Photocleavable peptide–oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS

Zhou, Guangyan; Khan, Fahd; Dai, Qing; Sylvester, Juliesta E.; Kron, Stephen J.

doi:10.1039/c2mb25163a

Cited by 18 publications

(16 citation statements)

References 73 publications

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“…2) Reaction of a free amino group on an oligonucleotide with an activated carboxylic group (NHS-ester), which produces amide linkage. The use of amino groups for conjugation has certain limitations; for example, the nucleophilicity of amino groups is pH dependent, which means that these groups are protonated at lower pH, which reduces their reactivity towards the electrophiles[163,164] (Fig. 4B2).…”

Section: Methods For Chemical Modification/conjugation Of Rna Nanmentioning

confidence: 99%

Stable RNA nanoparticles as potential new generation drugs for cancer therapy

Shu

Sharma

et al. 2014

Advanced Drug Delivery Reviews

213

180

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Human genome sequencing revealed that only ~1.5% of the DNA sequence coded for proteins. More and more evidence has uncovered that a substantial part of the 98.5% so-called “junk” DNAs actually code for noncoding RNAs. Two milestones, chemical drugs and protein drugs, have already appeared in the history of drug development, and it is expected that the third milestone in drug development will be RNA drugs or drugs that target RNA. This review focuses on the development of RNA therapeutics for potential cancer treatment by applying RNA nanotechnology. A therapeutic RNA nanoparticle is unique in that its scaffold, ligand, and therapeutic component can all be composed of RNA. The special physicochemical properties lend to the delivery of siRNA, miRNA, ribozymes, or riboswitches; imaging using fluogenenic RNA; and targeting using RNA aptamers. With recent advances in solving the chemical, enzymatic, and thermodynamic stability issues, RNA nanoparticles have been found to be advantageous for in vivo applications due to their uniform nano-scale size, precise stoichiometry, polyvalent nature, low immunogenicity, low toxicity, and target specificity. In vivo animal studies have revealed that RNA nanoparticles can specifically target tumors with favorable pharmacokinetic and pharmacodynamic parameters without unwanted accumulation in normal organs. This review summarizes the key studies that have led to the detailed understanding of RNA nanoparticle formation as well as chemical and thermodynamic stability issue. The methods for RNA nanoparticle construction, and the current challenges in the clinical application of RNA nanotechnology, such as endosome trapping and production costs, are also discussed.

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Section: Methods For Chemical Modification/conjugation Of Rna Nanmentioning

confidence: 99%

Stable RNA nanoparticles as potential new generation drugs for cancer therapy

Shu

Sharma

et al. 2014

Advanced Drug Delivery Reviews

213

180

View full text Add to dashboard Cite

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“…Given the advantage of the peptide‐maleimide and DNA‐thiol configuration, next, we tested a more cost‐effective method to synthesize POCs. Both the 5′‐thiol C6 and 5′‐amine C6 modifications are common in DNA synthesis. However, 5′‐amine modification is more frequently used and several times less expensive than 5′‐thiol‐modified DNAs.…”

Section: Resultsmentioning

confidence: 99%

“…POCs. Both the 5′-thiol C6 11,41-43 and 5′-amine C6 modifications 19, 28,44,45 are common in DNA synthesis. However, 5′-amine modification is more frequently used and several times less expensive than 5′-thiol-modified DNAs.…”

Section: Peptide and Dna Conjugation Via Thiolmaleimide Chemistrymentioning

confidence: 99%

Synthesis and purification of self‐assembling peptide‐oligonucleotide conjugates by solid‐phase peptide fragment condensation

Kye

Lim

2018

Journal of Peptide Science

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Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.

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“…A total of 150 µL of Sulfo-SMCC (5 mM) was dissolved into 100 nmol (10 µL) of TT probe (5′-NH 2 -mC-mU-mC-mG- T-T -mC-mG-mU-mU-mC-N 3 -3′) and the mixture was shaken at 1500 rpm for 1 h at RT. Next, 0.25 mL of D-SPION was added and the mixture was shaken at 500 rpm for an additional 2 h at RT [ 32 ]. D-SPION@TT-N 3 probe was then transferred to 500 μL of sodium bicarbonate buffer pH 8.8 using a MACS MS column.…”

Section: Methodsmentioning

confidence: 99%

Activatable MRI probes for the specific detection of bacteria

Prabu

Balian

et al. 2021

Anal Bioanal Chem

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Activatable fluorescent probes have been successfully used as molecular tools for biomedical research in the last decades. Fluorescent probes allow the detection of molecular events, providing an extraordinary platform for protein and cellular research. Nevertheless, most of the fluorescent probes reported are susceptible to interferences from endogenous fluorescence (background signal) and limited tissue penetration is expected. These drawbacks prevent the use of fluorescent tracers in the clinical setting. To overcome the limitation of fluorescent probes, we and others have developed activatable magnetic resonance probes. Herein, we report for the first time, an oligonucleotide-based probe with the capability to detect bacteria using magnetic resonance imaging (MRI). The activatable MRI probe consists of a specific oligonucleotide that targets micrococcal nuclease (MN), a nuclease derived from Staphylococcus aureus. The oligonucleotide is flanked by a superparamagnetic iron oxide nanoparticle (SPION) at one end, and by a dendron functionalized with several gadolinium complexes as enhancers, at the other end. Therefore, only upon recognition of the MRI probe by the specific bacteria is the probe activated and the MRI signal can be detected. This approach may be widely applied to detect bacterial infections or other human conditions with the potential to be translated into the clinic as an activatable contrast agent.

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Photocleavable peptide–oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS

Cited by 18 publications

References 73 publications

Stable RNA nanoparticles as potential new generation drugs for cancer therapy

Stable RNA nanoparticles as potential new generation drugs for cancer therapy

Synthesis and purification of self‐assembling peptide‐oligonucleotide conjugates by solid‐phase peptide fragment condensation

Activatable MRI probes for the specific detection of bacteria

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