Themed collection Nucleic acids: new life, new materials

Guest editors introduce this web collection highlighting recent achievements in nucleic acids research and applications in emerging areas. Featuring articles published in ChemComm, OBC and RSC Advances, the collection is dedicated to the memory of Professor Har Gobind Khorana (1922–2011) and Dr Daniel McGillivray Brown (1923–2012), acknowledging their legacy to the nucleic acids community.

We report an overview of c-di-GMP signaling in bacteria, the RNA and protein effectors that bind this second messenger, and recent advances in targeting these binding partners with synthetic dinucleotide analogs.

Here, we highlight the strategies for the synthesis and tuning of a variety of metal nanostructures and nanoassemblies with oligonucleotides and their applications.

Extension of aptamer selection from natural components to from unnatural components realizes the creation of new functional molecules.

The development and application of nucleic acid aptamers for targeted cancer therapy and cancer biomarker identification were reviewed.

In this review, we introduce our recently-developed simplified genetic code in order to discuss why the genetic code likely evolved from a simpler form encoding fewer than 20 amino acids.

This article covers glycoclusters prepared by DNA automated synthesis and click chemistry to their interactions with lectins studied with a DNA-based microarray

Pyrene chromophores attached to the 2′-position of short oligonucleotides affect the solubilisation of as-prepared single walled carbon nanotube solids when sonicated in an aqueous buffer solution.

The synthesis and incorporation of norbornene-modified nucleoside triphosphates for an efficient multiple labelling of DNA by inverse-electron-demand Diels–Alder reaction is described.

A pattern formed by self-assembly of 20 streptavidins in a V-shape on DNA origami was transferred to a biotin modified self-assembled monolayer.

A combination of end-modifications and 3D topology is shown to stabilize DNA triangular prisms in fetal bovine serum up to 62 hours.

Site-specific incorporation of photoswitches with tuneable thermal stability.

A novel G-quadruplex-selective luminescent iridium(III) complex has been employed as a sensitive and selective switch-on probe for the detection of sub-nanomolar human neutrophil elastase in homogenous solution.

Ordered 2,5-bis(2-thienyl)pyrrole (SNS) zipper arrays are formed by hybridization of complementary DNA oligomers each containing covalently bound SNS monomers.

Two new nitroxide-modified nucleosides, ^OxU and ^ImU, were synthesized and incorporated into DNA. ^ImU has lower mobility in duplex DNA due to an intramolecular hydrogen bond.

A G-quadruplex-selective luminescent iridium(III) switch-on probe has been developed for the detection of cysteine (Cys) in aqueous solution.

A general method has been developed using personal glucose meters to quantify different metal ions through an invasive DNA approach.

A cationic comb-type copolymer triggered rapid dimerization of a self-complementary stem-loop DNA. Reversible transformation was driven by successive addition of the copolymer and polyanion.

A finite state machine built from DNA with transitions between states triggered by a clock signal.

RNA templated molecular releasing reaction is applied to the protein expression in bacterial cells.

RNA aptamers to biologically active small ligands, such as tetracycline, dopamine, and streptomycin, are converted to modular fluorescent sensors that are amenable for ratiometric detection of the ligand.

This communication reports a novel intermolecular interaction for structural DNA nanotechnology.

A synthetic and organometallic nucleic acid analogue can be prepared by replacing repeating dinucleotide units in DNA with ferrocene units.

Oligonucleotides modified with consecutive incorporations of 5-(1-aryl-1,2,3-triazol-4-yl)-2′-deoxyuridine monomers display strong thermal affinity and binding specificity toward RNA targets, due to the formation of chromophore arrays in the major groove.

We report a biotin-labeled dinucleotide cap analogue that can be incorporated into transcripts to produce 5′-capped and biotinylated mRNAs which retain their biological functionality and may be employed for biotin-(strept)avidin technologies.

A photoresponsive peptide aptamer was selected using ribosome display from a random sequence library of peptides carrying azobenzene residues.

Reduction of metal ions by boranephosphonate DNA via a novel reaction pathway producing nanoparticles and phosphate diesters or triesters is described.

The T–Hg–T bond was utilized to cross-link two lateral loops of chair-type G-quadruplex DNA (G4-DNA) structures.

The size, shape and rigidity of the amine adduct influence the electrical current through the nanopore providing characteristic signatures.

Invasive binding event of PNA into DNA duplex was clearly observed both by atomic force microscope (AFM) imaging and electrophoretic mobility shift assay (EMSA) with the aid of nanomechanical DNA origami devices as ‘single-molecule’ visual probes.

Visualization of the intracellular distribution and stability of DNA origami was achieved with a label-free fluorescent cyanine molecule.

DNA containing the locked anti O⁶-alkylguanine analogue (right) is not repaired by MGMT, suggesting why O⁶-alkylguanines some are poor MGMT substrates.

Oligonucleotides containing cyclooctyne-labelled thymidines have been used to efficiently crosslink DNA strands and to orthogonally label fluorescent genetic probes.

