2-Substituted 2′-deoxyinosine 5′-triphosphates as substrates for polymerase synthesis of minor-groove-modified DNA and effects on restriction endonuclease cleavage

2020 ◽  
Vol 18 (2) ◽  
pp. 255-262 ◽  
Author(s):  
Ján Matyašovský ◽  
Michal Hocek
Keyword(s):  
Restriction Endonuclease ◽  
Enzymatic Synthesis ◽  
Minor Groove ◽  
Restriction Endonucleases ◽  
Modified Dna ◽  
Restriction Endonuclease Cleavage ◽  
Synthetic Transformations

Enzymatic synthesis of DNA modified in the minor groove and study of its post-synthetic transformations and cleavage by restriction endonucleases.

scholarly journals Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

2018 ◽  
Author(s):  
Bernardo Pollak ◽  
Ariel Cerda ◽  
Mihails Delmans ◽  
Simón Álamos ◽  
Tomás Moyano ◽  
...  
Keyword(s):  
Open Access ◽  
Restriction Endonuclease ◽  
Open System ◽  
High Efficiency ◽  
Restriction Endonucleases ◽  
Dna Assembly ◽  
Hybrid Assembly ◽  
Standard Level ◽  
Parallel Assembly ◽  
Restriction Endonuclease Cleavage

AbstractHigh efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.

scholarly journals Crystallization and preliminary X-ray analysis of the type IV restriction endonuclease ScoMcrA fromStreptomyces coelicolor, which cleaves both Dcm-methylated DNA and phosphorothioated DNA

2015 ◽  
Vol 71 (1) ◽  
pp. 57-60 ◽  
Author(s):  
Guang Liu ◽  
Zhenyi Zhang ◽  
Gong Zhao ◽  
Zixin Deng ◽  
Geng Wu ◽  
...  
Keyword(s):  
Restriction Endonuclease ◽  
Streptomyces Coelicolor ◽  
Restriction Endonucleases ◽  
Type I ◽  
Strand Breaks ◽  
Cell Parameters ◽  
Methylated Dna ◽  
Detailed Structural Analysis ◽  
Type Iv ◽  
Modified Dna

ScoMcrA is a type IV modification-dependent restriction endonuclease found in the model strainStreptomyces coelicolor. Unlike type I, II and III restriction endonucleases, which cleave unmodified DNA, type IV restriction endonucleases cleave modified DNA, including methylated, hydroxymethylated, glucosyl-hydroxymethylated and phosphorothioated DNA. ScoMcrA targets both Dcm-methylated DNA and phosphorothioated DNA, and makes double-strand breaks 16–28 nt away from the modified nucleotides or the phosphorothioate links. However, the mechanism by which ScoMcrA recognizes these two entirely different types of modification remains unclear. In this study, the ScoMcrA protein was overexpressed, purified and crystallized. The crystals diffracted to 3.35 Å resolution and belonged to space groupP212121. The unit-cell parameters were determined to bea= 130.19,b= 139.36,c= 281.01 Å, α = β = γ = 90°. These results will facilitate the detailed structural analysis of ScoMcrA and further elucidation of its biochemical mechanism.

Localization of kinetoplast DNA maxicircle transcripts in bloodstream and procyclic form Trypanosoma brucei

1982 ◽  
Vol 2 (7) ◽  
pp. 845-852
Author(s):  
K D Stuart ◽  
S B Gelvin
Keyword(s):  
Restriction Endonuclease ◽  
Trypanosoma Brucei ◽  
Variable Region ◽  
Cleavage Sites ◽  
Kinetoplast Dna ◽  
Coding Sequences ◽  
Procyclic Form ◽  
Restriction Endonuclease Cleavage ◽  
Mitochondrial Respiratory

Over 80% of the maxicircle and numerous minicircles of Trypanosoma brucei kinetoplast DNA have been cloned. The uncloned maxicircle segment contains few restriction endonuclease cleavage sites, varies in size among strains, and may be unstable in conventional cloning systems. cDNA prepared to bloodstream or procyclic trypomastigote RNA hybridized to all but one maxicircle segment, but did not hybridize to minicircles. Fourteen maxicircle transcripts were detected in RNA from both bloodstream and procyclic trypomastigotes. The coding sequences for these transcripts were localized and account for most of the maxicircle. One region of the maxicircle, which borders the variable region, was not found to be transcribed. We conclude that the maxicircle is largely but not completely transcribed in both bloodstream and procyclic trypomastigotes, whereas minicircle transcription is minimal or absent in these stages. Qualitative transcriptional differences which could account for mitochondrial respiratory differences between the bloodstream and procyclic trypomastigotes were not observed.

ChemInform Abstract: Enzymatic Synthesis of 8-Vinyl- and 8-Styryl-2′-deoxyguanosine Modified DNA - Novel Fluorescent Molecular Probes.

ChemInform ◽  
2012 ◽  
Vol 43 (39) ◽  
pp. no-no
Author(s):  
Bastian Holzberger ◽  
Julian Strohmeier ◽  
Vanessa Siegmund ◽  
Ulf Diederichsen ◽  
Andreas Marx
Keyword(s):  
Enzymatic Synthesis ◽  
Molecular Probes ◽  
Modified Dna ◽  
Fluorescent Molecular Probes
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