Reactions of Buffers in Cyanogen Bromide-Induced Ligations

Vogel, Heike; Gerlach, Claudia; Richert, Clemens

doi:10.1080/15257770.2012.744036

Cited by 10 publications

(11 citation statements)

References 29 publications

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“…Control reactions confirmed that the reactivity of aminoterminal strands is higher than that for strands with a 3′‐hydroxy group. When the ligation shown in Figure A was performed with a version of strand 1 that had a conventional deoxynucleoside at its 3′ terminus, incomplete conversion of the starting materials was found, even when the reaction time was extended from 3 to 24 h. This was also true for ligations with cyanogen bromide as the condensing agent, as well as for reactions induced by EDC . In all cases, no ligation product was detected in the absence of a template (Scheme S1 and Fig‐ ures S13–S16).…”

Section: Resultsmentioning

confidence: 88%

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

et al. 2016

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The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.

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Section: Resultsmentioning

confidence: 88%

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

et al. 2016

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“…The yield of enzyme-free chain extension is also dependent on the nucleophile found at the primer terminus. For straight DNA primers, no broadly applicable method exists for extension ( 21 ), but RNA primers with their terminal 2′/3′-diol are sufficiently reactive for extension to occur when allowed to react with monomers activated by one of the methods producing nucleotides with heterocyclic leaving groups. Still, the low reactivity of the ribose terminus often causes hydrolysis to compete successfully with extension, resulting in significant concentrations of free nucleotides that act as competitive inhibitors ( 22 ).…”

Section: Introductionmentioning

confidence: 99%

The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA

2016

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The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M−1 h−1. For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.

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“…Its buffering pH range (6.40 < pH < 7.80) makes BES suitable for biological studies. Recent studies describe the use of BES for this purpose [11][12][13][14][15]. There is evidence that BES complexes with Cu(II) [16]; however, this study only describes formation of CuL species.…”

Section: Introductionmentioning

confidence: 98%

Graphic data analysis and complex formation curves as modeling and optimization tools for characterization of Cu–(buffer)_x–(OH)_y systems involving BTP or BES in aqueous solution

Sadeghi

Ferreira

Vandenbogaerde

et al. 2015

Journal of Coordination Chemistry

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& Helena M.V.M. Soares (2015) Graphic data analysis and complex formation curves as modeling and optimization tools for characterization of Cu-(buffer) x -(OH) y systems involving BTP or BES in aqueous solution, Journal of Coordination Chemistry, 68:5, 777-793, Bis-tris propane or 1,3-bis(tris(hydroxymethyl)methylamino)propane (BTP) and N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES) are pH buffers which have been used in biological experiments. To characterize BTP and BES complexation properties with Cu(II), glass electrode potentiometry and direct current polarography were conducted using total ligand to total copper concentration ratios of different orders of magnitude and pH values at 25°C and 0.1 M KNO 3 ionic strength. The graphic analysis is a very powerful tool in the prediction and refinement operations of both systems. For the Cu-BTP system, six species were found to describe totally the system, CuL, CuL(OH), CuL(OH) 2 , CuL 2 , CuL 2 (OH), and CuL 2 (OH) 2 , with respective stability constants determined as 10.7 ± 0.1, 19.4 ± 0.4, 24.3 ± 0.2, 18.8 ± 0.1, 24.7 ± 0.2, and 29.8 ± 0.2. CuL 2 , CuL 2 (OH), and CuL 2 (OH) 2 were described for the first time. In the case of the Cu-BES system, complexation behavior was described by the model constituted by CuL, CuL(OH), and CuL(OH) 2 , the latter two described for the first time, with respective stability constants determined as 3.24 ± 0.08, 10.9 ± 0.2, and 16.0 ± 0.3, respectively. UV-vis results allowed us to establish coordination modes for the Cu-BTP and Cu-BES complexes.

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Reactions of Buffers in Cyanogen Bromide-Induced Ligations

Cited by 10 publications

References 29 publications

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA

Graphic data analysis and complex formation curves as modeling and optimization tools for characterization of Cu–(buffer)_x–(OH)_y systems involving BTP or BES in aqueous solution

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Reactions of Buffers in Cyanogen Bromide-Induced Ligations

Cited by 10 publications

References 29 publications

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures

The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA

Graphic data analysis and complex formation curves as modeling and optimization tools for characterization of Cu–(buffer)x–(OH)y systems involving BTP or BES in aqueous solution

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Graphic data analysis and complex formation curves as modeling and optimization tools for characterization of Cu–(buffer)_x–(OH)_y systems involving BTP or BES in aqueous solution