With Tag: Biochemical Methods

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Invariant Polymorphism in Virus Capsid Assembly

Hung D. Nguyen, Charles L. Brooks III, Vijay S. Reddy
J. Am. Chem. Soc. | 2009 | 10.1021/ja807730x

Directed self-assembly of designed viral capsids holds significant potential for applications in materials science and medicine. However, the complexity of preparing these systems for assembly and the difficulty of quantitative experimental measurements on...


Silica Encapsulation of Fluorescent Nanodiamonds for Colloidal Stability and Facile Surface Functionalization

Ambika Bumb, Martin W. Brechbiel, Neil Billington, Keir C. Neuman, Susanta K. Sarkar
J. Am. Chem. Soc. | 2013 | 10.1021/ja4016815

Fluorescent nanodiamonds (FNDs) emit in the near-IR and do not photobleach or photoblink. These properties make FNDs better suited for numerous imaging applications compared with commonly used fluorescence agents such as organic dyes and quantum dots....


Controlling Macromolecular Topology with Genetically Encoded SpyTag–SpyCatcher Chemistry

Fei Sun, Frances H. Arnold, Wen-Bin Zhang, David A. Tirrell
J. Am. Chem. Soc. | 2013 | 10.1021/ja4076452

Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole,...


Surface-Enhanced Raman Spectroscopy of DNA

Felicia Tam, Dongmao Zhang, Naomi J. Halas, Aoune Barhoumi
J. Am. Chem. Soc. | 2008 | 10.1021/ja800023j

We report a method for obtaining highly reproducible surface-enhanced Raman spectroscopy (SERS) of single and double-stranded thiolated DNA oligomers. Following a protocol that relaxes the DNA into an extended conformation, SERS spectra of DNA...


Pipette–Surface Interaction: Current Enhancement and Intrinsic Force

Alexander Zhukov, Nicholas Johnson, Owen Richards, Richard W. Clarke, David Klenerman, Victor Ostanin
J. Am. Chem. Soc. | 2012 | 10.1021/ja3094586

There is an intrinsic repulsion between glass and cell surfaces that allows noninvasive scanning ion conductance microscopy (SICM) of cells and which must be overcome in order to form the gigaseals used for patch clamping investigations of ion channels....


Full-Range Intracellular pH Sensing by an Aggregation-Induced Emission-Active Two-Channel Ratiometric Fluorogen

Yong Yu, Ben Zhong Tang, Sijie Chen, Ryan T. K. Kwok, Jianzhao Liu, Yuning Hong, Engui Zhao, Min Li, Chris W. T. Leung, Yang Liu, Jacky W. Y. Lam
J. Am. Chem. Soc. | 2013 | 10.1021/ja400337p

Intracellular pH (pH i ) is an important parameter associated with cellular behaviors and pathological conditions. Sensing pH i and monitoring its changes in live cells are essential but challenging due to the lack of effective probes. We herein report a...


Involvement of the LSPR Spectral Overlap for Energy Transfer between a Dye and Au Nanoparticle

Geoffrey F. Strouse, Mani Prabha Singh
J. Am. Chem. Soc. | 2010 | 10.1021/ja1022128

Nanometal surface energy transfer (NSET) is a molecular ruler technique that has been utilized to optically probe long distances in biomolecular structures. We investigate the useful spectral range of donor dyes and the importance of overlap between the...


Reversibly Photoswitchable Dual-Color Fluorescent Nanoparticles as New Tools for Live-Cell Imaging

James K. Hurst, Jason J. Han, Linyong Zhu, Alexander D. Q. Li, Ming-Qiang Zhu, Wuwei Wu
J. Am. Chem. Soc. | 2007 | 10.1021/ja068452k

Optically switchable dual-color fluorescent nanoparticles that incorporate two classes of dyes into the polymeric chains have been synthesized using an emulsion polymerization method. The nanoparticles consist of an organic photoisomerizable dye, spiropyran,...


Dip-Pen Nanolithography of Reactive Alkoxysilanes on Glass

Rajan Kulkarni, Hyungil Jung, C. Patrick Collier
J. Am. Chem. Soc. | 2003 | 10.1021/ja0363720

The use of organofunctional silane chemistry is a flexible and general method for immobilizing biomolecules on silicon oxide surfaces, including fabricating DNA, small-molecule, and protein microarrays. The biggest hurdle in employing dip-pen nanolithography...


Autopoietic Self-Reproduction of Chiral Fatty Acid Vesicles

Peter Walde, Stefano Colonna, Pier Luigi Luisi, Sabrina Dallavalle, Kenichi Morigaki
J. Am. Chem. Soc. | 1997 | 10.1021/ja961728b

The self-reproduction of vesicles formed by (S)- and (R)-2-methyldodecanoic acid (4) was investigated in order to relate the autocatalytic increase of the vesicle concentration with enantioselectivity. 4(R) and 4(S) were synthesized with an enantiomeric...


