keyword
https://read.qxmd.com/read/38499480/engineering-an-escherichia-coli-strain-for-production-of-long-single-stranded-dna
#21
JOURNAL ARTICLE
Konlin Shen, Jake J Flood, Zhihuizi Zhang, Alvin Ha, Brian R Shy, John E Dueber, Shawn M Douglas
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered Escherichia coli 'helper' strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E...
March 18, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38498914/competition-between-stacking-and-divalent-cation-mediated-electrostatic-interactions-determines-the-conformations-of-short-dna-sequences
#22
JOURNAL ARTICLE
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Interplay between divalent cations (Mg2+ and Ca2+ ) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30 , with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments...
March 18, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38497742/a-poly-aptamer-encoded-dna-nanocatcher-informs-efficient-virus-trapping
#23
JOURNAL ARTICLE
Yunhua Guo, Wenzhe Song, Yuhang Dong, Xuejun Wang, Guangjun Nie, Feng Li
Broad-spectrum antiviral platforms are always desired but still lack the ability to cope with the threats to global public health. Herein, we develop a poly aptamer encoded DNA nanocatcher platform that can trap entire virus particles to inhibit infection with a broad antiviral spectrum. Ultralong single-stranded DNA (ssDNA) containing repeated aptamers was synthesized as the scaffold of a nanocatcher via a biocatalytic process, wherein mineralization of magnesium pyrophosphate on the ssDNA could occur and consequently lead to the formation of nanocatcher with interfacial nanocaves decorated with virus-binding aptamers...
March 18, 2024: Nano Letters
https://read.qxmd.com/read/38497564/-in-silico-study-on-a-binding-mechanism-of-ssdna-aptamers-targeting-glycosidic-bond-containing-small-molecules
#24
JOURNAL ARTICLE
Jiaqing Li, Tong Xu, Yalan Zheng, Dongdong Liu, Chen Zhang, Jianjun Li, Zhuo A Wang, Yuguang Du
Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N -acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico , and analyzed factors contributing to their binding affinities...
March 18, 2024: Analytical Chemistry
https://read.qxmd.com/read/38497410/highly-selective-detection-of-deoxyribonucleic-acid-in-living-cells-using-reca-green-fluorescent-protein-single-stranded-deoxyribonucleic-acid-filament-fluorescence-resonance-energy-transfer-probe
#25
JOURNAL ARTICLE
Chunlei Wang, Yuanfu Zhang, Wenyue Gong, Shuhao Wang
A fluorescence resonance energy transfer (FRET) method was developed for double-stranded deoxyribonucleic acid (dsDNA) detection in living cells using the RecA-GFP (green fluorescent protein) fusion protein filament. In brief, the thiol-modified single-stranded DNA (ssDNA) was attached to gold nanoparticles (AuNPs); on the contrary, the prepared RecA-GFP fusion protein interacted with ssDNA. Due to the FRET between AuNPs and RecA-GFP, fluorescence of RecA-GFP fusion protein was quenched. In the presence of homologous dsDNA, homologous recombination occurred to release RecA-GFP fusion protein...
March 2024: Luminescence: the Journal of Biological and Chemical Luminescence
https://read.qxmd.com/read/38497408/novel-methods-for-the-rapid-and-sensitive-detection-of-nipah-virus-based-on-a-crispr-cas12a-system
#26
JOURNAL ARTICLE
Xi Yang, Kexin Xu, Siying Li, Jiangnian Zhang, Yinli Xie, Yongliang Lou, Xingxing Xiao
Nipah virus (NiV), a bat-borne zoonotic viral pathogen with high infectivity and lethality to humans, has caused severe outbreaks in several countries of Asia during the past two decades. Because of the worldwide distribution of the NiV natural reservoir, fruit bats, and lack of effective treatments or vaccines for NiV, routine surveillance and early detection are the key measures for containing NiV outbreaks and reducing its influence. In this study, we developed two rapid, sensitive and easy-to-conduct methods, RAA-CRISPR/Cas12a-FQ and RAA-CRISPR/Cas12a-FB, for NiV detection based on a recombinase-aided amplification (RAA) assay and a CRISPR/Cas12a system by utilizing dual-labeled fluorophore-quencher or fluorophore-biotin ssDNA probes...
