Adsorption of Cytosine and AZA Derivatives of Cytidine on Au Single Crystal Surfaces

Iakhnenko, Marianna; Feyer, Vitaliy; Tsud, Nataliya; Plekan, Oksana; Wang, Feng; Ahmed, Marawan; Slobodyanyuk, Oleksandr; Acres, Robert G.; Matolín, Vladimı́r; Prince, Kevin C.

doi:10.1021/jp404821t

Cited by 17 publications

(12 citation statements)

References 52 publications

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“…4g). Yet, the surface areas of the C (1.27 nm 2 ) and T (1.42 nm 2 ) are smaller than those of A and G. Furthermore, C adsorbs on gold surface with an angle tilted from the surface in solution phase 46 . As a result, many C and T molecules are covered in a hot spot on the AuNU tip that produces higher peak intensity, such as the “Both” spectrum in Fig.…”

Section: Resultsmentioning

confidence: 93%

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Huang¹,

Mousavi²,

Zhao³

et al. 2019

Nat Commun

175

154

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Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

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Section: Resultsmentioning

confidence: 93%

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Huang¹,

Mousavi²,

Zhao³

et al. 2019

Nat Commun

175

154

View full text Add to dashboard Cite

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“…3) manifested a doublet structure assigned as A (83.64 eV) -the surface state and B (83.98 eV) -the bulk state. 38,39 While peak B did not exhibit a shift, peak A shifted by 50 meV upon adsorption of uracil, and 100 meV upon adsorption of 2-thiouracil, with respect to the clean surface. The attenuated signal and shift in peak A suggest a strong adsorbate-substrate interaction.…”

Section: Anchored Monolayersmentioning

confidence: 87%

“…35 Band E was attributed to the 3a 00 (p 3 ) orbital. 39,40 At higher BEs, the spectra become more complex due to the overlapping structures formed by main peaks and satellites. In the BE range of B8-11 eV, where the broad feature F is located, four main transitions appeared: 2a 00 (p 2 ), 14a 0 (s), 13a 0 (s O ), and 1a 00 (p 1 ).…”

Section: Anchored Monolayersmentioning

confidence: 99%

Functionalisation and immobilisation of an Au(110) surface via uracil and 2-thiouracil anchored layer

Plekan¹,

Feyer

Cassidy

et al. 2015

Phys. Chem. Chem. Phys.

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We study surface functionalisation by uracil and 2-thiouracil, and immobilisation of several DNA moieties on functionalised gold surfaces. The combination of X-ray photoelectron and near-edge X-ray absorption spectroscopy allowed us to obtain a complete understanding of complex interfacial processes, starting from adsorption of biomolecules onto the metallic surface and progressing towards a specific surface functionality for interactions with other biologically related adsorbates. Au(110) surfaces were functionalised by deposition of uracil and 2-thiouracil molecules under vacuum conditions, and then tested for their selectivity by immobilisation of different DNA moieties deposited from aqueous solutions. We observed that adenine, adenosine, and RNA polymer (polyadenylic acid) from saturated solutions were immobilized successfully on the 2-thiouracil, but those from dilute (1%) solutions were not. However, cytosine failed to adsorb even from saturated solution. The chemical states of the biologically related adsorbates were investigated and the geometrical orientation of uracil and 2-thiouracil on the Au(110) surface was determined using both spectroscopic techniques.

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“… 81 In another example, deposition of cytosine on gold surfaces was used to assess the orientation of adsorption and ensuing electronic structure. 82 It adsorbed in two different ways: the vacuum deposited sample displayed a flat state where interaction through N3 nitrogen dominated, whereas deposition from an aqueous solution involved interaction through N3 and exocyclic amino group. Such studies provide insights into interesting behavior of nucleobase interaction with surfaces and the possibility of studying medium-range order in amorphous and glassy systems.…”

Section: Surface Modification By Cytosine (C)mentioning

confidence: 99%

Surface modification and pattern formation by nucleobases and their coordination complexes

et al. 2018

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This review presents recent progress concerning the organization of nucleobases on highly ordered pyrolytic graphite (HOPG), mica, Cu(110) and Au(111) surfaces, followed by their studies using microscopy methods such as atomic force microscopy (AFM), scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). Interesting research prospects related to surface patterning by nucleobases, nucleobase-functionalized carbon nanotubes (CNTs) and metal-nucleobase coordination polymers are also discussed, which offer a wide array of functional molecules for advanced applications. Nucleobases and their analogs are able to invoke non-covalent interactions such as p-p stacking and hydrogen bonding, and possess the required framework to coordinate metal ions, giving rise to fascinating supramolecular architectures. The latter could be transferred to conductive substrates, such as HOPG and gold, for assessment by high-end tunneling microscopy under various conditions. Clear understanding of the principles governing nucleobase self-assembly and metal ion complexation, and precise control over generation of functional architectures, might lead to custom assemblies for targeted nanotechnological and nanomaterial applications.

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Adsorption of Cytosine and AZA Derivatives of Cytidine on Au Single Crystal Surfaces

Cited by 17 publications

References 52 publications

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Functionalisation and immobilisation of an Au(110) surface via uracil and 2-thiouracil anchored layer

Surface modification and pattern formation by nucleobases and their coordination complexes

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