Stability and bioactivity of thrombin binding aptamers modified with<scp>d</scp>-/<scp>l</scp>-isothymidine in the loop regions

Cai, Baobin; Yang, Xiantao; Sun, Lidan; Fan, Xinmeng; Li, Liyu; Jin, Hongwei; Wu, Yun; Zhu, Ge; Zhang, Liangren; Zhang, Lihe; Yang, Zhenjun

doi:10.1039/c4ob01525h

Cited by 47 publications

(40 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…During this work, the authors found that when 3‐phenylpropionic acid was employed as a substrate, only the β‐keto sulfone was obtained with 1,2‐dichloroethane (DCE) as solvent under otherwise identical reaction conditions. Subsequent efforts have been devoted to the system, which was further advanced and applied to the oxysulfonylation of alkynes (Scheme ) …”

Section: Sulfonylationmentioning

confidence: 99%

Photoredox Catalysis in C–S Bond Construction: Recent Progress in Photo‐Catalyzed Formation of Sulfones and Sulfoxides

et al. 2017

View full text Add to dashboard Cite

The emergence of radical chemistry as well as green chemistry in organic synthesis has initiated an interest in photochemistry over the past decade. With catalytic amounts of photoredox catalysts under light irradiation, high active radical species are produced, which could trigger the subsequent organic transformations smoothly. Among the various photoredox reactions, photo‐catalytic C–S bond formation continues to thrive, as the C–S bond is indispensable in many important biological and pharmaceutical compounds. Great attention has been devoted to this area as illustrated by the series of papers on sulfone and sulfoxide skeleton synthesis under irradiation published in the past years. This review summarizing the recent advances in photo‐catalyzed sulfones and sulfoxide formation is arranged by reaction type together with the sulfur source covering sulfonylation and sulfinylation reactions. It is intended to provide readers with a comprehensive understanding of photo‐catalytic C‐S bond formation and offer help for future research.

show abstract

Section: Sulfonylationmentioning

confidence: 99%

Photoredox Catalysis in C–S Bond Construction: Recent Progress in Photo‐Catalyzed Formation of Sulfones and Sulfoxides

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The first thrombin binding aptamer, a 15-mer oligonucleotide, 5′-GGTTGGTGTGGTTGG-3′, was discovered through an in vitro combinatorial selection and polymerase chain reaction process by Bock et al [4]. An increasing number of modified TBAs have since been developed and used for diagnostic and therapeutic applications [5–9]. Unlike other thrombin-binding biomolecules and proteins, TBAs are smaller mass DNA molecules with high chemical and physiological stabilities, easier to synthesize and have high specificity and affinity for thrombin.…”

Section: Introductionmentioning

confidence: 99%

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

Zhang

Loo²,

Loo

2017

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA drug complexes.

show abstract

“…Numerous studies on modifications of TBA with non-natural nucleotides indicate that the improved anticoagulant properties or higher binding affinities of modified variants are often associated with the transformation of the TGT loop. In this way, a few advanced TBA analogs containing 2′-deoxyisoguanosine, 2′-deoxy-2′-fluoroarabinonucleotides, 4-thio-2′-deoxyuridine, 5-hydroxymethyl-2′-deoxyuridine, D-/L-isothymidine and UNA (unlocked nucleic acid) residues in the TGT loop have been described 7 8 9 10 11 12 .…”

mentioning

confidence: 99%

A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole

Цветков

Varizhuk

Pozmogova

et al. 2015

Sci Rep

View full text Add to dashboard Cite

In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a substantially increased clotting time and two-fold lower IC50 value compared to the unmodified prototype. Molecular modelling studies suggest that the improved anticoagulant properties of TBA-N8 result from changes in the binding mode of the analog. A modified central loop in TBA-N8 is presumed to participate in the binding of the target protein. Studies of FAM labelled TBA and TBA-N8 showed an improved binding affinity of the modified aptamer and provided evidence of a direct interaction between the modified central loop and thrombin. Our findings have implications for the design of new aptamers with improved binding affinities.

show abstract

Stability and bioactivity of thrombin binding aptamers modified withd-/l-isothymidine in the loop regions

Cited by 47 publications

References 50 publications

Photoredox Catalysis in C–S Bond Construction: Recent Progress in Photo‐Catalyzed Formation of Sulfones and Sulfoxides

Photoredox Catalysis in C–S Bond Construction: Recent Progress in Photo‐Catalyzed Formation of Sulfones and Sulfoxides

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole

Contact Info

Product

Resources

About