March 18, 2024: Analyst
https://read.qxmd.com/read/38490833/the-rna-tether-model-for-human-chromosomal-translocation-fragile-zones
#27
REVIEW
Di Liu, Chih-Lin Hsieh, Michael R Lieber
One of the two chromosomal breakage events in recurring translocations in B cell neoplasms is often due to the recombination-activating gene complex (RAG complex) releasing DNA ends before end joining. The other break occurs in a fragile zone of 20-600 bp in a non-antigen receptor gene locus, with a more complex and intriguing set of mechanistic factors underlying such narrow fragile zones. These factors include activation-induced deaminase (AID), which acts only at regions of single-stranded DNA (ssDNA). Recent work leads to a model involving the tethering of AID to the nascent RNA as it emerges from the RNA polymerase...
March 14, 2024: Trends in Biochemical Sciences
https://read.qxmd.com/read/38490040/enhanced-cellular-internalization-of-near-infrared-fluorescent-single-walled-carbon-nanotubes-facilitated-by-a-transfection-reagent
#28
JOURNAL ARTICLE
Naamah Levin, Adi Hendler-Neumark, Dotan Kamber, Gili Bisker
Functionalized single-walled carbon nanotubes (SWCNTs) hold immense potential for diverse biomedical applications due to their biocompatibility and optical properties, including near-infrared fluorescence. Specifically, SWCNTs have been utilized to target cells as a vehicle for drug delivery and gene therapy, and as sensors for various intracellular biomarkers. While the main internalization route of SWCNTs into cells is endocytosis, methods for enhancing the cellular uptake of SWCNTs are of great importance...
March 6, 2024: Journal of Colloid and Interface Science
https://read.qxmd.com/read/38489095/microrna-sensors-based-on-crispr-cas12a-technologies-evolution-from-indirect-to-direct-detection
#29
REVIEW
Songcheng Yu, Xueying Lei, Chenling Qu
MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a...
March 15, 2024: Critical Reviews in Analytical Chemistry
https://read.qxmd.com/read/38488707/a-dual-reference-study-design-for-understanding-and-improving-aav-genome-size-analysis
#30
JOURNAL ARTICLE
Yali Sun, Zhi-Xiang Lu, Michael Miller, Ying Valcour, Anis H Khimani, Jana Bauer, Michael Salomon, Yanhong Tong
Recombinant adeno-associated virus (rAAV) is the leading platform of gene delivery for its long-lasting gene transformation and low immunogenicity. Characterization of the integrity and purity of the rAAV genome is critical to ensure clinical potency and safety. However, current rAAV genome characterization methods that can provide size assessment are either time-consuming or not easily accessible to general labs. Additionally, there is a lack of right reference standard for analyzing long single-stranded DNA (ssDNA) fragments...
March 15, 2024: Electrophoresis
https://read.qxmd.com/read/38487270/timeless-tipin-interactions-with-mcm-and-rpa-mediate-dna-replication-stress-response
#31
JOURNAL ARTICLE
Paulina Prorok, Eva Wolf, M Cristina Cardoso
The accuracy of replication is one of the most important mechanisms ensuring the stability of the genome. The fork protection complex prevents premature replisome stalling and/or premature disassembly upon stress. Here, we characterize the Timeless-Tipin complex, a component of the fork protection complex. We used microscopy approaches, including colocalization analysis and proximity ligation assay, to investigate the spatial localization of the complex during ongoing replication in human cells. Taking advantage of the replication stress induction and the ensuing polymerase-helicase uncoupling, we characterized the Timeless-Tipin localization within the replisome...
2024: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/38484860/studying-the-ssdna-loaded-adeno-associated-virus-aggregation-using-coarse-grained-molecular-dynamics-simulations
#32
JOURNAL ARTICLE
Tibo Duran, Shivangi Naik, Leila Sharifi, Willow R DiLuzio, Arani Chanda, Bodhisattwa Chaudhuri
The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i...
March 12, 2024: International Journal of Pharmaceutics
https://read.qxmd.com/read/38481135/structural-motifs-at-the-telomeres-and-their-role-in-regulatory-pathways
#33
REVIEW
Abeer F R Alanazi, Gary N Parkinson, Shozeb Haider
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand...
March 14, 2024: Biochemistry
https://read.qxmd.com/read/38478499/amplification-free-analysis-of-bladder-cancer-micrornas-on-wrinkled-silica-nanoparticles-with-dna-functionalized-quantum-dots
#34
JOURNAL ARTICLE
Pei Wang, Xiaowei Wei, Luming Shen, Kexin Xu, Zhongting Wen, Nengjiao Gao, Ting Fan, Shenmei Xun, Qingyi Zhu, Xiaojun Qu, Yefei Zhu
Bladder cancer (BC) occurrence and progression are accompanied by alterations in microRNAs (miRNAs) expression levels. Simultaneous detection of multiple miRNAs contributes to the accuracy and reliability of the BC diagnosis. In this work, wrinkled silica nanoparticles (WSNs) were applied as the microreactor for multiplex miRNAs analysis without enzymes or nucleic acid amplification. Conjugated on the surface of WSNs, the S9.6 antibody was adopted as the universal module for binding DNA/miRNA duplexes, regardless of their sequence...
