| Publication |
Sentence |
Publish Date |
Extraction Date |
Species |
| Svetlana V Baranova, Polina V Zhdanova, Anastasia D Koveshnikova, Pavel E Pestryakov, Ivan P Vokhtantsev, Alexander A Chernonosov, Vladimir V Kova. Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features. International journal of molecular sciences. vol 25. issue 19. 2024-10-16. PMID:39409191. |
we show that mismatches in the complementarity of the sgrna/dna duplex at different positions relative to the protospacer adjacent motif (pam) sequence tend to decrease the cleavage efficiency and increase the half-maximal reaction time. |
2024-10-16 |
2024-10-18 |
Not clear |
| Shishi Liu, Yao He, Tingting Fan, Meirui Zhu, Caiyan Qi, Yanqin Ma, Mengqiao Yang, Liang Yang, Xu Tang, Jianping Zhou, Zhaohui Zhong, Xueli An, Yiping Qi, Yong Zhan. PAM-relaxed and temperature-tolerant CRISPR-Mb3Cas12a single transcript unit systems for efficient singular and multiplexed genome editing in rice, maize, and tomato. Plant biotechnology journal. 2024-10-10. PMID:39387219. |
protospacer adjacent motif (pam) requirements, editing efficiencies, and editing profiles are compared in rice. |
2024-10-10 |
2024-10-16 |
Not clear |
| Sofia Lemak, Greg Brown, Kira S Makarova, Eugene V Koonin, Alexander F Yakuni. Biochemical plasticity of the Escherichia coli CRISPR Cascade revealed by in vitro reconstitution of Cascade activities from purified Cas proteins. The FEBS journal. 2024-10-08. PMID:39375921. |
the escherichia coli cascade complex consists of 11 protein subunits and functions as an effector through crispr rna (crrna) binding, protospacer adjacent motif (pam)-specific double-stranded dna targeting, r-loop formation, and cas3 helicase-nuclease recruitment for target dna cleavage. |
2024-10-08 |
2024-10-10 |
Not clear |
| Shen Huang, Yongliang Lou, Laibao Zhen. Synergistic effect of split DNA activators of Cas12a with exon-unwinding and induced targeting effect. Nucleic acids research. 2024-09-11. PMID:39258555. |
we demonstrate that upon binding of split dna activators adjacent to the protospacer adjacent motif (pam) to the cas12a ribonucleoprotein (cas12a-rnp), a ternary complex form that can capture and interact with distal split dna activators to achieve synergistic effects. |
2024-09-11 |
2024-09-13 |
Not clear |
| Qiaochu Wang, Gundra Sivakrishna Rao, Tin Marsic, Rashid Aman, Magdy Mahfou. Fusion of FokI and catalytically inactive prokaryotic Argonautes enables site-specific programmable DNA cleavage. The Journal of biological chemistry. 2024-08-30. PMID:39214308. |
prokaryotic argonaute (pago) proteins have received much attention as biotechnological tools due to their ability to recognize specific target sequences without a protospacer adjacent motif (pam), but their lack of intrinsic double-stranded dna (dsdna) unwinding activity limits their utility in key applications such as gene editing. |
2024-08-30 |
2024-09-04 |
Not clear |
| Dhawane Yogi, Karuppannasamy Ashok, Cholenahalli Narayanappa Anu, Thalooru Shashikala, Chalapathy Pradeep, Chikmagalur Nagaraja Bhargava, Madhusoodanan Sujatha Parvathy, M N Jithesh, Maligeppagol Manamohan, Girish Kumar Jha, Ramasamy Asoka. CRISPR/Cas12a ribonucleoprotein mediated editing of tryptophan 2,3-dioxygenase of Spodoptera frugiperda. Transgenic research. 2024-08-29. PMID:39210187. |
as opposed to cas9 which requires a gc-rich protospacer adjacent motif (pam), cas12a requires a t-rich pam and causes staggered cleavage in the target dna, opening possibilities for multiplexing. |
