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Bad Münster am Stein-Ebernburg, Germany

Seela F.,Center for Nanotechnology | Seela F.,University of Osnabruck | Ingale S.A.,University of Osnabruck
Journal of Organic Chemistry | Year: 2010

(Chemical Equation Presented) The 7-tripropargylamine-7-deaza-2′- deoxyguanosine (2) containing two terminal triple bonds in the side chain was synthesized by the Sonogashira cross-coupling reaction from the corresponding 7-iodo nucleoside 1b. This was protected at the 2-amino group with an iso-butyryl residue, affording the protected intermediate 5. Then, compound 5 was converted to the 5′-O-DMT derivative 6, which on phosphitylation afforded the phosphoramidite 7. This was employed in solid-phase synthesis of a series of oligonucleotides. Tm measurements demonstrate that a covalently attached tripropargylamine side chain increases duplex stability. Both terminal triple bonds of nucleoside 2 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition "double click reaction" with 1-azidomethyl pyrene 3, decorating the side chain with two proximalpyrenes.While themonomeric tripropargylamine nucleosidewith two proximal pyrenes (4) shows strong excimer fluorescence, the ss-oligonucleotide containing 4 does not. This was also observed for ds-oligonucleotides when the complementary strand was unmodified. However, duplex DNA bearing pyrene residues in both strands exhibits strong excimer fluorescence when each strand contains two pyrene residues linked to the tripropargylamine moiety. This pyrene-pyrene interstrand interaction occurs when the pyrene modification sites of the duplex are separated by two base pairs which bring the fluorescent dyes in a proximal position. Molecular modeling indicates that only two out of four pyrene residues are interacting forming the exciplex while the other two do not communicate. © 2009 American Chemical Society.

Renault C.,University of Texas at Austin | Koehne J.,Center for Nanotechnology | Ricco A.J.,NASA | Crooks R.M.,University of Texas at Austin
Langmuir | Year: 2014

In this paper we describe a method for three-dimensional wax patterning of microfluidic paper-based analytical devices (μPADs). The method is rooted in the fundamental details of wax transport in paper and provides a simple way to fabricate complex channel architectures such as hemichannels and fully enclosed channels. We show that three-dimensional μPADs can be fabricated with half as much paper by using hemichannels rather than ordinary open channels. We also provide evidence that fully enclosed channels are efficiently isolated from the exterior environment, decreasing contamination risks, simplifying the handling of the device, and slowing evaporation of solvents. © 2014 American Chemical Society.

Xiong H.,Center for Nanotechnology | Xiong H.,University of Osnabruck | Seela F.,Center for Nanotechnology | Seela F.,University of Osnabruck
Bioconjugate Chemistry | Year: 2012

Heterodimeric interstrand cross-linked DNA was constructed by the "bis-click" reaction carried out on preformed oligonucleotide duplexes with the bis-azide 1. For this, alkynylated 8-aza-7-deazapurine or corresponding 5-substituted pyrimidine nucleosides were synthesized. Cross-linking resulted in chemoselective formation of heterodimeric duplexes while homodimers were suppressed. For product identification, heterodimeric DNA was prepared by the "stepwise click" reaction, while noncomplementary homodimers were accessible by "bis-click" chemistry, unequivocally. Studies on duplex melting of complementary cross-linked duplexes (heterodimers) revealed significantly increased Tm values compared to the non-cross-linked congeners. The stability of this cross-linked DNA depends on the linker length and the site of modification. Cross-linked homodimers hybridized with single-stranded complementary oligonucleotides show much lower stability. (Chemical Equation Presented) © 2012 American Chemical Society.

Jiang D.,Center for Nanotechnology | Jiang D.,Sichuan University | Seela F.,Center for Nanotechnology | Seela F.,University of Osnabruck
Journal of the American Chemical Society | Year: 2010

8-Aza-2′-deoxyisoguanosine (4) is the first fluorescent shape mimic of 2′-deoxyisoguanosine (1a); its fluorescence is stronger in alkaline medium than under neutral conditions. Nucleoside 4, which was synthesized from 8-aza-2′-deoxyguanosine via a 4,6-diamino intermediate after selective deamination, was incorporated in oligodeoxyribonucleotides using phosphoramidite 11. Duplexes with 4·m5iCd(5-methyl-2′- deoxyisocytidine) base pairs are more stable than those incorporating dG-dC pairs, thereby expanding the genetic alphabet by a fluorescent orthogonal base pair. As demonstrated by Tm measurements, the base pair stability decreases in the order m5iCd·4 dG·4 > dT·4 ≥ dC·4 dA·4. A better base pairing selectivity of 4 against the canonical nucleosides dT, dC, dA, and dG is observed than for the degenerated base pairing of 1a. The base pair stability changes can be monitored by nucleobase anion fluorescence sensing. The fluorescence change correlates to the DNA base pair stability. Oligonucleotide 5′-d(T44 4T4) (22), containing short runs of nucleoside 4, forms stable multistranded assemblies (ionophores) with K+ in the central cavity. They are quite stable at elevated temperature but are destroyed at high pH value. © 2010 American Chemical Society.

Ming X.,Center for Nanotechnology | Seela F.,Center for Nanotechnology | Seela F.,University of Osnabruck
Chemistry - A European Journal | Year: 2012

New pyrrolo-dC click adducts (4 and 5) tethered with a 1,2,3-triazole skeleton were synthesized and oligonucleotides were prepared. The triazole system was either directly linked to the pyrrolo moiety (5) or connected via an n-butyl linker (4). The quantum yield of nucleoside 5 (φ=0.32), which is 10 times higher than those of 8-methylpyrrolo-dC (1 b, φ=0.026) or the long linker derivative 4 (φ=0.03), is maintained in oligonucleotides. Compound 5 was used as a nucleobase-discriminating fluorescence sensor in duplex DNA. Excellent mismatch discrimination was observed when 5 was positioned opposite the four canonical nucleosides. Compound 5 has the potential to be used for SNP detection in long DNA targets when conventional techniques such as high resolution melt analysis fail. Nucleobase analogues: Compound 1 (see scheme) was designed to act as a nucleobase-discriminating fluorescence sensor for duplex DNA. Excellent mismatch discrimination was observed when nucleoside 1 was positioned opposite the four canonical nucleosides within the DNA duplex. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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