March 13, 2024: Analytical Chemistry
https://read.qxmd.com/read/38477377/determinants-of-crispr-cas12a-nuclease-activation-by-dna-and-rna-targets
#35
JOURNAL ARTICLE
Eric A Nalefski, Remy M Kooistra, Ishira Parikh, Samantha Hedley, Karunya Rajaraman, Damian Madan
The RNA-guided CRISPR-associated (Cas) enzyme Cas12a cleaves specific double-stranded (ds-) or single-stranded (ss-) DNA targets (in cis), unleashing non-specific ssDNA cleavage (in trans). Though this trans-activity is widely coopted for diagnostics, little is known about target determinants promoting optimal enzyme performance. Using quantitative kinetics, we show formation of activated nuclease proceeds via two steps whereby rapid binding of Cas12a ribonucleoprotein to target is followed by a slower allosteric transition...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477342/an-autocatalytic-crispr-cas-amplification-effect-propelled-by-the-lna-modified-split-activators-for-dna-sensing
#36
JOURNAL ARTICLE
Ke Sun, Lei Pu, Chuan Chen, Mutian Chen, Kaiju Li, Xinqiong Li, Huanqing Li, Jia Geng
CRISPR-Cas systems with dual functions offer precise sequence-based recognition and efficient catalytic cleavage of nucleic acids, making them highly promising in biosensing and diagnostic technologies. However, current methods encounter challenges of complexity, low turnover efficiency, and the necessity for sophisticated probe design. To better integrate the dual functions of Cas proteins, we proposed a novel approach called CRISPR-Cas Autocatalysis Amplification driven by LNA-modified Split Activators (CALSA) for the highly efficient detection of single-stranded DNA (ssDNA) and genomic DNA...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38472229/znf827-is-a-single-stranded-dna-binding-protein-that-regulates-the-atr-chk1-dna-damage-response-pathway
#37
JOURNAL ARTICLE
Sile F Yang, Christopher B Nelson, Jadon K Wells, Madushan Fernando, Robert Lu, Joshua A M Allen, Lisa Malloy, Noa Lamm, Vincent J Murphy, Joel P Mackay, Andrew J Deans, Anthony J Cesare, Alexander P Sobinoff, Hilda A Pickett
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827...
March 12, 2024: Nature Communications
https://read.qxmd.com/read/38472177/functionalized-graphene-oxide-grids-enable-high-resolution-cryo-em-structures-of-the-snf2h-nucleosome-complex-without-crosslinking
#38
JOURNAL ARTICLE
Un Seng Chio, Eugene Palovcak, Anton A A Smith, Henriette Autzen, Elise N Muñoz, Zanlin Yu, Feng Wang, David A Agard, Jean-Paul Armache, Geeta J Narlikar, Yifan Cheng
Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). Here, to address this issue, we develop graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitate collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking...
March 12, 2024: Nature Communications
https://read.qxmd.com/read/38470036/the-intrinsically-disordered-linker-in-the-single-stranded-dna-binding-protein-influences-dna-replication-restart-and-recombination-pathways-in-escherichia-coli-k-12
#39
JOURNAL ARTICLE
Steven J Sandler, Nina J Bonde, Elizabeth A Wood, Michael M Cox, James L Keck
Tetrameric single-stranded (ss) DNA-binding proteins (SSBs) stabilize ssDNA intermediates formed during genome maintenance reactions in Bacteria . SSBs also recruit proteins important for these processes through direct SSB-protein interactions, including proteins involved in DNA replication restart and recombination processes. SSBs are composed of an N-terminal oligomerization and ssDNA-binding domain, a C-terminal acidic tip that mediates SSB-protein interactions, and an internal intrinsically disordered linker (IDL)...
March 12, 2024: Journal of Bacteriology
https://read.qxmd.com/read/38467834/atr-limits-rad18-mediated-pcna-monoubiquitination-to-preserve-replication-fork-and-telomerase-independent-telomere-stability
#40
JOURNAL ARTICLE
Siyuan Chen, Chen Pan, Jun Huang, Ting Liu
Upon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18...
March 11, 2024: EMBO Journal
keyword
keyword
117373
2
3
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.