In Vitro Selection of N‐Peptide‐Binding RNA on a Quartz‐Crystal Microbalance to Study a Sequence‐Specific Interaction between the Peptide and Loop RNA

Furusawa, Hiroyuki; Murakawa, Akiko; Fukusho, Shinobu; Okahata, Yoshio

doi:10.1002/cbic.200390034

Cited by 13 publications

(16 citation statements)

References 19 publications

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“…The QCM frequency responded to three steps in polymerase reactions, namely binding of DNA polymerase to the primer on the QCM (mass increase), elongation of complementary nucleotides along the template (mass increase), and release of the enzyme from the completely polymerized DNA (mass decrease), as a function of elapsed time. [77] In vitro selection of Npeptide-binding RNA to study a sequence-specific interaction between the peptide and loop RNA [78] and direct monitoring of enzymatic glucan hydrolysis [79] were also successfully demonstrated with the QCM method. Parallelized platforms for QCM measurement are expected to be developed.…”

Section: Detection Methodsmentioning

confidence: 97%

“…Although the most suitable detection method that meets such criteria is still under consideration, there are several candidates, such as 1) fluorescent labeling, [31,32] 2) isotopic labeling, [33,49] 3) chemiluminesent labeling, [69] 4) mass spectrometry, [70] 5) surface plasmon resonance (SPR) spectroscopy, [71][72][73][74][75] 6) anomalous reflections (AR) of the gold surface, [76] 7) quartz-crystal microbalance (QCM) analysis, [77][78][79] 8) fluorescence correlation spectroscopy (FCS), [80][81][82] and 9) electrochemical detection ( Figure 3). It is necessary to label with fluorescent probes for the methods 1 and 8, with radioisotopes for method 2, with an adequate functional group/molecule for method 3, and with electrically active probes for method 9, but no labeling at all is necessary for the other methods (4-7).…”

Section: Detection Methodsmentioning

confidence: 99%

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Protein‐Detecting Microarrays: Current Accomplishments and Requirements

2005

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The sequencing of the human genome has been successfully completed and offers the chance of obtaining a large amount of valuable information for understanding complex cellular events simply and rapidly in a single experiment. Interestingly, in addressing these proteomic studies, the importance of protein-detecting microarray technology is increasing. In the coming few years, microarray technology will become a significantly promising and indispensable research/diagnostic tool from just a speculative technology. It is clear that the protein-detecting microarray is supported by three independent but strongly related technologies (surface chemistry, detection methods, and capture agents). Firstly, a variety of surface-modification methodologies are now widely available and offer site-specific immobilization of capture agents onto surfaces in such a way as to keep the native conformation and activity. Secondly, sensitive and parallel detection apparatuses are being developed to provide highly engineered microarray platforms for simultaneous data acquisition. Lastly, in the development of capture agents, antibodies are now probably the most prominent capture agents for analyzing protein abundances. Alternative scaffolds, such as phage-displayed antibody and protein fragments, which provide the advantage of increasing diversity of proteinic capture agents, however, are under development. An approach involving recombinant proteins fused with affinity tag(s) and coupled with a highly engineered surface chemistry will provide simple production protocols and specific orientations of capture agents on the microarray formats. Peptides and other small molecules can be employed in screening highly potent ligands as well as in measuring enzymatic activities. Protein-detecting microarrays supported by the three key technologies should contribute in accelerating diagnostic/biological research and drug discovery.

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Section: Detection Methodsmentioning

confidence: 97%

Section: Detection Methodsmentioning

confidence: 99%

Protein‐Detecting Microarrays: Current Accomplishments and Requirements

2005

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“…Stengel et al (2005) used the same approach but employed QCM-D and noted the changes in frequency and dissipation arising from variations in the viscoelastic properties and therefore advise that changes in frequency alone may not be ideal for estimations of coupled mass and kinetics. The technique has also been employed to analyse enzymatic DNA cleavage (Yan and Sadik, 2001 the in vitro selection of N-peptide-binding RNA for sequence-specific interaction between the peptide and loop RNA (Furusawa et al, 2003).…”

Section: Detection Of Hybridizationmentioning

confidence: 99%

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

Cooper¹,

Singleton²

2007

J of Molecular Recognition

335

205

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The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.

