Co-reporter:Xiao Wang;Dr. Ruojie Sha;Dr. Martin Kristiansen;Carina Hernez;Yudong Hao; Chengde Mao; James W. Canary; Nadrian C. Seeman
Angewandte Chemie 2017 Volume 129(Issue 23) pp:6545-6548
Publication Date(Web):2017/06/01
DOI:10.1002/ange.201700462
AbstractA 3D array of organic semiconductors was assembled using a DNA scaffold. An octameric aniline molecule (“octaniline”) was incorporated into a DNA building block based on a dimeric tensegrity triangle. The construct self-assembled to form a 3D crystal. Reversible redox conversion between the pernigraniline and leucoemeraldine states of the octaniline is retained in the crystal. Protonic doping gave emeraldine salt at pH 5, corresponding to the conductive form of polyaniline. Redox cycling within the crystal was visualized by color changes and Raman microscopy. The ease of conversion between the octaniline states suggests that it is a viable electronic switch within a unique 3D structure.
Co-reporter:Xiao Wang;Dr. Ruojie Sha;Dr. Martin Kristiansen;Carina Hernez;Yudong Hao; Chengde Mao; James W. Canary; Nadrian C. Seeman
Angewandte Chemie International Edition 2017 Volume 56(Issue 23) pp:6445-6448
Publication Date(Web):2017/06/01
DOI:10.1002/anie.201700462
AbstractA 3D array of organic semiconductors was assembled using a DNA scaffold. An octameric aniline molecule (“octaniline”) was incorporated into a DNA building block based on a dimeric tensegrity triangle. The construct self-assembled to form a 3D crystal. Reversible redox conversion between the pernigraniline and leucoemeraldine states of the octaniline is retained in the crystal. Protonic doping gave emeraldine salt at pH 5, corresponding to the conductive form of polyaniline. Redox cycling within the crystal was visualized by color changes and Raman microscopy. The ease of conversion between the octaniline states suggests that it is a viable electronic switch within a unique 3D structure.
Co-reporter:Dadong Li, Xiaojian Wang, Fubo Shi, Ruojie Sha, Nadrian C. Seeman and James W. Canary
Organic & Biomolecular Chemistry 2014 vol. 12(Issue 44) pp:8823-8827
Publication Date(Web):06 Oct 2014
DOI:10.1039/C4OB01552E
We describe two DNA-templated ligation strategies: native chemical ligation (NCL), and thiol-disulfide exchange. Both systems result in successful ligation in the presence of a DNA template. The stability of the product from the NCL reaction relies on exogenous thiol, while the thiol-disulfide reaction proceeds in a catalyst-free manner.
Co-reporter:Yuning Zhang;Pei Che Soon; Alexej Jerschow; James W. Canary
Angewandte Chemie International Edition 2014 Volume 53( Issue 13) pp:3396-3399
Publication Date(Web):
DOI:10.1002/anie.201310284
Abstract
Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) have become important techniques in many research areas. One major limitation is the relatively low sensitivity of these methods, which recently has been addressed by hyperpolarization. However, once hyperpolarization is imparted on a molecule, the magnetization typically decays within relatively short times. Singlet states are well isolated from the environment, such that they acquire long lifetimes. We describe herein a model reaction for read-out of a hyperpolarized long-lived state in dimethyl maleate using thiol conjugate addition. This type of reaction could lend itself to monitoring oxidative stress or hypoxia by sensitive detection of thiols. Similar reactions could be used in biosensors or assays that exploit molecular switching. Singlet lifetimes of about 4.7 min for 1H spins in [D4]MeOH are seen in this system.
Co-reporter:Miao Ye, Johan Guillaume, Yu Liu, Ruojie Sha, Risheng Wang, Nadrian C. Seeman and James W. Canary
Chemical Science 2013 vol. 4(Issue 3) pp:1319-1329
Publication Date(Web):25 Jan 2013
DOI:10.1039/C2SC21775A
We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2′-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.
