A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA

2018 ◽  
Vol 185 (2) ◽  
Author(s):  
Haiyan Ma ◽  
Zongbing Li ◽  
Ning Xue ◽  
Zhiyuan Cheng ◽  
Xiangmin Miao
Keyword(s):  
Gold Nanoparticle ◽  
Fluorescent Probe ◽  
Single Stranded Dna ◽  
Double Stranded Dna

A Requirement for Recombinational Repair in Saccharomyces cerevisiae Is Caused by DNA Replication Defects of mec1 Mutants

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 595-605 ◽  
Author(s):  
Bradley J Merrill ◽  
Connie Holm
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Synthetic Lethality ◽  
Velocity Sedimentation ◽  
Recombinational Repair ◽  
Repair Pathway ◽  
Dna Breaks ◽  
Single Stranded Dna ◽  
Double Stranded Dna

Abstract To examine the role of the RAD52 recombinational repair pathway in compensating for DNA replication defects in Saccharomyces cerevisiae, we performed a genetic screen to identify mutants that require Rad52p for viability. We isolated 10 mec1 mutations that display synthetic lethality with rad52. These mutations (designated mec1-srf for synthetic lethality with rad-fifty-two) simultaneously cause two types of phenotypes: defects in the checkpoint function of Mec1p and defects in the essential function of Mec1p. Velocity sedimentation in alkaline sucrose gradients revealed that mec1-srf mutants accumulate small single-stranded DNA synthesis intermediates, suggesting that Mec1p is required for the normal progression of DNA synthesis. sml1 suppressor mutations suppress both the accumulation of DNA synthesis intermediates and the requirement for Rad52p in mec1-srf mutants, but they do not suppress the checkpoint defect in mec1-srf mutants. Thus, it appears to be the DNA replication defects in mec1-srf mutants that cause the requirement for Rad52p. By using hydroxyurea to introduce similar DNA replication defects, we found that single-stranded DNA breaks frequently lead to double-stranded DNA breaks that are not rapidly repaired in rad52 mutants. Taken together, these data suggest that the RAD52 recombinational repair pathway is required to prevent or repair double-stranded DNA breaks caused by defective DNA replication in mec1-srf mutants.

scholarly journals DNA Binding by the Methanothermobacter thermautotrophicus Cdc6 Protein Is Inhibited by the Minichromosome Maintenance Helicase

2006 ◽  
Vol 188 (12) ◽  
pp. 4577-4580 ◽  
Author(s):  
Rajesh Kasiviswanathan ◽  
Jae-Ho Shin ◽  
Zvi Kelman
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Minichromosome Maintenance ◽  
Single Stranded Dna ◽  
Mutant Proteins ◽  
Dna Binding Activity ◽  
Double Stranded Dna ◽  
Mcm Helicase ◽  
Methanothermobacter Thermautotrophicus

ABSTRACT The Cdc6 proteins from the archaeon Methanothermobacter thermautotrophicus were previously shown to bind double-stranded DNA. It is shown here that the proteins also bind single-stranded DNA. Using minichromosome maintenance (MCM) helicase mutant proteins unable to bind DNA, it was found that the interaction of MCM with Cdc6 inhibits the DNA binding activity of Cdc6.

scholarly journals Archaeal Orc1 protein interacts with T-rich single-stranded DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Katarzyna Wegrzyn ◽  
Igor Konieczny
Keyword(s):  
Dna Replication ◽  
Replication Initiation ◽  
Single Stranded Dna ◽  
Dna Replication Initiation ◽  
Double Stranded Dna ◽  
Nucleoprotein Complexes ◽  
Eukaryotic Organisms ◽  
Replication Initiation Proteins ◽  
Hydrolysis Of ◽  
Replication Activity

Abstract Objective The ability to form nucleoprotein complexes is a fundamental activity of DNA replication initiation proteins. They bind within or nearby the region of replication origin what results in melting of a double-stranded DNA (dsDNA) and formation of single-stranded DNA (ssDNA) region where the replication machinery can assemble. For prokaryotic initiators it was shown that they interact with the formed ssDNA and that this interaction is required for the replication activity. The ability to interact with ssDNA was also shown for Saccharomyces cerevisiae replication initiation protein complex ORC. For Archaea, which combine features of both prokaryotic and eukaryotic organisms, there was no evidence whether DNA replication initiators can interact with ssDNA. We address this issue in this study. Results Using purified Orc1 protein from Aeropyrum pernix (ApOrc1) we analyzed its ability to interact with ssDNA containing sequence of an AT-rich region of the A. pernix origin Ori1 as well as with homopolymers of thymidine (polyT) and adenosine (polyA). The Bio-layer interferometry, surface plasmon resonance and microscale thermophoresis showed that the ApOrc1 can interact with ssDNA and it binds preferentially to T-rich ssDNA. The hydrolysis of ATP is not required for this interaction.

Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation

The Analyst ◽  
2019 ◽  
Vol 144 (7) ◽  
pp. 2284-2290 ◽  
Author(s):  
Wei Zhou ◽  
Ze Yu ◽  
Ge Ma ◽  
Tian Jin ◽  
Yunchao Li ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Thioflavin T ◽  
Duplex Dna ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Double Stranded Dna ◽  
Nucleotide Mutation

Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).

