Methods for measuring aptamer-protein equilibria: A review

Meng, Jing; Bowser, Michael T.

doi:10.1016/j.aca.2010.10.032

Cited by 195 publications

(176 citation statements)

References 130 publications

(113 reference statements)

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“…The formation of this complex blocks the electron transfer and consequently the R et increases. Ultraviolet-visible (UV-vis) absorption method [35] was used to prove the interaction between APTs and proteins. for further experiments.…”

Section: The Principle Of Eca Impedimetric Biosensormentioning

confidence: 99%

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

Queirós

de‐los‐Santos‐Álvarez

Noronha

et al. 2013

Sensors and Actuators B: Chemical

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a b s t r a c tA label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins (OMPs) was developed. Two single stranded DNA sequences were tested as recognition elements and compared. The aptamer capture probes were immobilized, with and without 6-mercapto-1-hexanol (MCH) on a gold electrode. Each step of the modification process was characterized by Faradaic impedance spectroscopy (FIS). A linear relationship between the electron-transfer resistance (R et ) and E. coli OMPs concentration was demonstrated in a dynamic detection range of 1 × 10 −7 -2 × 10 −6 M. Moreover, the aptasensor showed selectivity despite the presence of other possible water contaminates and could be regenerated under low pH condition. The developed biosensor shows great potential to be incorporated in a biochip and used for in situ detection of E. coli OMPs in water samples.

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Section: The Principle Of Eca Impedimetric Biosensormentioning

confidence: 99%

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

Queirós

de‐los‐Santos‐Álvarez

Noronha

et al. 2013

Sensors and Actuators B: Chemical

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“…1 Conversely, in immunoassay applications, a tunable affinity is often desired to enable sensor reusability. 2 Therefore, it is not surprising that the study of binding site affinities is of great scientific and industrial importance. In order to fully characterize the binding site affinity, it is necessary to perform measurements using both free and fixed molecules.…”

mentioning

confidence: 99%

“…However, while there are numerous methods for determining the affinity with free molecules, the approaches for fixed molecules are limited. 2 The primary approach for fixed molecule characterization is based on surface plasmon resonance (SPR) sensors. This technique relies on the decaying evanescent optical field generated by the SPR, which is established at the interface of a metal film and the solution, and is approximately $50 nm long.…”

mentioning

confidence: 99%

Determination of binding kinetics using whispering gallery mode microcavities

Soteropulos

Hunt

Armani

2011

Applied Physics Letters

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Silica optical microcavity sensors show great promise in the kinetic evaluation of binding pairs, fundamental in understanding biomolecular interactions. Here, we develop and demonstrate a novel platform, based on bioconjugated silica microsphere resonators, to study the binding kinetics of the biotin-streptavidin system. We characterize the optical performance, verify the covalent attachment of biotin to the surface, and perform streptavidin detection experiments. We perform preliminary kinetic analysis of the detection data which shows the potential of whispering gallery mode resonators in the determination of the dissociation constant of the binding pair, which is in good agreement with previously published values. The binding site affinity of an enzyme or antibody (i.e., its ability to bind to its specific complement), determines its utility in a given application. For example, in designing therapeutics, a strong affinity for a specific target is desired to maximize the effectiveness of the therapeutic.1 Conversely, in immunoassay applications, a tunable affinity is often desired to enable sensor reusability.2 Therefore, it is not surprising that the study of binding site affinities is of great scientific and industrial importance. In order to fully characterize the binding site affinity, it is necessary to perform measurements using both free and fixed molecules. However, while there are numerous methods for determining the affinity with free molecules, the approaches for fixed molecules are limited. 2The primary approach for fixed molecule characterization is based on surface plasmon resonance (SPR) sensors. This technique relies on the decaying evanescent optical field generated by the SPR, which is established at the interface of a metal film and the solution, and is approximately $50 nm long.3 When a molecule is located within the evanescent field, it modifies the effective refractive index. This change is detected as an increase in the SPR wavelength. While current SPR systems are ideal for characterizing single interaction pairs, they often experience difficulties resolving multi-valent interactions. This limitation is a result of the short interaction time between the photon and the molecule, limited bioconjugation protocols for attachment of one half of the binding pair to metal surfaces, and restricted mass transport across the sensor surface.

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“…In the general case ligands such as L-tyrosinamide bind by electrostatic, hydrophobic and hydrogen bonding interactions [53]. Typically, a conformational change in the RNA or DNA aptamer is a hallmark of the small molecule binding [54]. However, the driving force for binding by the small molecules has a large electrostatic component.…”

Section: Thermodynamics Of Rna and Dna Aptamer Bindingmentioning

confidence: 99%

Thermodynamics of Nucleic Acid Structural Modifications for Biotechnology Applications

Franzen¹

2011

Biotechnology of Biopolymers

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IntroductionThe repertoire of chemistry available to native nucleotides in DNA and RNA is limited to the purine and pyrimidine functional groups, along with the special role of the 2'-hydroxyl of RNA. The nucleobases have exocyclic amino groups and imines, neither of which is highly reactive or a good candidate for catalytic function. One might argue that the limited range of chemical reactivity is an evolutionary advantage in molecules whose functions are primarily to store (DNA) and process (RNA) genetic information. The most important attribute of both DNA and RNA is the molecular recognition through base pairing. The hydrogen bond pattern combined with the conformation of the ribose sugar gives rise to the specific B-form double helix in DNA and A-form helix with a range of additional standard folds in RNA, loops, bulges and pseudoknots. These structures are well known for their ability to interact with proteins to provide a scaffold for transcription (DNA → RNA) to create messenger RNA (mRNA), and processing of mRNA by enzymes that have active components composed of RNA molecules. The chemical action of RNA on other RNAs by means of the 2'-hydroxyl is an exception to the lack or reactivity of DNA and RNA. Selfsplicing by action of the 2'-hydroxyl as a nucleophile was the process that broke the dogma that RNA is always a passive molecule that simply transmits information [1]. Indeed, RNA i s v e r y a c t i v e i n p r o c e s s i n g o t h e r R N A s u s i n g t h e 2 ' -h y d r o x y l a s a n u c l e o p h i l e f o r hydrolysis of the phosphodiester bond leading to cleavage or to rearrangements of structure such as RNA splicing. Outside of this reactivity, the components of the purine and pyrimidine rings are largely inert. Aromatic amines are poor nucleophiles, and imines are even less reactive. The purine and pyrimidine rings are not particularly electrophilic because of the nitrogen heteroatoms and carbonyls. Using in vitro selection (also known as SELEX) [2][3][4], and appropriate modification, RNA and DNA have been developed for numerous applications that transcend their biological functions. In this chapter we will consider the modifications of the nucleobase as a means to expand upon the native function. The extensive literature on modifications of the phosphodiester backbone and the ribose sugar will not be considered in this chapter due to space limitations. Base modifications may consist of expansions of the purine/pyrimidine ring, appended functional group or chemical modification to increase the stability of the backbone with respect to hydrolysis. Expanded DNA or xDNA has been developed as mimics of native DNA with potential biotechnology applications [5,6]. In these molecules, the purine and pyrimidine rings are fused to phenyl or naphthyl rings to give rise to

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Methods for measuring aptamer-protein equilibria: A review

Cited by 195 publications

References 130 publications

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

Determination of binding kinetics using whispering gallery mode microcavities

Thermodynamics of Nucleic Acid Structural Modifications for Biotechnology Applications

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