The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers

被引：40

作者：

Leal, Leonardo Andres Espinosa ^{[1
]}

Karpenko, Alexander ^{[1
]}

Swasey, Steven ^{[2
]}

Gwinn, Elisabeth G. ^{[3
]}

Rojas-Cervellera, Victor ^{[4
,5
]}

Rovira, Carme ^{[4
,5
]}

Lopez-Acevedo, Olga ^{[1
]}

机构：

[1] Aalto Univ, Dept Appl Phys, COMP Ctr Excellence, Aalto 00076, Finland

[2] Univ Calif Santa Barbara, Dept Chem & Biochem, Santa Barbara, CA 93106 USA

[3] Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA

[4] Univ Barcelona, Dept Quim Organ, Barcelona 08208, Spain

[5] Univ Barcelona, Inst Quim Teor & Computac IQTCUB, Barcelona 08208, Spain

来源：

JOURNAL OF PHYSICAL CHEMISTRY LETTERS | 2015年 / 6卷 / 20期

基金：

美国国家科学基金会; 芬兰科学院;

关键词：

SILVER(I)-MEDIATED BASE-PAIR; NUCLEIC-ACIDS; FORCE-FIELD; DNA; CLUSTERS; SURFACE;

D O I：

10.1021/acs.jpclett.5b01864

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.

引用

页码：4061 / 4066

页数：6

共 36 条

[1] Atomically Precise Arrays of Fluorescent Silver Clusters: A Modular Approach for Metal Cluster Photonics on DNA Nanostructures [J].

Copp, Stacy M. ;

Schultz, Danielle E. ;

Swasey, Steven ;

Gwinn, Elisabeth G. .

ACS NANO, 2015, 9 (03) :2303-2310

[2] Base Motif Recognition and Design of DNA Templates for Fluorescent Silver Clusters by Machine Learning [J].

Copp, Stacy M. ;

Bogdanov, Petko ;

Debord, Mark ;

Singh, Ambuj ;

Gwinn, Elisabeth .

ADVANCED MATERIALS, 2014, 26 (33) :5839-5845

[3] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

GOULD, IR ;

MERZ, KM ;

FERGUSON, DM ;

SPELLMEYER, DC ;

FOX, T ;

CALDWELL, JW ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197

[4] DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental Theoretical Case Study of the AT Homo-Oligonucleotide [J].

Di Meo, Florent ;

Pedersen, Morten N. ;

Rubio-Magnieto, Jenifer ;

Surin, Mathieu ;

Linares, Mathieu ;

Norman, Patrick .

JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2015, 6 (03) :355-359

[5] Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method [J].

Enkovaara, J. ;

Rostgaard, C. ;

Mortensen, J. J. ;

Chen, J. ;

Dulak, M. ;

Ferrighi, L. ;

Gavnholt, J. ;

Glinsvad, C. ;

Haikola, V. ;

Hansen, H. A. ;

Kristoffersen, H. H. ;

Kuisma, M. ;

Larsen, A. H. ;

Lehtovaara, L. ;

Ljungberg, M. ;

Lopez-Acevedo, O. ;

Moses, P. G. ;

Ojanen, J. ;

Olsen, T. ;

Petzold, V. ;

Romero, N. A. ;

Stausholm-Moller, J. ;

Strange, M. ;

Tritsaris, G. A. ;

Vanin, M. ;

Walter, M. ;

Hammer, B. ;

Hakkinen, H. ;

Madsen, G. K. H. ;

Nieminen, R. M. ;

Norskov, J. K. ;

Puska, M. ;

Rantala, T. T. ;

Schiotz, J. ;

Thygesen, K. S. ;

Jacobsen, K. W. .

JOURNAL OF PHYSICS-CONDENSED MATTER, 2010, 22 (25)

[6] Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C-Ag-C and C-Ag-A Systems [J].

Fortino, Mariagrazia ;

Marino, Tiziana ;

Russo, Nino .

JOURNAL OF PHYSICAL CHEMISTRY A, 2015, 119 (21) :5153-5157

[7]

Frisch M. J., 2016, GAUSSIAN 16

[8] Separable dual-space Gaussian pseudopotentials [J].

Goedecker, S ;

Teter, M ;

Hutter, J .

PHYSICAL REVIEW B, 1996, 54 (03) :1703-1710

[9] Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems [J].

Goedecker, S .

JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (21) :9911-9917

[10] DNA-Protected Silver Clusters for Nanophotonics [J].

Gwinn, Elisabeth ;

Schultz, Danielle ;

Copp, Stacy M. ;

Swasey, Steven .

NANOMATERIALS, 2015, 5 (01) :180-207

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