2024-08-29 |
2024-09-04 |
drosophila_melanogaster |
| Xiao Chen, Zhaohui Zhong, Xu Tang, Suxin Yang, Yaohua Zhang, Shoudong Wang, Yiqian Liu, Ye Zhang, Xuelian Zheng, Yong Zhang, Xianzhong Fen. Advancing PAM-less genome editing in soybean using CRISPR-SpRY. Horticulture research. vol 11. issue 8. 2024-08-07. PMID:39108580. |
although crispr-cas9 technology has been rapidly applied in soybean genetic improvement, it is difficult to achieve the targeted editing of the specific loci in the soybean complex genome due to the limitations of the classical protospacer adjacent motif (pam). |
2024-08-07 |
2024-08-09 |
Not clear |
| Akiyoshi Nakamura, Hiroshi Yamamoto, Tsubasa Yano, Reika Hasegawa, Yoichi Makino, Nobutaka Mitsuda, Teruhiko Terakawa, Seiichiro Ito, Shigeo S Sugan. Expanding the Genome-Editing Toolbox with The CRISPR journal. 2024-08-07. PMID:39111827. |
expanding the genome-editing toolbox with the genome-editing efficiency of the crispr-cas9 system hinges on the recognition of the protospacer adjacent motif (pam) sequence, which is essential for cas9 binding to dna. |
2024-08-07 |
2024-08-10 |
Not clear |
| Fuqiang Huang, Xin Li, Yule Zhou, Wenqiang Tang, Zhisheng Dang, Jun Kui, Chunxia Zhang, Xu Zhan. Optimization of CRISPR/Cas12a detection assay and its application in the detection of Echinococcus granulosus. Veterinary parasitology. vol 331. 2024-08-01. PMID:39089176. |
in this study, we present a one-pot crispr/cas12a detection method for e. granulosus (genotype g1, sheep strain) integrating recombinase polymerase amplification (rpa) with suboptimal protospacer adjacent motif (pam) and structured crispr rna (crrna) to enhance reaction efficiency. |
2024-08-01 |
2024-08-05 |
dog |
| Yunqian Zhang, Jingjing Wei, Hongyan Wang, Yongming Wan. Characterization of NiCas12b for In Vivo Genome Editing. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2024-07-30. PMID:39076074. |
particularly noteworthy is the nicas12b derived from nitrospira sp., which recognizes a "ttn" protospacer adjacent motif (pam) and facilitates efficient genome editing in various cell lines. |
2024-07-30 |
2024-08-02 |
mouse |
| Kelly E W Carufe, Nicholas G Economos, Peter M Glaze. Peptide Nucleic Acid-Mediated Regulation of CRISPR-Cas9 Specificity. Nucleic acid therapeutics. 2024-07-22. PMID:39037032. |
our findings reveal that pnas bound in the region distal to the protospacer adjacent motif (pam) site effectively enhance specificity in both on-target/off-target and allele-specific scenarios. |
2024-07-22 |
2024-07-24 |
Not clear |
| Tao Hu, Quanquan Ji, Xinxin Ke, Hufeng Zhou, Senfeng Zhang, Shengsheng Ma, Chenlin Yu, Wenjun Ju, Meiling Lu, Yu Lin, Yangjing Ou, Yingsi Zhou, Yibei Xiao, Chunlong Xu, Chunyi H. Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV). Communications biology. vol 7. issue 1. 2024-07-13. PMID:39003402. |
this type i-a crispr-cas3 system not only exhibits an expanded protospacer adjacent motif (pam) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. |
2024-07-13 |
2024-07-16 |
human |
| Chenyu Cui, Guihuan Guo, Ting-Hsuan Che. Toehold region triggered CRISPR/Cas12a trans-cleavage for detection of uracil-DNA glycosylase activity. Biotechnology journal. vol 19. issue 7. 2024-07-10. PMID:38987221. |
this protospacer adjacent motif (pam)-free approach achieves remarkable sensitivity and specificity in detecting udg, with a detection limit as low as 0.000368 u ml |
