Hairpin‐Spacer crRNA‐Enhanced CRISPR/Cas13a System Promotes the Specificity of Single Nucleotide Polymorphism (SNP) Identification

Ke, Yuqing; Huang, Shiyi; Ghalandari, Behafarid; Li, Sijie; Warden, Antony R.; Dang, Jingqi; Kang, Lin Woo; Zhang, Yu; Wang, Yunqing; Sun, Yiqing; Wang, Jinglin; Cui, Daxiang; Zhi, Xiao; Li, Yiyang

doi:10.1002/advs.202003611

Cited by 49 publications

(58 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The contact surface area (CSA) and binding energy between the three model proteins and CDS-PMo12@PVPx(x=0,1) NPs were calculated using molecular docking. [45] As shown in Figure 3c-d, the CSA of proteins on CDS-PMo12@PVP0 is larger than that on CDS-PMo12@PVP1. Importantly, the CSA of Cyt-C is larger than that of Hb/BSA on CDS-PMo12@PVPx(x=0,1) NPs.…”

Section: Molecular Docking Study Of Cds-pmo12@pvpx(x=01) Nps and Protein Interactionsmentioning

confidence: 80%

“…During CDS-PMo12@PVP0 interacts with the proteins, the primary force is hydrophobic and the secondary forces is electrostatic (Figure 3a). Molecular docking [45] results show that CDS-PMo12@PVP1 binds with Cyt-C, Hb, and BSA mainly through electrostatic interaction, but also Van der Waals force as the second action force (Figure 3b).…”

Section: Molecular Docking Study Of Cds-pmo12@pvpx(x=01) Nps and Protein Interactionsmentioning

confidence: 99%

See 1 more Smart Citation

Poly (N-vinylpyrrolidone) Modification Mitigates Plasma Protein Corona Formation on Phosphomolybdate-based Nanoparticles

Ghalandari

Shen³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Phosphomolybdate-based nanoparticles (PMo12-based NPs) have been commonly applied in nanomedicine. However, upon contact with biofluids, proteins are quickly adsorbed onto the NPs surface to form a protein corona, which induces the opsonization and facilitates the rapid clearance of the NPs by macrophage uptake. Herein, we introduce a family of structurally homologous PMo12-based NPs (CDS-PMo12@PVPx(x = 0 ~ 1) NPs) capping diverse content of zwitterionic polymer poly (N-vinylpyrrolidone) (PVP) to regulate the protein corona formation on PMo12-based NPs. The fluorescence quenching data indicate that the introduction of PVP effectively reduces the number of binding sites of proteins on PMo12-based NPs. Molecular docking simulations results show that the contact surface area and binding energy of proteins to CDS-PMo12@PVP1 NPs are smaller than the CDS-PMo12@PVP0 NPs. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) is further applied to analyze and quantify the compositions of the human plasma corona formation on CDS-PMo12@PVPx(x = 0 ~ 1) NPs. The number of plasma protein groups adsorption on CDS-PMo12@PVP1 NPs, compared to CDS-PMo12@PVP0 NPs, decreases from 372 to 271. In addition, 76 differentially adsorption proteins are identified between CDS-PMo12@PVP0 and CDS-PMo12@PVP1 NPs, in which apolipoprotein is up-regulated in CDS-PMo12@PVP1 NPs. The apolipoprotein adsorption onto the NPs is proposed to have dysoponic activity and enhance the circulation time of NPs. Our findings demonstrate that PVP grafting on PMo12-based NPs is a promising strategy to improve the anti-biofouling property for PMo12-based nanodrug design.

show abstract

Section: Molecular Docking Study Of Cds-pmo12@pvpx(x=01) Nps and Protein Interactionsmentioning

confidence: 80%

Section: Molecular Docking Study Of Cds-pmo12@pvpx(x=01) Nps and Protein Interactionsmentioning

confidence: 99%

Poly (N-vinylpyrrolidone) Modification Mitigates Plasma Protein Corona Formation on Phosphomolybdate-based Nanoparticles