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“…After the addition of 1% Triton X-100 for solubilization, IgG binding proteins were purified by IgG-Sepharose affinity chromatography. 27 MHz QCM setup and its calibration in aqueous solutions AFFINIXQ4 was used as a QCM instrument (Initium Co. Ltd, Tokyo: http://www.initium2000.com) with four 500 mL cells equipped with a 27 MHz QCM plate (8.7 mm quartz plate diameter and a 4.9 mm 2 Au electrode area) at the bottom of the cell and a stirring bar with a temperature control system (Ebara and Okahata, 1994;Sato et al, 1996;Okahata et al, 1998a,b;Furusawa et al, 2002Furusawa et al, , 2003). Sauerbrey's equation (Sauerbrey, 1959) was obtained for the AT-cut shear mode QCM in the air phase,…”

Section: Preparation Of Lppbx and B5mentioning

confidence: 99%

“…The 27 MHz QCM is a very sensitive mass-measuring device in aqueous solutions, as well as in air, and the resonance frequency has been proven to decrease linearly with increasing mass on the Au electrode of the QCM at a nanogram level. The QCM has been employed to quantitatively analyze DNA hybridizations (Okahata et al, 1992(Okahata et al, , 1998a, DNA-peptide/protein interactions (Okahata et al, 1998b;Furusawa et al, 2002Furusawa et al, , 2003, and glycolipid-protein interactions (Ebara and Okahata, 1994;Sato et al, 1996) in aqueous solutions.…”

Section: Introductionmentioning

confidence: 99%

IgG binding kinetics to oligo B protein A domains on lipid layers immobilized on a 27 MHz quartz‐crystal microbalance

Mitomo

Shigematsu

Kobatake

et al. 2007

J of Molecular Recognition

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Although molecular recognitions between membrane receptors and their soluble ligands have been analyzed using their soluble proteins in bulk solutions, molecular recognitions of membrane receptors should be studied on lipid membranes considering their orientation and dynamics on membrane surfaces. We employed Staphylococcal Protein A (SpA) oligo B domains with long trialkyl-tags from E. coli (LppBx, x = 1, 2, and 5) and immobilized LppBx on lipid layers using hydrophobic interactions from the trialkyl-tag, while maintaining the orientation of B domain-chains on a 27 MHz quartz-crystal microbalance (QCM; AT-cut shear mode). The binding of IgG Fc regions to LppBx on lipid layers was detected by frequency decreases (mass increases) on the QCM. The maximum amount bound (Delta m(max)), association constants (K(a)), association and dissociation rate constants (k(1) and k(-1), respectively) were obtained. Binding kinetics of IgG to LppB2 and LppB5 were quite similar, showing a simple 1:1 binding of the IgG Fc region to the B domain, when the surface coverage of LppB2 and LppB5 on the lipid surface is low (1.4%). When LppB5 was immobilized at the high surface coverage of 3.5%, the complex bindings of IgG such as one IgG bound to one or two LppB5 on the membrane could be observed. IgG-LppB1 binding was largely restricted because of steric hindrance on lipid surfaces. This gives a suggestion why Protein A has five IgG binding domains.

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In Vitro Selection of N‐Peptide‐Binding RNA on a Quartz‐Crystal Microbalance to Study a Sequence‐Specific Interaction between the Peptide and Loop RNA

Cited by 13 publications

References 19 publications

Protein‐Detecting Microarrays: Current Accomplishments and Requirements

Protein‐Detecting Microarrays: Current Accomplishments and Requirements

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

IgG binding kinetics to oligo B protein A domains on lipid layers immobilized on a 27 MHz quartz‐crystal microbalance

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