2024-07-10 |
2024-07-13 |
Not clear |
| Wenjing Li, Xuan Li, Chunyang Wang, Guanzhong Huo, Xinru Zhang, Jintai Yu, Xiaoxiao Yu, Jing Li, Chao Zhang, Jianjun Zhao, Yan Li, Jun L. Expanding the targeting scope of CRISPR/Cas9-mediated genome editing by Cas9 variants in aBIOTECH. vol 5. issue 2. 2024-07-08. PMID:38974859. |
however, the strict requirement for a protospacer adjacent motif (pam) has hindered the application of the crispr/cas9 system because the number of targetable genomic sites is limited. |
2024-07-08 |
2024-07-11 |
Not clear |
| Jian Wang, Ke Wang, Zhe Deng, Zhiyu Zhong, Guo Sun, Qing Mei, Fuling Zhou, Zixin Deng, Yuhui Su. Engineered cytosine base editor enabling broad-scope and high-fidelity gene editing in Streptomyces. Nature communications. vol 15. issue 1. 2024-07-06. PMID:38971862. |
base editing (be) faces protospacer adjacent motif (pam) constraints and off-target effects in both eukaryotes and prokaryotes. |
2024-07-06 |
2024-07-11 |
Not clear |
| Wei Qin, Fang Liang, Sheng-Jia Lin, Cassidy Petree, Kevin Huang, Yu Zhang, Lin Li, Pratishtha Varshney, Philippe Mourrain, Yanmei Liu, Gaurav K Varshne. ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish. Nature communications. vol 15. issue 1. 2024-07-04. PMID:38965236. |
however, base editors are restricted by protospacer adjacent motif (pam) sequences and specific editing windows, hindering their applicability to a broad spectrum of genetic variants. |
2024-07-04 |
2024-07-08 |
zebrafish |
| Yao Yao, Zhiwei Zhou, Xiaoling Wang, Zhirui Liu, Yixin Zhai, Xiaolin Chi, Jingyi Du, Liheng Luo, Zhigang Zhao, Xiaoyue Wang, Chaoyou Xue, Shuquan Ra. SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. Cell genomics. 2024-06-18. PMID:38889719. |
crispr mutagenesis screens conducted with spcas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (pam) sequences. |
2024-06-18 |
2024-06-21 |
Not clear |
| Hyogu Han, Se Hee Jang, Jun Ki Ahn, Chang Yeol Le. DNA repair-retarded isothermal CRISPR amplification for rapid, sensitive base excision repair enzyme assay. Analytica chimica acta. vol 1314. 2024-06-14. PMID:38876521. |
after isothermal amplification, a crispr/cas reagent should be separately added with extra manual steps and its guide rna (grna) should be designed, considering the presence of protospacer adjacent motif (pam) site. |
2024-06-14 |
2024-06-17 |
Not clear |
| Pengda Liang, Bei Lv, Ke Chen, Dawei L. Sensitive aptasensing of ATP based on a PAM site-regulated CRISPR/Cas12a activation. Mikrochimica acta. vol 191. issue 7. 2024-06-12. PMID:38867016. |
in the current study, the duplex protospacer adjacent motif (pam) in the activator of crispr/cas12a was used as a molecular switch, and a sensitive adenosine triphosphate (atp) detection biosensor was constructed using an allosteric probe-conjugated pam site formation in hybridization chain reaction (hcr) integrated with the crispr/cas12a system (apf-crispr). |
2024-06-12 |
2024-06-15 |
Not clear |
| Jianlin Zheng, Yuwei Zhu, Tengjin Huang, Wenbo Gao, Jiale He, Zhiwei Huan. Inhibition mechanisms of CRISPR-Cas9 by AcrIIA25.1 and AcrIIA32. Science China. Life sciences. 2024-06-06. PMID:38842649. |
we found that both acriia25.1 and acriia32 directly interact with the wed domain, where they spatially obstruct conformational changes of the wed and pi domains, thereby inhibiting spycas9 from recognizing protospacer adjacent motif (pam) and unwinding double-stranded dna. |
2024-06-06 |
2024-06-08 |
human |