A fluorescence assay for microRNA let-7a by a double-stranded DNA modified gold nanoparticle nanoprobe combined with graphene oxide

The Analyst ◽  
2020 ◽  
Vol 145 (4) ◽  
pp. 1190-1194 ◽  
Author(s):  
Yuanyuan Gao ◽  
Jingjing Tian ◽  
Xing Zhang ◽  
Bin Qiao ◽  
Yang Cao ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Gold Nanoparticle ◽  
Fluorescence Assay ◽  
Double Stranded Dna ◽  
Fluorescence Switching

A fluorescence switching platform was developed to monitor target microRNA let-7a by coupling dsDNA–AuNPs with the GO nanosheet.

scholarly journals How to copy and paste DNA microarrays

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefan D. Krämer ◽  
Johannes Wöhrle ◽  
Philipp A. Meyer ◽  
Gerald A. Urban ◽  
Günter Roth
Keyword(s):  
Real Time ◽  
Dna Microarray ◽  
Dna Microarrays ◽  
Label Free ◽  
Binding Assays ◽  
Single Stranded Dna ◽  
Whole Process ◽  
Double Stranded Dna ◽  
Cost Efficient ◽  
Copy And Paste

Abstract Analogous to a photocopier, we developed a DNA microarray copy technique and were able to copy patterned original DNA microarrays. With this process the appearance of the copied DNA microarray can also be altered compared to the original by producing copies of different resolutions. As a homage to the very first photocopy made by Chester Charlson and Otto Kornei, we performed a lookalike DNA microarray copy exactly 80 years later. Those copies were also used for label-free real-time kinetic binding assays of apo-dCas9 to double stranded DNA and of thrombin to single stranded DNA. Since each DNA microarray copy was made with only 5 µl of spPCR mix, the whole process is cost-efficient. Hence, our DNA microarray copier has a great potential for becoming a standard lab tool.

scholarly journals Effects of recJ, recQ, and recFOR Mutations on Recombination in Nuclease-Deficient recB recD Double Mutants of Escherichia coli

2005 ◽  
Vol 187 (4) ◽  
pp. 1350-1356 ◽  
Author(s):  
Ivana Ivančić-Baće ◽  
Erika Salaj-Šmic ◽  
Krunoslav Brčić-Kostić
Keyword(s):  
Escherichia Coli ◽  
Double Mutant ◽  
Reca Protein ◽  
Recq Helicase ◽  
Single Stranded Dna ◽  
Double Stranded Dna ◽  
Recf Pathway ◽  
Recombination Pathway ◽  
Recbcd Enzyme ◽  
Dna Ends

ABSTRACT The two main recombination pathways in Escherichia coli (RecBCD and RecF) have different recombination machineries that act independently in the initiation of recombination. Three essential enzymatic activities are required for early recombinational processing of double-stranded DNA ends and breaks: a helicase, a 5′→3′ exonuclease, and loading of RecA protein onto single-stranded DNA tails. The RecBCD enzyme performs all of these activities, whereas the recombination machinery of the RecF pathway consists of RecQ (helicase), RecJ (5′→3′ exonuclease), and RecFOR (RecA-single-stranded DNA filament formation). The recombination pathway operating in recB (nuclease-deficient) mutants is a hybrid because it includes elements of both the RecBCD and RecF recombination machineries. In this study, genetic analysis of recombination in a recB (nuclease-deficient) recD double mutant was performed. We show that conjugational recombination and DNA repair after UV and gamma irradiation in this mutant are highly dependent on recJ, partially dependent on recFOR, and independent of recQ. These results suggest that the recombination pathway operating in a nuclease-deficient recB recD double mutant is also a hybrid. We propose that the helicase and RecA loading activities belong to the RecBCD recombination machinery, while the RecJ-mediated 5′→3′ exonuclease is an element of the RecF recombination machinery.

scholarly journals Spontaneous ssDNA stretching on graphene and hexagonal boron nitride in plane heterostructures

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Binquan Luan ◽  
Ruhong Zhou
Keyword(s):  
Boron Nitride ◽  
Genome Analysis ◽  
Hexagonal Boron Nitride ◽  
Persistence Length ◽  
Atomic Resolution ◽  
Two Dimensional ◽  
Planar Surface ◽  
Single Stranded Dna ◽  
Double Stranded Dna ◽  
Material Fabrication

Abstract Single-stranded DNA (ssDNA) molecules in solution typically form coiled structures, therefore stretching ssDNA is extremely crucial before applying any nanotechnology for ssDNA analysis. Recent advances in material fabrication enable the deployment of nanochannels to manipulate, stretch, sort and map double-stranded DNA (dsDNA) molecules, however nanochannels fail to stretch ssDNA molecules due to the ultra-short persistence length and the potential nonspecific-interaction-induced clogging. Given the significance of ssDNA stretching in genome analysis, here we report an ssDNA stretching platform: two dimensional in-plane heterostructure comprising graphene and hexagonal boron nitride (h-BN), and show that ssDNA can be stretched on a h-BN nanostripe sandwiched between two adjacent graphene domains (“nanochannel”). We further show that with a biasing voltage the stretched ssDNA can be electrophoretically transported along the “nanochannel”, allowing easy controls/manipulations. When being conveniently integrated with existing atomic resolution sensors, the heterostructure platform paves the way for sequencing DNA on a planar surface.

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