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Themed collection Nucleic Acid Modifications

29 items
Review Article

25 years and still going strong: 2′-O-(pyren-1-yl)methylribonucleotides – versatile building blocks for applications in molecular biology, diagnostics and materials science

This review highlights the synthesis, biophysical properties, and wide range of applications of oligonucleotides modified with 2′-O-(pyren-1-yl)methyl-RNA monomers reported over the past 25 years.

Graphical abstract: 25 years and still going strong: 2′-O-(pyren-1-yl)methylribonucleotides – versatile building blocks for applications in molecular biology, diagnostics and materials science
From the themed collection: Nucleic Acid Modifications
Review Article

Synthesis and biological applications of fluoro-modified nucleic acids

The present review highlights recent progress in the synthesis of fluoro-modified nucleic acids, and their applications in diagnostics, and therapeutics, and as tools for probing the structure and function of nucleic acids by 19F NMR and MRI.

Graphical abstract: Synthesis and biological applications of fluoro-modified nucleic acids
From the themed collection: Nucleic Acid Modifications
Communication

Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries

DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities.

Graphical abstract: Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries
From the themed collection: Nucleic Acid Modifications
Communication

Oxidative activation of leinamycin E1 triggers alkylation of guanine residues in double-stranded DNA

From the themed collection: Nucleic Acid Modifications
Open Access Communication

Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA

A synthetic access to stable isotope modified large RNAs for structural biology is introduced.

Graphical abstract: Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA
From the themed collection: Nucleic Acid Modifications
Communication

Reversible modification of DNA by methyltransferase-catalyzed transfer and light-triggered removal of photo-caging groups

We developed analogs of S-adenosyl-L-methionine with photo-caging (PC) groups and demonstrated enzymatic transfer and light-triggered removal based on a DNA-methyltransferase and plasmid DNA.

Graphical abstract: Reversible modification of DNA by methyltransferase-catalyzed transfer and light-triggered removal of photo-caging groups
From the themed collection: Nucleic Acid Modifications
Open Access Communication

5-(Hydroxymethyl)uracil and -cytosine as potential epigenetic marks enhancing or inhibiting transcription with bacterial RNA polymerase

5-(Hydroxymethyl)uracil and -cytosine in DNA templates regulate transcription by bacterial RNA polymerase depending on the promoter, indicating that they may act as epigenetic marks.

Graphical abstract: 5-(Hydroxymethyl)uracil and -cytosine as potential epigenetic marks enhancing or inhibiting transcription with bacterial RNA polymerase
From the themed collection: Nucleic Acid Modifications
Communication

Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing

Methods to map small-molecule binding sites on cellular RNAs are important for understanding interactions with both endogenous and exogenous compounds. Here, ‘Pt-Seq’ is presented as a high-throughput method to identify Pt adducts on RNA resulting from cisplatin treatment.

Graphical abstract: Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing
From the themed collection: Nucleic Acid Modifications
Communication

Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase

The structural basis for selective incorporation of BenziMP opposite O6-MeG by KlenTaq DNA polymerase is elucidated by X-ray crystallography.

Graphical abstract: Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase
From the themed collection: Nucleic Acid Modifications
Communication

Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants

Thermostable T7 RNA polymerase variants were explored for genetic alphabet expansion transcription involving the unnatural Ds–Pa pair.

Graphical abstract: Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants
From the themed collection: Nucleic Acid Modifications
Communication

Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides

The 10DM24 deoxyribozyme can site-specifically label RNAs with fluorophore-GTP conjugates. The phosphorothioate modification prevents enzymatic cleavage of the 2′,5′-branched RNA.

Graphical abstract: Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides
From the themed collection: Nucleic Acid Modifications
Communication

Substoichiometric ribose methylations in spliceosomal snRNAs

Sequencing-based profiling of spliceosomal snRNA demonstrates substoichiometric methylation at cap-proximal and internal sites that may impact splicing and protein production.

Graphical abstract: Substoichiometric ribose methylations in spliceosomal snRNAs
From the themed collection: Nucleic Acid Modifications
Communication

Programmable fusion of liposomes mediated by lipidated PNA

Lipidated peptide nucleic acids as tools for efficient liposome fusion at elevated temperatures – in a zipper and a double-zipper fusion design. An potent alternative to DNA-mediated membrane fusion.

Graphical abstract: Programmable fusion of liposomes mediated by lipidated PNA
From the themed collection: Nucleic Acid Modifications
Communication

Origins of the enhanced affinity of RNA–protein interactions triggered by RNA phosphorodithioate backbone modification

A single phosphorodithioate in place of a phosphate in a 19mer hairpin-RNA regio-specifically boosts its affinity for MS2 phage coat protein.

Graphical abstract: Origins of the enhanced affinity of RNA–protein interactions triggered by RNA phosphorodithioate backbone modification
From the themed collection: Nucleic Acid Modifications
Paper

Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications

Structural information provides important insight to how major groove-modified triazole-containing siRNAs selectively knockout their intended target.

Graphical abstract: Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications
From the themed collection: Nucleic Acid Modifications
Paper

Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA)

Transcriptome In Vivo Analysis (TIVA) probes capable of single cell mRNA isolation were generated with stabilizing oligonucleotide modifications, with the goal of enabling transcriptomic applications in a wide range of biological specimens.

Graphical abstract: Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA)
From the themed collection: Nucleic Acid Modifications
Paper

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

Energetically activated double-stranded probes with interstrand arrangements of intercalator-functionalized nucleotides enable recognition of mixed-sequence DNA hairpins with excellent binding specificity.