Co-reporter:Maksim Royzen, James W. Canary
Polyhedron 2013 Volume 58() pp:85-91
Publication Date(Web):13 July 2013
DOI:10.1016/j.poly.2012.11.027
Tripodal ligands containing 8-hydroxyquinoline moieties have been reported with strong binding but perplexing fluorescence properties. Herein we describe the synthesis, photophysical properties and structural characterization of three 8-hydroxyquinoline-based fluorescent Zn(II) probes. Incorporation of the chromophore into a tripodal scaffold resulted in femtomolar sensitivity to the analyte. All three ligands were determined to bind Zn(II) in a 1:1 metal–ligand stoichiometry. Strong zinc affinity was complemented by more than 10-fold fluorescence turn-on. An X-ray crystallographic study revealed very different ligand geometries in the zinc complexes that may influence their spectroscopic behavior.Graphical abstractHerein we describe the synthesis, photophysical properties and structural characterization of three 8-hydroxyquinoline-based fluorescent Zn(II) probes. Structural parameters of the Zn(II) complexes affect fluorescence quantum yields.Highlights► Tripodal ligands with femtomolar zinc affinity. ► X-ray crystal structures of zinc complexes of the 8-hydroxyquinoline-based tripodal ligands. ► Photophysical properties of the 8-hydroxyquinoline-based tripodal ligands and their zinc complexes.
Co-reporter:Shahab Mortezaei ; Noelle R. Catarineu
Journal of the American Chemical Society 2012 Volume 134(Issue 19) pp:8054-8057
Publication Date(Web):May 2, 2012
DOI:10.1021/ja302283s
A redox-reconfigurable catalyst derived from l-methionine and incorporating catalytic urea groups has been synthesized. This copper complex catalyzes the enantioselective addition of diethyl malonate to trans-β-nitrostyrene. Either enantiomer of the product can be predetermined by selection of the oxidation state of the copper ion. Enantiomeric excesses of up to 72% (S) and 70% (R) were obtained in acetonitrile. The ability of the catalyst to invert enantiomeric preference was reproduced with several different solvents and bases. Facile interconversion between the Cu2+ and Cu+ redox states allowed easy access to both active helical forms of the complex and, therefore, dial-in enantioselectivity.
Co-reporter:Yu Liu, Risheng Wang, Liang Ding, Roujie Sha, Nadrian C. Seeman and James W. Canary
Chemical Science 2012 vol. 3(Issue 6) pp:1930-1937
Publication Date(Web):08 Mar 2012
DOI:10.1039/C2SC20129A
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis; coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2′-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
Co-reporter:Dr. Francesca Gruppi;Xiang Xu;Boyang Zhang;Dr. Joel A. Tang; Alexej Jerschow; James W. Canary
Angewandte Chemie International Edition 2012 Volume 51( Issue 47) pp:11787-11790
Publication Date(Web):
DOI:10.1002/anie.201204403
Co-reporter:Joel A. Tang, Francesca Gruppi, Roman Fleysher, Daniel K. Sodickson, James W. Canary and Alexej Jerschow
Chemical Communications 2011 vol. 47(Issue 3) pp:958-960
Publication Date(Web):15 Nov 2010
DOI:10.1039/C0CC03421E
A system that provides a sustained hyperpolarized 1H NMR signal in an aqueous medium is reported. The enhanced signal lasts much longer than typical 1H T1 values, uncovering new possibilities for implementing hyperpolarized 1H NMR/MRI experiments or performing kinetics studies that would not otherwise be detectable.
