 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane (1)) and an azacrown-crown ether (i.e., 14,17,20,23,26-pentaoxa-2,6,10-triaza-spiro[11.15]heptacosane (2)), to promote the cleavage of the phosphoester linkage of dinucleoside 3',5'-phosphates and the phosphoric anhydride bridge of dinucleoside 5',5'-triphosphates was studied. In both reactions, the bimetallic homonuclear Cu2+ and Zn2+ complexes were better catalysts than their monometallic counterparts. The acceleration was two- to five-fold with the phosphoester cleavage and 3- to 20-fold with the phosphoric anhydride cleavage. Interestingly, the most-efficient catalyst of the phosphoester cleavage was the heterodinuclear Ni2+,Zn2+ complex of 1, the catalytic activity of which was up to 5- and 100-fold that of the homodinuclear Zn2+ and Ni2+ complexes, respectively. Moreover, this cooperative acceleration was observed to depend on the identity of the 5'-linked nucleoside: 3',5'-UpU and 3',5'-ApU were cleaved much faster than 3',5'-UpA, and no cooperative acceleration was observed with 3',5'-ApA. The reaction was second-order in hydroxide ion concentration, suggesting that a double deprotonation took place on going from the initial to the transition state. Evidently, in addition to deprotonation of the attacking 2'-OH group, N(3)H of the 5'-linked uridine was displaced by one of the metal ions of the cleaving agent. With the phosphoric anhydride cleavage, no similar cooperativity of two different metal ions was observed, but the greatest rate-acceleration was achieved with the homodinuclear Cu2+ complexes.

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“…However, supramolecular complexes that operate in aqueous solution are rare (10)(11)(12)(13)(14). While working on molecular recognition of imide functions by zinc(II) complexes of 12-membered tetraamine [Zn 2ϩ -1,4,7,10-tetraazacyclododecane (cyclen)] in aqueous solution (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28), we tested interaction of cyanuric acid (CA) containing C 3 -symmetric three-imide functions with a C 3 -symmetric trinuclear zinc(II)-cyclen, Tris(Zn 2ϩ -cyclen) 1 [Zn 3 L 1 ; L 1 ϭ 1,3,5-Tris(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene]. We have discovered quantitative formation of a 2:3 1-dianionic CA (CA 2Ϫ ) complex at neutral pH that is represented schematically as a trigonal prism 2 ( Fig.…”

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confidence: 99%

New supramolecular trigonal prisms from zinc(II)– 1,4,7,10-tetraazacyclododecane (cyclen) complexes and trithiocyanurate in aqueous solution

Aoki

Zulkefeli

Shiro

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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The multiple bonding between multinuclear zinc(II)-1,4,7,10-tetraazacyclododecane (cyclen, a 12-membered tetraamine) complexes and multidentate ligands is an effective method for constructing supramolecular complexes having well defined and distinct structures in aqueous solution. Herein we present examples of supramolecular D 3h prisms formed by self-assembly of linearly dimeric or trimeric zinc(II)-cyclen complexes with a potentially trianionic C 3 subunit trithiocyanuric acid (TCA 3؊ ), wherein Zn 2؉ OS ؊ or Zn 2؉ ON ؊ coordination bonds and hydrogen bonds are responsible for stability of the multicomponent architectures in aqueous solution at neutral pH.A rtificial supramolecular hosts with stable and well defined structures formed by spontaneous self-assembly of molecular building blocks in organic solvents have shown great potential for inclusion phenomena, molecular recognition, or catalysis (1-12). However, supramolecular complexes that operate in aqueous solution are rare (10)(11)(12)(13)(14). While working on molecular recognition of imide functions by zinc(II) complexes of 12-membered tetraamine [Zn 2ϩ -1,4,7,10-tetraazacyclododecane (cyclen)] in aqueous solution (15-28), we tested interaction of cyanuric acid (CA) containing C 3 -symmetric three-imide functions with a C 3 -symmetric trinuclear zinc(II)-cyclen, Tris(Zn 2ϩ -cyclen) 1 [Zn 3 L 1 ; L 1 ϭ 1,3,5-Tris(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene]. We have discovered quantitative formation of a 2:3 1-dianionic CA (CA 2Ϫ ) complex at neutral pH that is represented schematically as a trigonal prism 2 ( Fig. 1; ref. 29). More interestingly, we accidentally isolated a 4:4 assembly [(Zn 3 L 1 ) 4 -(CA 3Ϫ ) 4 ] from basic aqueous solution. The x-ray crystal structure showed four sets of completely deprotonated CA (CA 3Ϫ ) binding to three Zn 2ϩ -cyclen units from three different Zn 3 L 1 at each N Ϫ rim (29). Its outer shape may be viewed as a cuboctahedron 3a with 12 vertices occupied by Zn 2ϩ and its inner shell as a truncated tetrahedron 4a. It was unfortunate, however, to find that this 4:4 cuboctahedral complex collapsed in neutral H 2 O, possibly because of the extremely high pK a value of the third imide proton of CA. More recently (30), this problem was overcome by replacing CA for TCA, the thioimide functions of which possess lower pK a values [5.12 (pK 1 ), 8.24 (pK 2 ), and 11.69 (pK 3 )] than those of CA [6.85 (pK 1 ), 10.91 (pK 2 ), and Ͼ12 (pK 3 )]. As anticipated, TCA acted as a tridentate donor for three Zn 3 L 1 at neutral pH to yield a similar type of the 4:4 self-assembling supercomplex 3b, in which the deprotonated TCA 3Ϫ in an aromatic 1,3,5-triazine bound to 1 through Zn 2ϩ OS Ϫ (exocyclic) coordination bonds, and thus the 4:4 assembly is a chiral, twisted cuboctahedron. More interestingly, 3b [(Zn 3 L 1 ) 4 -(TCA 3Ϫ ) 4 ] encapsulates various sizematched and hydrophobic guest molecules such as adamantane in its inner cavity, which is represented as a twisted, truncated tetrahedron 4b. Thus, we discovered an approach to de...

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Novel Recognition of Thymine Base in Double-Stranded DNA by Zinc(II)−Macrocyclic Tetraamine Complexes Appended with Aromatic Groups

Cited by 125 publications

References 45 publications

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

New supramolecular trigonal prisms from zinc(II)– 1,4,7,10-tetraazacyclododecane (cyclen) complexes and trithiocyanurate in aqueous solution

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