Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

Marino, Tiziana; Russo, Nino; Toscano, Marirosa; Pavelka, Matěj

doi:10.1039/c1dt11028d

Cited by 21 publications

(21 citation statements)

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“…This value is lower than the BE previously found (42.9 kcal/mol), at almost the same level of theory (B3LYP-D3) but in a gas-phase environment, for the GC naturally occurring nucleobases that incorporate the silver ion. 35 The formation of this kind of WC structure has been observed experimentally also in the case of a silver ion interacting with artificial pyridine and imidazole. 36−38 As far as the (dC−Ag−dC) 2 complex is concerned, the optimized structure depicted in Figure 2 shows a planar geometry on the upper base pair fragment, characterized by Ag−N distances of 2.169 and 2.147 Å with two H-bonds involving the CO and H 2 N groups equal to 3.062 and 3.497 Å.…”

Section: ■ Results and Discussionmentioning

confidence: 92%

Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C–Ag–C and C–Ag–A Systems

2014

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Silver-mediated base pairs applied to DNA represent a new biomacromolecular nanomaterial useful for generating nanodevices as ion sensors. Reported herein is a full quantum chemical study devoted to give further knowledge on the electronic and energetic properties of C-Ag-C and mixed C-Ag-A mismatched base pairs. The B3LYP functional in conjunction with the dispersion effects (D3) has been applied. Single-point calculations have been also performed by using the M06-L functional. The investigation of their behavior has been extended to the duplex DNA modeled by the (dC-Ag-dC)2 and (dC-Ag-dA)2 more complex systems. The solvent effect has been taken into account by the conductor-like screening model, COSMO. In the case of mixed C-Ag-A and (dC-Ag-dA)2 systems, both the Watson-Crick and Hoogsteen arrangements have been taken into account. Results show that for (dC-Ag-dA)2 systems, the binding energies are almost double that of the corresponding values of C-Ag-A ones.

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Section: ■ Results and Discussionmentioning

confidence: 92%

Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C–Ag–C and C–Ag–A Systems

2014

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“…The available results only consider the lowest energetic tautomers [69,99]. Therefore, our results in energetics and stabilization can not be directly compared.…”

Section: A(n1)-t(o4) > A(n1)-t(o2) > A(n6)-t(o4) > A(n3) > A(n7)mentioning

confidence: 85%

“…Here, the authors studied the binding sites for cationic silver in adenine. In the following years, several computational studies appeared; these mainly focused on DNA/RNA-gold/silver hybrid structure properties by fixing the charge state (neutral, cationic, or anionic) [64][65][66] or by considering a reduced number of nucleobases [67,68] (or base pairs) [69] in gas phase. In recent years, with the need to understand the aforementioned phenomena in more complex systems, the investigations in hybrid DNA/ RNA metallic nanoclusters (MNCs) have opened new fields of research such as the interaction with large clusters [70,71], expanded nucleobases [72][73][74], influence of solvent [75], importance of the sugar backbone [76,77], among others.…”

Section: Metal-dna Interaction: Historical Pathmentioning

confidence: 99%

“…Even though other methodologies have been used: Mulliken analysis [52,68] or natural bond orbital (NBO) analysis [53,69,110], in this work, we used Brought to you by | New York University Bobst Library Technical Services Authenticated Download Date | 6/8/15 2:30 PM the Bader charge population analysis method [81], previously used in the description of the charge transfer in the interaction of silver neutral clusters with nucleobases [64]. In our particular methodology, our results are free of the basis-set dependency issues of other methods [110].…”

Section: Bader Chargementioning

confidence: 99%

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On the interaction between gold and silver metal atoms and DNA/RNA nucleobases – a comprehensive computational study of ground state properties

Leal

Lopez-Acevedo

2015

Nanotechnology Reviews

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On the interaction between gold and silver metal atoms and DNA/RNA nucleobasesa comprehensive computational study of ground state properties Abstract: The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an exhaustive study of the ground state electronic properties of DNA/RNA nucleobases interacting with gold and silver atoms at three charge states: neutral, cationic, and anionic. We describe the nature of the stability and electronic properties in each hybrid metallic structure. In addition to the metal interacting with the five isolated nucleobases, we included their respective DNA-WC base pairs and one case with the protonated sugarphosphate backbone. As a general trend, we discerned that the energetic ordering of isomers follows simple electrostatic rules as expected from previous studies. Also, we found that although the metal localizes almost all of the extra charge in the anionic system, a donation of charge is shared almost equally in the cationic system. Furthermore, the frontier orbitals of the cationic system tend to have more effects from the pairing and inclusion of the backbone than the anionic system. Finally, the electronic gap varies greatly among all of the considered structures and could be further used as a fingerprint when searching DNA-metal hybrid structures. -Acevedo: DNA/RNA nucleobases interacting with gold and silver atoms 191 University, Finland. Her research interest focuses on the quantum modeling of hybrid soft-nano systems and the development of computational methods for multi-scale simulations. She obtained her Bachelor's and Master's degrees in physics from the University of Strasbourg, France. In 2006, she obtained a PhD in theoretical physics working on quantum algorithmics from the University of Cergy-Pontoise, France. Her postdoctoral experience includes stays at

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“…The silver (I) leaching from the electrodes would bind to phosphate groups of the RNA backbone or to electron donor atoms on nucleobases [59], [60]. This binding forms ternary complexes between Ag (I) and nucleotides, cytosine and guanine [59], [60]. As a result of this binding, there would be a reduction in reverse-transcription of the mRNA.…”

Section: Resultsmentioning

confidence: 99%

RNase A Does Not Translocate the Alpha-Hemolysin Pore

Krasniqi

Lee

2014

PLoS ONE

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The application of nanopore sensing utilizing the α-hemolysin pore to probe proteins at single-molecule resolution has expanded rapidly. In some studies protein translocation through the α-hemolysin has been reported. However, there is no direct evidence, as yet, that proteins can translocate the α-hemolysin pore. The biggest challenge to obtaining direct evidence is the lack of a highly sensitive assay to detect very low numbers of protein molecules. Furthermore, if an activity based assay is applied then the proteins translocating by unfolding should refold back to an active confirmation for the assay technique to work. To overcome these challenges we selected a model enzyme, ribonuclease A, that readily refolds to an active conformation even after unfolding it with denaturants. In addition we have developed a highly sensitive reverse transcription polymerase chain reaction based activity assay for ribonuclease A. Initially, ribonuclease A, a protein with a positive net charge and dimensions larger than the smallest diameter of the pore, was subjected to nanopore analysis under different experimental conditions. Surprisingly, although the protein was added to the cis chamber (grounded) and a positive potential was applied, the interaction of ribonuclease A with α-hemolysin pore induced small and large blockade events in the presence and the absence of a reducing and/or denaturing agent. Upon measuring the zeta potential, it was found that the protein undergoes a charge reversal under the experimental conditions used for nanopore sensing. From the investigation of the effect of voltage on the interaction of ribonuclease A with the α-hemolysin pore, it was impossible to conclude if the events observed were translocations. However, upon testing for ribonuclease A activity on the trans chamber it was found that ribonuclease A does not translocate the α-hemolysin pore.

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Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

Cited by 21 publications

References 74 publications

Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C–Ag–C and C–Ag–A Systems

Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C–Ag–C and C–Ag–A Systems

On the interaction between gold and silver metal atoms and DNA/RNA nucleobases – a comprehensive computational study of ground state properties

RNase A Does Not Translocate the Alpha-Hemolysin Pore

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