Ghalandari

Shen³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…SNPs in the disease-causing pathogens such as bacteria or viruses provide information of pathogens such as endemicity, transmission mode, and clinical outcomes, making it a useful biomarker for the diagnosis and the appropriate treatments [36]. For example, detection of SNPs in the hepatitis B virus (HBV), the most common viral infection in humans, tells the genotypes of the HBV, B or C, where genotype C is associated with more active disease and higher risk of liver cirrhosis comparing with genotype B [37,38].…”

Section: Snp Detectionmentioning

confidence: 99%

“…Only the target RNA possessing a single-point mutation can bind to the Cas13a-gRNA complex activating its trans-cleavage activity for the surrounding ssRNA because it possesses the perfect complementarity with gRNA, not the wild-type DNA. In this way, the SNPs (C347G and C369T in HBV and T2573G in EGFR) were detected by monitoring the increase in the fluorescence signal caused by the cleavage of FQ-labeled ssRNA at the level of attomolar [20,37]. Harrington et al detected the SNP of the HERC2 gene that decides the eye color (brown or blue eye).…”

Section: Snp Detectionmentioning

confidence: 99%

CRISPR as a Diagnostic Tool

Kim

Koh

2021

Biomolecules

View full text Add to dashboard Cite

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.

show abstract

“…The more e cient crRNA adopted a conserved stem-loop structure [26] and showed lower minimum free energy (MFE) [27]. Therefore, we predicted the second structure and MFE of the 12 crRNAs using the NUPACK online tools (Additional le 2).…”

Section: Design and Preparation Of Crrnas For Gbs Detectionmentioning

confidence: 99%

CRISPR/Cas12a-Based Assay for the Rapid and High-Sensitivity Detection of Streptococcus Agalactiae Colonization in Pregnant Women with Premature Rupture of Membrane

Yu¹,

Bin

et al. 2021

Preprint

View full text Add to dashboard Cite

Background Streptococcus agalactiae or group B Streptococcus (GBS) is a leading infectious cause of neonatal morbidity and mortality. This study aims to establish a novel method, termed as the CRISPR-GBS assay, for the rapid and sensitive detection of GBS that is based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system. Results The CRISPR-GBS assay detected GBS in the samples within 35 min. The limit of detection was as low as 5 copies/µL and showed no cross-reactivity with other microorganisms. The clinical performance was assessed using vaginal or cervical swab samples that were collected from 179 pregnant women with premature rupture of membrane. Compared with the culture-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry method, the CRISPR-GBS assay demonstrated a sensitivity of 96.64% (144/149, 95% confidence interval [CI] = 92.39–98.56%) and a specificity of 100% (30/30, 95% CI = 88.65–100%). It also had a high concordance rate of 98.88% with the real-time fluorescence polymerase chain reaction assay. Conclusions The CRISPR-GBS assay can be used for rapid and high-sensitivity detection of GBS in a simple and cost-efficient manner; thus, it offers a novel method for intrapartum screening.

show abstract

Hairpin‐Spacer crRNA‐Enhanced CRISPR/Cas13a System Promotes the Specificity of Single Nucleotide Polymorphism (SNP) Identification

Cited by 49 publications

References 47 publications

Poly (N-vinylpyrrolidone) Modification Mitigates Plasma Protein Corona Formation on Phosphomolybdate-based Nanoparticles

Poly (N-vinylpyrrolidone) Modification Mitigates Plasma Protein Corona Formation on Phosphomolybdate-based Nanoparticles

CRISPR as a Diagnostic Tool

CRISPR/Cas12a-Based Assay for the Rapid and High-Sensitivity Detection of Streptococcus Agalactiae Colonization in Pregnant Women with Premature Rupture of Membrane

Contact Info

Product

Resources

About