Co-reporter:Jian Liang
Chirality 2011 Volume 23( Issue 1) pp:24-33
Publication Date(Web):
DOI:10.1002/chir.20833
Abstract
A tetradentate tripodal ligand containing a chiral center and three different coordinating arms was designed and synthesized. Its complexation properties with ZnII and CuI were studied by NMR and optical spectroscopy. NMR experiments demonstrated the formation of two diastereomers, indicating the stabilization of the central tertiary amine configuration by metal coordination. The inversion of pyramidalization of the central tertiary amine of the ligand was found to be highly dependent upon metal ion, solvent, and temperature. Dynamic NMR measurements were used to estimate the energy of activation required for nitrogen atom inversion. Finally, absorption and circular dichroism measurements confirmed the expectation that metal complexes of the ligand gave rise to circular dichroism but that such spectra were not characterized by exciton-coupling, in contrast to previously described ligands containing two identical arms with strong chromophores. Chirality 2011. © 2010 Wiley-Liss, Inc.
Co-reporter:Jian Liang ; Jing Zhang ; Lei Zhu ; Alexander Duarandin ; Victor G. Young; ; Jr.; Nicholas Geacintov
Inorganic Chemistry 2009 Volume 48(Issue 23) pp:11196-11208
Publication Date(Web):October 30, 2009
DOI:10.1021/ic901662z
Metal complexes of tris((6-phenyl-2-pyridyl)methyl)amine (2) have hydrophobic cavities that potentially accommodate small molecules. However, the utility of this attractive motif has been hampered by the poor solubility of such complexes in many common solvents. In this study, two tripodal ligands (3, tris-[6-(3,4,5-trimethoxy-phenyl)-pyridin-2-ylmethyl]-amine, and 4, tris((6-(3,4,5-tris(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)phenyl)pyridin-2-yl)methyl)amine) derived from 2 were prepared with enhanced solubility in organic and aqueous solvents. The X-ray crystallographic analyses of selected ligands and complexes revealed that the hydrophobic cavities inside the zinc complexes were retained after derivatization. Fluorescence, nuclear magnetic resonance (NMR), and potentiometric titration studies, which were enabled by the improved solubility, were performed to investigate the binding properties of the soluble ligands (3 and 4) with metal ions such as Zn2+ and Cu2+. When saturating quantities of Zn2+ ions are added to ligand 3 in acetonitrile, the fluorescence emission maximum exhibits a pronounced red shift of ∼80 nm (from 376 to 457 nm) and is enhanced by a factor of >100 when measured at 520 nm. The fluorescence properties of the Zn2+ ion-coordinated ligands in the Zn(3) complex are consistent with a charge-transfer character in the excited state, with possible contributions from a planarization of the pyridyl-trimethoxyphenyl groups in the excited state, and from excitonic interactions.
Co-reporter:Debasis Das;Zhaohua Dai;Andrea Holmes
Chirality 2008 Volume 20( Issue 3-4) pp:585-591
Publication Date(Web):
DOI:10.1002/chir.20519
Abstract
N,N-Bis(arylmethyl)methionine derivatives are chiral ligands whose complexes with metal ions may show molecular helicity that can be modulated by defined structural processes. It was shown previously that exciton-coupled circular dichroism (ECCD) spectral amplitude could be modulated by one-electron copper redox chemistry in copper complexes of these ligands. Here we describe the further development of novel systems that show conformational changes resulting in the inversion of exciton chirality. The phenomenon was probed in a N,N-bis(arylmethyl)methionine derivative containing quinoline/pyridine moieties and a methionine carboxylate moiety. The sign of the ECCD of the complex formed between this ligand and CoCl2 is negative, which suggests that the deprotonated carboxylate oxygen coordinates to the metal, but the sulfur atom does not. The sign of the ECCD inverts to positive upon addition of ascorbic acid, which can be turned back to negative upon further treatment with persulfate. X-ray quality crystals of three cobalt complexes and one nickel complex were obtained. The ascorbate-treated cobalt complex of the ligand and the same ligand with nickel, however, vary from the behavior expected from their X-ray crystal structures. It is clear that the solution and crystallographic structures of these complexes differ in several cases. Chirality, 2008. © 2008 Wiley-Liss, Inc.
Co-reporter:Yu Liu;Risheng Wang;Liang Ding Dr.;Ruojie Sha Dr.;Philip S. Lukeman Dr. Dr.;Nadrian C. Seeman Dr.
