Electrospray‐Ionization Mass Spectrometry for Screening the Specificity and Stability of Single‐Stranded‐DNA Templated Self‐Assemblies

Abstract

Supramolecular complexes consisting of a single-stranded oligothymine (dTn) as the host template and an array of guest molecules equipped with a complementary diaminotriazine hydrogen-bonding unit have been studied with electrospray-ionization mass spectrometry (ESI-MS). In this hybrid construct, a supramolecular stack of guest molecules is hydrogen bonded to dTn. By changing the hydrogen-bonding motif of the DNA host template or the guest molecules, selective hydrogen bonding was proven. We were able to detect single-stranded-DNA (ssDNA)-guest complexes for strands with lengths of up to 20 bases, in which the highest complex mass detected was 15 kDa; these complexes constitute 20-component self-assembled objects. Gas-phase breakdown experiments on single- and multiple-guest-DNA assemblies gave qualitative information on the fragmentation pathways and the relative complex stabilities. We found that the guest molecules are removed from the template one by one in a highly controlled way. The stabilities of the complexes depend mainly on the molecular weight of the guest molecules, a fact suggesting that the complexes collapse in the gas phase. By mixing two different guests with the ssDNA template, a multicomponent dynamic library can be created. Our results demonstrate that ESI-MS is a powerful tool to analyze supramolecular ssDNA complexes in great detail.

High‐Strength Hydrogels with Integrated Functions of H‐bonding and Thermoresponsive Surface‐Mediated Reverse Transfection and Cell Detachment

“…PNIPAAm components in hydrogels allowed for the attachment and detachment of cultured cells by temperature change without the need for enzymatic treatment 11, 12. It was established that VDT moieties were capable of forming complementary hydrogen bonding with base pairs of nucleic acid 13–15. Thus, it is anticipated that VDT moieties on the surface of HT hydrogels could be hydrogen‐bonded with DNA to realize local gene delivery.…”

Encapsulation of DNA‐Templated Chromophore Assemblies within Virus Protein Nanotubes

“…[5][6][7][8][9][10][11] Viruses have also been used as robust and monodisperse scaffolds for the incorporation of chemical entities both in their inner cavities and on their exterior surfaces. [18][19][20][21] Herein, we describe a unique strategy to assemble chromophoric molecules into very long helical stacks by using both types of biological scaffolds outlined above, that is, DNA to template the chromophore assembly [22][23][24] and the Cowpea chlorotic mottle virus (CCMV) protein to create nanotubes that can hold the DNA-chromophore architectures.CCMV [25,26] is an icosahedral virus with an outer diameter of 28 nm and an inner cavity 18 nm in diameter. [18][19][20][21] Herein, we describe a unique strategy to assemble chromophoric molecules into very long helical stacks by using both types of biological scaffolds outlined above, that is, DNA to template the chromophore assembly [22][23][24] and the Cowpea chlorotic mottle virus (CCMV) protein to create nanotubes that can hold the DNA-chromophore architectures.…”

“…[12][13][14][15][16][17] Filamentous viruses such as the Tobacco mosaic virus and M13 viruses can be used to construct one-dimensional arrays, mainly through the attachment of small building blocks to their surfaces. [18][19][20][21] Herein, we describe a unique strategy to assemble chromophoric molecules into very long helical stacks by using both types of biological scaffolds outlined above, that is, DNA to template the chromophore assembly [22][23][24] and the Cowpea chlorotic mottle virus (CCMV) protein to create nanotubes that can hold the DNA-chromophore architectures.CCMV [25,26] is an icosahedral virus with an outer diameter of 28 nm and an inner cavity 18 nm in diameter. The capsid shell is formed by 180 coat protein (CP) subunits that assemble with T = 3 Caspar-Klug symmetry around a central RNA matrix.…”

Synthesis and 2D self-assembly at the liquid–solid interface of novel H-bonding linear π-conjugated oligomers terminated by uracil and melamine units

“…These were then converted into the bis-melamine derivatives GR2 and GR3 by treatment with dicyanodimide. 31,32 The optical absorption and emission spectra of the dialokoxybenzene derivative GR2 are similar to those of GR1, with two absorption maxima in the UV region (at 308 and 374 nm) and a single emission band peaking at B512 nm (Fig. S10, ESI †) By contrast, the dialkyl derivative GR3 shows only one absorption band peaking at B295 nm and a blue-shifted emission band peaking at B430 nm (Fig.…”