Graphical abstract: Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers
From the themed collection: Nucleic Acid Modifications
Paper

Decoration of trastuzumab with short oligonucleotides: synthesis and detailed characterization

Trastuzumab, an antibody prescribed for the treatment of metastatic breast cancer, was covalently conjugated to oligonucleotides and characterized by high resolution MALDI-ToF MS.

Graphical abstract: Decoration of trastuzumab with short oligonucleotides: synthesis and detailed characterization
From the themed collection: Nucleic Acid Modifications
Paper

Efficient liposome fusion mediated by lipid–nucleic acid conjugates

Highly efficient fusion and content mixing of liposomes encoded by lipidated oligonucleotides (LiNAs). “Hot fusion of biomembranes” – a low leakage process at elevated temperature.

Graphical abstract: Efficient liposome fusion mediated by lipid–nucleic acid conjugates
From the themed collection: Nucleic Acid Modifications
Paper

Exploration of a Au(I)-mediated three-component reaction for the synthesis of DNA-tagged highly substituted spiroheterocycles

A gold(I)-mediated reaction to a DNA-tagged spirocycle, and the tolerance of different nucleic acids to the reaction conditions are demonstrated.

Graphical abstract: Exploration of a Au(i)-mediated three-component reaction for the synthesis of DNA-tagged highly substituted spiroheterocycles
From the themed collection: Nucleic Acid Modifications
Paper

Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes

Pseudouridine modifications in helix 69 of bacterial ribosomes impact aminoglycoside interactions by altering the RNA conformational states and accessibility to chemical probes.

Graphical abstract: Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes
From the themed collection: Nucleic Acid Modifications
Paper

8-Oxo-7,8-dihydro-2′-deoxyguanosine and abasic site tandem lesions are oxidation prone yielding hydantoin products that strongly destabilize duplex DNA

8-Oxo-2′-deoxyguanosine in a tandem lesion context is two orders of magnitude more susceptible to oxidation than in a context of native DNA yielding hydantoin products.

Graphical abstract: 8-Oxo-7,8-dihydro-2′-deoxyguanosine and abasic site tandem lesions are oxidation prone yielding hydantoin products that strongly destabilize duplex DNA
From the themed collection: Nucleic Acid Modifications
Paper

Structural basis of interstrand cross-link repair by O6-alkylguanine DNA alkyltransferase

Conformation of the alkylene lesion may play a role in interstrand cross-link repair by O6-alkylguanine DNA alkyltransferases.

Graphical abstract: Structural basis of interstrand cross-link repair by O6-alkylguanine DNA alkyltransferase
From the themed collection: Nucleic Acid Modifications
Paper

Synthesis and thermal stabilities of oligonucleotides containing 2′-O,4′-C-methylene bridged nucleic acid with a phenoxazine base

BNAP-modified ODNs showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2′,4′-BNA/LNA with 5-methylcytosine or 2′-deoxyribonucleoside with phenoxazine.

Graphical abstract: Synthesis and thermal stabilities of oligonucleotides containing 2′-O,4′-C-methylene bridged nucleic acid with a phenoxazine base
From the themed collection: Nucleic Acid Modifications
Paper

Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer

The Na+-specific Ce13d DNAzyme is rigid showing no global folding in the presence of Na+, but splitting it at the cleavage site enables its Na+-specific folding detected by FRET.

Graphical abstract: Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer
From the themed collection: Nucleic Acid Modifications
Open Access Paper

Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA

New phenothiazine-modified nucleotides were prepared and used for enzymatic synthesis of labelled DNA for electrochemical detection and redox coding of DNA bases.

Graphical abstract: Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA
From the themed collection: Nucleic Acid Modifications
Paper

Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking

Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.

Graphical abstract: Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking
From the themed collection: Nucleic Acid Modifications
Paper

Isonucleotide incorporation into middle and terminal siRNA duplexes exhibits high gene silencing efficacy and nuclease resistance

D-/L-Isonucleotides were used to explore the local conformation requirement at specific sites of siRNA; both silencing activity and nuclease resistant character were improved, respectively.

Graphical abstract: Isonucleotide incorporation into middle and terminal siRNA duplexes exhibits high gene silencing efficacy and nuclease resistance
From the themed collection: Nucleic Acid Modifications
Paper

On the enzymatic incorporation of an imidazole nucleotide into DNA

We have evaluated the possibility for using an imidazole modified nucleoside triphosphate for the enzymatic construction of artificial metal base pair with view on an expansion of the genetic code.

Graphical abstract: On the enzymatic incorporation of an imidazole nucleotide into DNA
From the themed collection: Nucleic Acid Modifications
29 items

About this collection

Nucleic acids are known for their predictable base-pairing that forms a key basis for their biological function as well as for various applications in chemistry, materials science, diagnostics, therapeutics, and elsewhere. Beyond the handful of canonical nucleic acid building blocks, scientists and nature itself have been very inventive in the creation of non-standard nucleic acids with augmented chemical functionalities.

This issue, Guest Edited by Professors Mark Helm, P. I. Pradeepkumar and Scott K. Silverman is dedicated to nucleic acid modifications and encompasses:

1. Synthetic modifications of DNA, RNA, or chemically related polymers; their characterization or application

2. Naturally occurring modifications of RNA or DNA; their synthesis, detection, or function

Articles in this themed collection will be added below as soon as possible after they are published.

Please return to this page frequently to see the collection grow.

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