ChemBioChem 2008 Volume 9( Issue 10) pp:1641-1648
Publication Date(Web):
DOI:10.1002/cbic.200800032
Abstract
The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1–5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 °C increase in the thermal transition temperature (Tm) for five linkages) and RNA (around 15 °C increase in Tm for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2′-position of ribose and recovery of stability upon linkage of the side chains.
Co-reporter:Zhaohua Dai;Xiaodong Xu
Chirality 2005 Volume 17(Issue S1) pp:S227-S233
Publication Date(Web):10 JUN 2005
DOI:10.1002/chir.20130
Chiral rigidified piperidine and quinuclidine analogues of tris(2-pyridylmethyl)amine (TPA) derivatives were examined for asymmetric recognition of amino compounds by cyclic voltammetry and fluorescence. A Cu(II) complex of a piperidine analogue discriminated the enantiomers of some chiral amines and amino alcohols, giving differences in electrochemical potential for diastereomeric complexes. Protonated piperidine and quinuclidine analogues were able to differentiate the two enantiomers of certain amino alcohols by fluorescence spectroscopy. The quinuclidine analogue gave a 3-fold difference in response to the two enantiomers of phenyglycinol. Chirality 17:S227–S233, 2005. © 2005 Wiley-Liss, Inc.
Co-reporter:Andrea E. Holmes;Jing Zhang;Neil R. Brooks;Ry S. Rarig;Jon Zubieta;Akanksha Sharma
Chirality 2003 Volume 15(Issue 2) pp:180-189
Publication Date(Web):8 JAN 2003
DOI:10.1002/chir.10158
We report here a sensitive method for the determination of the absolute configurations of primary amines using exciton-coupled circular dichroism (ECCD). The method works on a microgram scale by derivatization of chiral amines with quinoline chromophores. Complexation of the chiral ligands with metal ion fixes the geometry of the chromophores, resulting in a twist that is governed by the asymmetric carbon configuration and steric environment of the amine. The absolute configurations of the primary amines can be interpreted from the couplets of the ECCD spectra of the derivatized complexes. Crystal structures, 2D NMR studies, and semiempirical calculations provide structural evidence for our model. Chirality 15:180–189, 2003. © 2003 Wiley-Liss, Inc.
Co-reporter:Zhaohua Dai, Xiaodong Xu and James W. Canary
Chemical Communications 2002 (Issue 13) pp:1414-1415
Publication Date(Web):05 Jun 2002
DOI:10.1039/B111259G
Stereochemistry plays a major role in the selectivity toward zinc ion over copper(II) of some tripodal ligands with a central piperidine scaffold, one of which acts as a fluorescent zinc sensor with nanomolar sensitivity.
Co-reporter:James W. Canary
Advanced Synthesis & Catalysis 2002 Volume 344(Issue 5) pp:
Publication Date(Web):2 AUG 2002
DOI:10.1002/1615-4169(200207)344:5<563::AID-ADSC563>3.0.CO;2-M
Co-reporter:Steffen Zahn;Andrea E. Holmes
Chirality 2002 Volume 14(Issue 6) pp:471-477
Publication Date(Web):21 MAY 2002
DOI:10.1002/chir.10079
We report a method to determine the absolute configuration of α-amino acids by exciton coupled circular dichroism (ECCD). Naturally occurring amino acids were successfully derivatized with 2-bromomethylquinoline. Complexation of these conformationally flexible ligands with Cu(II) salts yielded defined propeller-like structures. The direction of the twist (i.e., the relative orientation of the chromophores to each other) is governed by the asymmetric amino acid carbon center. The transition moments of the chromophores couple and yield a bisignate circular dichroism spectrum, the sign of which corresponds to the absolute configuration of the chiral center of the amino acid. Enantiomeric excess (e.e.) of amino acid derivatives is linearly related to the differential extinction coefficient Δε and can be assessed easily utilizing a standard curve. This efficient, sensitive technique requires low analyte concentrations, offers several advantages over established methods, and could be applied in medicinal, pharmaceutical, or chemical retail and manufacturing industry. Chirality 14:471–477, 2002. © 2002 Wiley-Liss, Inc.
