Assembly of Two‐Dimensional DNA Crystals Carrying N4‐[2‐(tert‐Butyldisulfanyl)ethyl]cytosine Residues

Garibotti, Alejandra V.; Sisquella, Xavier; Martínez, Elena; Eritja, Ramón

doi:10.1002/hlca.200900186

Cited by 8 publications

(13 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the presence of thiol-modified oligonucleotides within the DNA origami stamp provides additional anchor points, and extra stability of the DNA structure to remain on the surface in comparison with non-modified DNA origami ( Figure S2); result that is in agreement with previous work in our laboratory. [17] The DNA origami stamp was then denatured in 0.05-0.1 M NaOH allowing the removal of the DNA origami frame (i.e. the staple strands and the M13 scaffold).…”

mentioning

confidence: 99%

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

Self Cite

View full text Add to dashboard Cite

The programmability [1] and self-assembly properties of DNA provides means of precise organization of matter at the nanoscale. [2] DNA origami allows the folding of DNA into twodimensional [3] and three-dimensional [4] structures, and has been used to organize biomolecules, [2b, e, 5] nanophotonic [2a, c, f, 6] and electronic [7] components with a resolution of 6 nm / pixel. [8] Two-dimensional DNA origami has been also used as a platform to organize other chemical [9] species that can then be placed on technologically relevant substrates. [2c, 10] Nevertheless, these approaches have only used the DNA nanostructure to hold the chemical species on the surface and, to the best of our knowledge, have never been utilized to immobilize nucleic acids patterns on surfaces with sub-10 nm resolution providing an enable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 2 platform for potential applications such as multiplexed biochemical assays. [11] to the creation of metasurfaces [12] with potentially reconfigurable features. Revised ManuscriptHerein we report on the use of a two-dimensional DNA origami as a template to covalently attach DNA with a pre-programmed pattern on a surface (see Scheme 1). The method utilizes the incorporation of modified staple strands in programmed positions of the DNA origami (DNA origami stamp), acting as DNA ink. Once the DNA origami is immobilized on the surface, the modified staples can react with the surface creating a defined DNA pattern (Stamping step). The pattern can then be exposed upon denaturation of the DNA origami stamp (Unmasking step), allowing the non-bound staples to be rinsed off of the surface. As a proof-of-principle of this methodology, we have created a linear pattern of thiolmodified DNA ink on gold surfaces. The formation of the linear pattern was revealed by the successful formation of bead-on-a-string-like structures (here named "chains" for simplicity) composed of gold nanoparticles conjugated with thiol-oligonucleotides (OGNP) that are hybridized to the DNA ink pattern (Development step). The linear pattern provided a direct evidence of the stamping process and was chosen as a simple geometry that can be statistically analysed in our experimental setup. Montecarlo Simulations have been used for better understanding of our statistical results and to determine key elements governing the process that can be used for future optimization of pattern information transfer with DNA origami stamp methodology. Furthermore, we have studied the development of more complex patterns using Montecarlo Simulations.We demonstrate that our approach can be employed to form DNA patterns with sub-10 nm resolution to flat gold surfaces, an unsolved goal to date. This methodology can thus be extended to other surfaces utilizing different covalent strategies. [10b, 13] M...

show abstract

mentioning

confidence: 99%

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…The excellent molecular recognition properties of synthetic oligonucleotides are being exploited for the rational construction of 2-D DNA lattices with well defined structures [ 23 , 24 ]. A step ahead is to incorporate chemical groups at specific sites of 2-D DNA lattices to direct the deposition of specific molecules or nanomaterials [ 25 ] or to direct deposition to surfaces [ 17 ]. In this article we have described the synthesis of the 2’-deoxy- N 4 -[2-(t-butyldisulfanyl)ethyl]-5-methylcytidine phosphoramidite building block.…”

Section: Discussionmentioning

confidence: 99%

“…We are interested in the incorporation of thiol groups into two-dimensional DNA lattices [ 17 ] by introducing a single thiol group per DNA unit. Thiol groups have a strong affinity for gold surfaces and they can be used for the introduction of peptides, proteins and a large number of molecules functionalized with maleimido- or bromo- or iodo-acetyl groups.…”

Section: Introductionmentioning

confidence: 99%

“…Thiol groups have a strong affinity for gold surfaces and they can be used for the introduction of peptides, proteins and a large number of molecules functionalized with maleimido- or bromo- or iodo-acetyl groups. Previous work has demonstrated that bidimensional DNA arrays carrying N 4 -[2-(t-butyldisulfanyl)ethyl]cytosine residues at the apex of the topological markers can be deposited on gold surfaces [ 17 ]. The starting material for the synthesis of the 2’-deoxycytidine phosphoramidite building block carrying the N 4 -( t -butyldisulfanyl)ethyl group was 2’-deoxyuridine [ 15 ], which is expensive and the synthetic route is long and tedious.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Solid-Phase Synthesis of Oligodeoxynucleotides Containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine Moieties

2010

View full text Add to dashboard Cite

An efficient route for the synthesis of the phosphoramidite derivative of 5-methylcytosine bearing a tert-butylsulfanyl group protected thiol is described. This building block is used for the preparation of oligonucleotides carrying a thiol group at the nucleobase at the internal position of a DNA sequence. The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence.

show abstract

“…138 The exocyclic amino group has been used to attach fluorophores, 139 for the introduction of ethanethiol (via a disulfide bond) such that once the thiol is reduced it is capable of forming disulfide bonds between oligonucleotide duplexes such that DNA arrays are formed (see section 3.6). 140 Addition of bulky substituents such as a crown ether onto the exocyclic amine has been used as a method for stabilising 2'-O-methyl-RNA with short RNA targets. 141 The modified cytosines are incorporated onto each terminus of the probe and the bulky residues can act as an endcap with short RNA's, i.e.…”

Section: Oligonucleotide Synthesismentioning

confidence: 99%

Nucleotides and nucleic acids; oligo- and polynucleotides

Loakes¹

Organophosphorus Chemistry

View full text Add to dashboard Cite

Assembly of Two‐Dimensional DNA Crystals Carrying N⁴‐[2‐(tert‐Butyldisulfanyl)ethyl]cytosine Residues

Abstract: DNA lattices carrying two cytosine residues bearing the N 4 - [(t-butyldithio)ethyl] group at the apex of hairpin topological markers are prepared for first time. We show that these residues are important for the deposition of DNA lattices on gold surfaces.--

Cited by 8 publications

References 19 publications

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

Solid-Phase Synthesis of Oligodeoxynucleotides Containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine Moieties

Nucleotides and nucleic acids; oligo- and polynucleotides

Contact Info

Product

Resources

About