Polymerase synthesis of modified DNA containing cytosine in major groove

2011 ◽  
Author(s):  
Pavel Kielkowski ◽  
Michal Hocek
Keyword(s):  
Major Groove ◽  
Modified Dna

Modulation of RNase H activity by modified DNA probes: Major groove vs minor groove effects

1997 ◽  
Vol 5 (6) ◽  
pp. 1037-1042 ◽  
Author(s):  
Andrew T. Daniher ◽  
Jin Xie ◽  
Shashank Mathur ◽  
James K. Bashkin
Keyword(s):  
Minor Groove ◽  
Dna Probes ◽  
Rnase H ◽  
Major Groove ◽  
Modified Dna

Benzophenone modified DNA for photocatalysis

2011 ◽  
Author(s):  
Michael J. Weinberger ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Modified Dna

Polymerase synthesis of base-modified DNA: new methods and new applications

2014 ◽  
Author(s):  
Jana Balintová ◽  
Jitka Daďová ◽  
Pavel Kielkowski ◽  
Petra Ménová ◽  
Zuzana Vaníková ◽  
...  
Keyword(s):  
New Methods ◽  
Modified Dna ◽  
New Applications

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities

2020 ◽  
Author(s):  
Yuru Wang ◽  
Christopher D Katanski ◽  
Christopher Watkins ◽  
Jessica N Pan ◽  
Qing Dai ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Screening Method ◽  
Targeted Mutagenesis ◽  
Rna Repair ◽  
Dna And Rna ◽  
Modified Dna ◽  
Dna Substrates ◽  
Trna Sequencing

Abstract AlkB is a DNA/RNA repair enzyme that removes base alkylations such as N1-methyladenosine (m1A) or N3-methylcytosine (m3C) from DNA and RNA. The AlkB enzyme has been used as a critical tool to facilitate tRNA sequencing and identification of mRNA modifications. As a tool, AlkB mutants with better reactivity and new functionalities are highly desired; however, previous identification of such AlkB mutants was based on the classical approach of targeted mutagenesis. Here, we introduce a high-throughput screening method to evaluate libraries of AlkB variants for demethylation activity on RNA and DNA substrates. This method is based on a fluorogenic RNA aptamer with an internal modified RNA/DNA residue which can block reverse transcription or introduce mutations leading to loss of fluorescence inherent in the cDNA product. Demethylation by an AlkB variant eliminates the blockage or mutation thereby restores the fluorescence signals. We applied our screening method to sites D135 and R210 in the Escherichia coli AlkB protein and identified a variant with improved activity beyond a previously known hyperactive mutant toward N1-methylguanosine (m1G) in RNA. We also applied our method to O6-methylguanosine (O6mG) modified DNA substrates and identified candidate AlkB variants with demethylating activity. Our study provides a high-throughput screening method for in vitro evolution of any demethylase enzyme.

scholarly journals Membrane-Interacting DNA Nanotubes Induce Cancer Cell Death

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2003
Author(s):  
Samet Kocabey ◽  
Aslihan Ekim Kocabey ◽  
Roger Schneiter ◽  
Curzio Rüegg
Keyword(s):  
Drug Delivery ◽  
Cell Death ◽  
Cytochrome C ◽  
Membrane Permeability ◽  
Cancer Cell ◽  
Cell Membrane Permeability ◽  
Caspase Activity ◽  
Cancer Cell Death ◽  
Modified Dna ◽  
Dna Nanotubes

DNA nanotechnology offers to build nanoscale structures with defined chemistries to precisely position biomolecules or drugs for selective cell targeting and drug delivery. Owing to the negatively charged nature of DNA, for delivery purposes, DNA is frequently conjugated with hydrophobic moieties, positively charged polymers/peptides and cell surface receptor-recognizing molecules or antibodies. Here, we designed and assembled cholesterol-modified DNA nanotubes to interact with cancer cells and conjugated them with cytochrome c to induce cancer cell apoptosis. By flow cytometry and confocal microscopy, we observed that DNA nanotubes efficiently bound to the plasma membrane as a function of the number of conjugated cholesterol moieties. The complex was taken up by the cells and localized to the endosomal compartment. Cholesterol-modified DNA nanotubes, but not unmodified ones, increased membrane permeability, caspase activation and cell death. Irreversible inhibition of caspase activity with a caspase inhibitor, however, only partially prevented cell death. Cytochrome c-conjugated DNA nanotubes were also efficiently taken up but did not increase the rate of cell death. These results demonstrate that cholesterol-modified DNA nanotubes induce cancer cell death associated with increased cell membrane permeability and are only partially dependent on caspase activity, consistent with a combined form of apoptotic and necrotic cell death. DNA nanotubes may be further developed as primary cytotoxic agents, or drug delivery vehicles, through cholesterol-mediated cellular membrane interactions and uptake.

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