Co-reporter:Xiaodong Xu Dr.;Kevin J. Maresca Dr.;Debasis Das Dr.;Steffen Zahn Dr.;Jon Zubieta
Chemistry - A European Journal 2002 Volume 8(Issue 24) pp:
Publication Date(Web):13 DEC 2002
DOI:10.1002/1521-3765(20021216)8:24<5679::AID-CHEM5679>3.0.CO;2-A
The ligand in [Cu(6)CH3CN](ClO4)2 adopts two conformations that may be described as “pseudo-enantiomers” in that they possess approximately mirror-image molecular helicity, although they differ in the orientation of a single methyl substituent. The two conformations differ in energy as judged by analogy to other compounds studied previously, computation of the relative free energies of formation of the isomers, and measurement of solution circular dichroism spectra. The solid-state structures of both single enantiomer and racemic forms of the complex were determined by X-ray crystallography. In the chiral complex, a quasi-racemate was observed with both pseudo-enantiomeric conformers present in the asymmetric unit. Packing forces induce a higher energy conformation in order to achieve higher apparent symmetry in the solid state. In contrast, the racemic complex only displayed a single conformation corresponding to the lower energy one of the two observed in the single enantiomer structure.
Co-reporter:Steffen Zahn;Gloria Proni Dr.;Gian Piero Spada ;James W. Canary Dr.
Chemistry - A European Journal 2001 Volume 7(Issue 1) pp:
Publication Date(Web):5 JAN 2001
DOI:10.1002/1521-3765(20010105)7:1<88::AID-CHEM88>3.0.CO;2-0
Tripodal tetradentate ligands may act as chemosensor molecules. Their ability to torque a nematic into a cholesteric phase increases upon complexation with copper ion. Moreover, changes in overall shape of the complexes induced by different metals and counter ions were transferred sensitively to the supramolecular level, observed by proportionate changes in the degree of twisting. Modification of the oxidation state of the metal center also gave large changes in twisting power; this suggests potential application in electrochemical molecular switches. The handedness of the induced cholesteric phase is related to the stereochemistry of the ligand: The small amount of chiral dopant needed for the LC technique (less than 2 nmol) suggests the possible determination of the absolute configuration of the parent primary amines of the ligands.
Ligandi tetradentati tripodali possono agire da chemosensori; la loro capacità di trasformare una fase nematica in colesterica aumenta a seguito della complessazione con ioni rame. Inoltre le variazioni di forma dei complessi indotte dai diversi metalli e controioni sono state apprezzabilmente trasferite a livello supramolecolare e osservate attraverso le corrispondenti variazioni del grado di twist. Modifiche dello stato di ossidazione del centro metallico hanno portato a grosse variazioni di potere torcente suggerendo possibili applicazioni in dispositivi molecolari elettrochimici. Il senso del colesterico indotto è in relazione con la stereochimica del ligando: la piccola quantità di soluto chirale necessaria per la tecnica a cristalli liquidi (meno di 2 nmol) ne suggerisce il possibile uso nella determinazione della configurazione assoluta delle ammine primarie da cui i ligandi sono ottenuti.
Co-reporter:Steffen Zahn
Angewandte Chemie International Edition 1998 Volume 37(Issue 3) pp:
Publication Date(Web):17 DEC 1998
DOI:10.1002/(SICI)1521-3773(19980216)37:3<305::AID-ANIE305>3.0.CO;2-T
Intense chiroptical properties and efficient reversibility of the chemical redox cycle support the adaptability of the CuI/CuII complex system 1/2 for the development of a binary molecular device. Reduction proceeds with ascorbic acid, and oxidation with ammonium persulfate.
