Electrostatic investigation of metal cation binding to DNA bases and base pairs

Gadre, Shridhar R.; Pundlik, Savita S.; Limaye, Ajay; Rendell, Alistair P.

doi:10.1039/a708372f

Cited by 23 publications

(22 citation statements)

References 11 publications

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“…Although the exact structural transition mechanism is not clear, several factors may play important roles in Eu-valine complex inducing polydA and polyrA self-structured. For example, the favorable electrostatic interaction between the phosphate backbone and the free amino groups of Valine and Eu ions; another important issue concerning interactions between DNA and the Eu-valine complex is the relative energetic preference of the various ion-pair sites in the bases [20,24,25] and the N7 sites of adenine residues have been considered as metal common binding sites since they are exposed and accessible for metal ion binding. The ability of Eu-valine complex which could induce polydA and polyrA self-structured might be duo to the unique structure of the complex and the complex DNA structural selectivity will be further discussed and compared with another europium amino acid complex, europium-L L-aspartic acid complex in the later section.…”

Section: Resultsmentioning

confidence: 99%

“…The synthesis and crystallization of [Eu 8 (L L-Val) 16 (H 2 O) 32 ]-Cl 24 were described in detail in Section 2. Supporting Table 1 shows the details of final refinement of the complex.…”

Section: Resultsmentioning

confidence: 99%

“…We are reporting the newly synthesized europium-L L-valine complex can facilitate the self-structuring of single-stranded nucleic acid polydA and polyrA. 32 ]Cl 24 Different types of amino acids (about 2 mmol) were added as solid individually in an aqueous solution of EuCl 3 (0.1 M, 20 ml) prepared by dissolution of Eu 2 O 3 [20]. The amount of amino acids was slightly less than that of EuCl 3 .…”

Section: Introductionmentioning

confidence: 99%

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PolydA and polyrA self‐structured by a europium and amino acid complex

Zhang

Ren

et al. 2006

FEBS Letters

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Different DNA selectivity was found for the newly synthesized europium-L L-valine complex. Unexpected DNA and RNA selection results showed that europium-L L-valine complex can cause single-stranded polydA and polyrA to self-structure. The sigmoidal melting curve profiles indicate the transition is cooperative, similar to the cooperative melting of a duplex DNA. This is different from another europium amino acid complex, europium-L L-aspartic acid complex which can induce B-Z transition under the low salt condition. To our knowledge, there is no report to show that a metal-amino acid complex can cause the self-structuring of single-stranded DNA and RNA.

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Section: Resultsmentioning

confidence: 99%

“…The synthesis and crystallization of [Eu 8 (L L-Val) 16 (H 2 O) 32 ]-Cl 24 were described in detail in Section 2. Supporting Table 1 shows the details of final refinement of the complex.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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PolydA and polyrA self‐structured by a europium and amino acid complex

Zhang

Ren

et al. 2006

FEBS Letters

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“…Recently, a density functional study of the influence of C5 cytosine substitution in base pairs with guanine has been performed by Moser et al [14]. On the other hand, many studies have analyzed the interaction of different metal cations to G and their influence on base pairing [15][16][17][18][19][20][21][22][23][24]. The variation of dissociation energy and H-bond character of the G-C ?…”

Section: Introductionmentioning

confidence: 99%

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Ebrahimi

Habibi‐Khorassani

Delarami

et al. 2010

J Comput Aided Mol Des

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The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

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“…Ab initio calculations were further used to characterize proton‐transfer processes in base pairs90 and base‐pair radical cations 91–93. QM calculations are now routinely used in studies of various aspects of nucleobase H‐bonding, and other valuable papers can be found in the literature 93–110…”

Section: Introductionmentioning

confidence: 99%

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

Šponer¹,

Leszczyński²,

Hobza³

2001

Biopolymers

427

357

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This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio‐base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C—H … O interbase contacts, sugar–base stacking, intrinsically nonplanar base pairs, out‐of‐plane hydrogen bonds, and amino–acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation–π interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 3–31, 2002; DOI 10.1002/bip.10048

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Electrostatic investigation of metal cation binding to DNA bases and base pairs

Cited by 23 publications

References 11 publications

PolydA and polyrA self‐structured by a europium and amino acid complex

PolydA and polyrA self‐structured by a europium and amino acid complex

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

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