Synthesis and Characterization of Fluorescent Displacers for Online Monitoring of Displacement Chromatography

Scott A. McCallum, Chester Simocko, Sun Kyu Park, J. A. Moore, Christopher J. Morrison, Steven M. Cramer
J. Am. Chem. Soc. | 2008 | 10.1021/ja806279x

One of the major impediments to the implementation of displacement chromatography for the purification of biomolecules is the need to collect fractions from the column effluent for time-consuming offline analysis. The ability to employ direct online...


Simple and Versatile Method for Tagging Phenyldiazirine Photophores

Yutaka Sadakane, Hiroyuki Nakashima, Yasumaru Hatanaka, Makoto Hashimoto, Takenori Tomohiro
J. Am. Chem. Soc. | 2006 | 10.1021/ja066479y

The first effective method for the introduction of a versatile substituent on 3-phenyl-3-trifluoromethyldiazirine has been developed. The simple preparation of a useful aldehyde intermediate allows easy access to various elaborated photoaffinity ligands,...


Three-Dimensional DNA Crystals as Molecular Sieves

Paul J. Paukstelis
J. Am. Chem. Soc. | 2006 | 10.1021/ja061322r

DNA has proved to be a successful nanoscale building block because of its inherent programmability and its predictable structural features. One long-standing goal of DNA nanotechnology has been the rational design and assembly of three-dimensional (3D) DNA...


Catalytic Beacons for the Detection of DNA and Telomerase Activity

Moshe Kotler, Yi Xiao, Itamar Willner, Valeri Pavlov, Tamara Niazov, Arnon Dishon
J. Am. Chem. Soc. | 2004 | 10.1021/ja031875r

DNA and telomerase activity are detected by a DNAzyme generated upon hybridization and opening of a functional catalytic beacon.


Ensemble Calculations of Unstructured Proteins Constrained by RDC and PRE Data: A Case Study of Urea-Denatured Ubiquitin

Jie-rong Huang, Stephan Grzesiek
J. Am. Chem. Soc. | 2009 | 10.1021/ja907974m

The detailed, quantitative characterization of unfolded proteins is a largely unresolved task due to the enormous experimental and theoretical difficulties in describing the highly dimensional space of their conformational ensembles. Recently, residual...


Direct Observation of Nitrosylated Heme in Myoglobin and Hemoglobin by Electrospray Ionization Mass Spectrometry

Rita K. Upmacis, David P. Hajjar, Brian T. Chait, Urooj A. Mirza
J. Am. Chem. Soc. | 1997 | 10.1021/ja964249l

Using electrospray ionization mass spectrometry (ESI-MS), we demonstrate the direct observation of NO attached to the heme moiety in horse heart myoglobin (Mb) and in the α- and β-chains of human hemoglobin (Hb). It was found that a narrow range of ESI-MS...


Immobilization of Ligands with Precise Control of Density to Electroactive Surfaces

Eugene W. L. Chan, Muhammad N. Yousaf
J. Am. Chem. Soc. | 2006 | 10.1021/ja065828l

We report a broadly applicable surface chemistry methodology to immobilize ligands, proteins, and cells to an electroactive substrate with precise control of ligand density. This strategy is based on the coupling of soluble aminooxy terminated ligands with an...


A Polymeric Domain That Promotes Cellular Internalization

Laura L. Kiessling, Erin M. Kolonko
J. Am. Chem. Soc. | 2008 | 10.1021/ja8001716

Polymers have emerged as powerful biological tools; however, their ability to gain access to the intracellular environment is limited. To expand the biological utility of polymer scaffolds, we have synthesized an internalization domain using the ring-opening...


Two-Photon Fluorescence Microscopy Imaging of Cellular Oxidative Stress Using Profluorescent Nitroxides

Vanessa Lussini, Kathryn E. Fairfull-Smith, Benjamin J. Morrow, Bosung Kim, Hyo-Yang Ahn, Kevin D. Belfield, Mykhailo V. Bondar, Steven E. Bottle
J. Am. Chem. Soc. | 2012 | 10.1021/ja210315x

A range of varying chromophore nitroxide free radicals and their nonradical methoxyamine analogues were synthesized and their linear photophysical properties examined. The presence of the proximate free radical masks the chromophore’s usual fluorescence...


Phosphorescent Sensor for Biological Mobile Zinc

Kei Ohkubo, Weon-Sik Chae, Youngmin You, Sumin Lee, Shunichi Fukuzumi, Taehee Kim, Wonwoo Nam, Gil-Ja Jhon, Stephen J. Lippard
J. Am. Chem. Soc. | 2011 | 10.1021/ja207163r

A new phosphorescent zinc sensor (ZIrF) was constructed, based on an Ir(III) complex bearing two 2-(2,4-difluorophenyl)pyridine (dfppy) cyclometalating ligands and a neutral 1,10-phenanthroline (phen) ligand. A zinc-specific di(2-picolyl)amine (DPA) receptor...

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