Co-reporter:Steffen Zahn;James W. Canary
Angewandte Chemie 1998 Volume 110(Issue 3) pp:
Publication Date(Web):12 MAR 1999
DOI:10.1002/(SICI)1521-3757(19980202)110:3<321::AID-ANGE321>3.0.CO;2-E
Intensive chiroptische Eigenschaften und hervorragende Reversibilität der chemischen Redoxcyclen empfehlen das CuI/CuII-Komplexpaar 1/2 als Basis für die Entwicklung eines molekularen Schalters. Reduziert wird mit Ascorbinsäure, oxidiert mit Ammoniumpersulfat.
Co-reporter:Jesus M. Castagnetto;Xiaodong Xu;Nina D. Berova
Chirality 1997 Volume 9(Issue 5‐6) pp:616-622
Publication Date(Web):7 DEC 1998
DOI:10.1002/(SICI)1520-636X(1997)9:5/6<616::AID-CHIR32>3.0.CO;2-P
The solution configuration of labile coordination complexes may be difficult to determine, even in cases in which the solid state structure is known. We have previously synthesized a series of chiral ligands which form pseudo-C3-symmetric complexes with ZnII and CuII salts that possess an available electrophilic coordination site. Molecular modeling of ZnII complexes of the chiral ligand N,N-bis[(2-quinolyl)methyl]-1-(2-pyridyl)ethanamine (α-MeBQPA) showed that the spatial arrangement of the heterocyclic arms is controlled by a substituent on one methylene arm, resulting in the adoption of an enantiomeric conformation displaying a propeller-like asymmetry. In this paper we report the application of the exciton chirality method to the determination of the conformation of asymmetric metal-ligand complexes in solution. There is a good correlation between the predicted and the observed Cotton effects, demonstrating that the geometry in solution closely resembles that predicted by computational simulations and those obtained by X-ray crystallographic studies of metal complexes with racemic and enantiomerically pure ligands. The X-ray crystallographic structure of the first optically pure complex in this series is reported. Chirality 9:616–622, 1997. © 1997 Wiley-Liss, Inc.
Co-reporter:Miao Ye, Johan Guillaume, Yu Liu, Ruojie Sha, Risheng Wang, Nadrian C. Seeman and James W. Canary
Chemical Science (2010-Present) 2013 - vol. 4(Issue 3) pp:NaN1329-1329
Publication Date(Web):2013/01/25
DOI:10.1039/C2SC21775A
We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2′-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.
Co-reporter:Joel A. Tang, Francesca Gruppi, Roman Fleysher, Daniel K. Sodickson, James W. Canary and Alexej Jerschow
Chemical Communications 2011 - vol. 47(Issue 3) pp:NaN960-960
Publication Date(Web):2010/11/15
DOI:10.1039/C0CC03421E
A system that provides a sustained hyperpolarized 1H NMR signal in an aqueous medium is reported. The enhanced signal lasts much longer than typical 1H T1 values, uncovering new possibilities for implementing hyperpolarized 1H NMR/MRI experiments or performing kinetics studies that would not otherwise be detectable.
Co-reporter:Yu Liu, Risheng Wang, Liang Ding, Roujie Sha, Nadrian C. Seeman and James W. Canary
Chemical Science (2010-Present) 2012 - vol. 3(Issue 6) pp:NaN1937-1937
Publication Date(Web):2012/03/08
DOI:10.1039/C2SC20129A
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis; coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2′-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
Co-reporter:Dadong Li, Xiaojian Wang, Fubo Shi, Ruojie Sha, Nadrian C. Seeman and James W. Canary
Organic & Biomolecular Chemistry 2014 - vol. 12(Issue 44) pp:NaN8827-8827
Publication Date(Web):2014/10/06
DOI:10.1039/C4OB01552E
We describe two DNA-templated ligation strategies: native chemical ligation (NCL), and thiol-disulfide exchange. Both systems result in successful ligation in the presence of a DNA template. The stability of the product from the NCL reaction relies on exogenous thiol, while the thiol-disulfide reaction proceeds in a catalyst-free manner.