A programmable DNA switch based on a molecular beacon including strategically positioned FRET pairs allows the specific addressing of five discrete states with variable fluorescence readout; the structure and switching of the beacon strongly depends on the type of fluorophores used.

It is revealed that the excess electron hopping rate between T's in DNA hairpins is faster than that of the hole.

The effect of 5′-labeling on RNAi activity has been explored, by comparing a guanine sugar edge label to 5′-phosphate labeled siRNA.

A site-specific labeling method for large RNA molecules, by combining the unnatural base pair transcription system and the post-transcriptional modification using click chemistry, has been developed.

A high-throughput screening assay based on fluorescence readout was used to screen mutant libraries of T7 RNA polymerase to identify a mutant with increased acceptance of 2′-methylseleno-2′-deoxyuridine 5′-triphosphate.

A designed DNA-b-PPO copolymer can undergo in situ transition between diblock and triblock, and alter assembly morphologies accordingly upon pH changes.

Dehydration during conformational transition of the add-A riboswitch in response to a binding of ligand.

Triplex DNA recognition is utilized to direct inter-strand cross-linking reactions at precise locations within a pre-assembled DNA nanostructure.

We developed fluorogenic probes, which are photoactivated in the presence of specific nucleic acid templates with the release of fluorescent dyes.

A G-quadruplex-based switch-on luminescence assay has been developed for the detection of gene deletion using a cyclometallated iridium(III) complex as a G-quadruplex-selective probe.

Reversible disulfide crosslinks between thionucleosides in DNA substrates demonstrate double nucleotide unpairing is required for structure-sensing nuclease specificity.

A convergent synthesis is developed to give efficiently all four 2′-C-α-aminomethyl-2′-deoxynucleosides 15a–d (U, C, A, G) in 38%, 42%, 12%, 12–42% yield, respectively.

Modified nucleotides play a paramount role in many cutting-edge biomolecular techniques.

Designed DNA bases and fluorogenic templated chemistry have been used to detect enzymatic removal of damaged bases in double-stranded DNA.

Preparation of ribonucleoprotein fragments of unprecedented complexity comprising solid-phase peptide and reverse RNA synthesis on a single solid support.

Guanine-responsive allosteric ribozymes were designed and used to control mammalian gene expression via two mechanisms.

A 26 kilobase ssDNA obtained from long-range PCR amplification was folded into a super-sized DNA origami nanostructure with 792 staple strands.

Short DNA duplexes carrying TTF units at the same termini exhibit a high increase in melting temperature.

Double-headed nucleotides are used to organize additional nucleobases in the minor groove of the DNA duplex. By UV, cross-linking between two thymines is obtained.

Enantiomerically pure (R_p)- and (S_p)-4-azido[2.2]paracyclophane was incorporated into DNA using copper-catalysed azide–alkyne cycloaddition. UV-vis and CD data indicate that the transfer of chirality from paracylophane-DNA to the perylene is dependent on the arrangement of the chiral paracyclophanes in the preformed duplex.

Proton chemical shifts in modified DNA oligonucleotides are accurately predicted using DFT-NMR calculations during MD simulations in a (QM/)MM framework.

HOXC13 is a homeobox containing gene that plays crucial roles in hair development and origin of replication. Herein, we investigated the biochemical functions of HOXC13 and explored its potential roles in tumor cell viability.

A convenient, versatile method to organize discrete length single-walled carbon nanotubes (SWNT) into complex geometries using 2D DNA origami structures is developed here.

Double-stranded synthetic oligoribonucleotides (dsORNs) of 50-mer length show potent TLR3 activation in vitro and in vivo in mice and non-human primates.

Terminal Cu²⁺-mediated base pairs dramatically stabilize short oligonucleotide duplexes, without compromising sequence-selectivity.

Phosphorothiolate linkages are now shown to stabilise RNA·RNA duplexes and G-quadruplex structures.

Nucleotides bearing terpyridine ligands attached via a flexible octadiynyl tether were prepared and enzymatically incorporated into DNA where formation of intra-strand complexes with Fe²⁺ and Ni²⁺ was observed.

Locking/freezing the sugar conformation in the S-type geometry in 2′–5′ DNA would improve the strength of RNA binding through entropic advantage.

It is shown that a [2.2.2]heptamethinecyanine dye binds selectively to quadruplex DNA. The association with the nucleic acid leads to a significant increase of the emission intensity of the otherwise weakly fluorescent dye, thus enabling the fluorimetric detection of quadruplex DNA.

A nucleoside with desmethyl thiazole orange dyes has been developed for live-cell RNA imaging.

Oligonucleotides containing 4′-carboxythymidine had an increased binding affinity to RNA complements compared to a natural oligonucleotide.

Short and high-yielding syntheses based on cheap and readily available starting compounds for the nucleobases preQ₁ base, Q base, and (ent)-Q base are described. For the latter two bases, preQ₁ served as a central synthon.

Methodology and synthesis of different m₃G-CAP constructs equipped with an azide handle and their attachment by “click reaction” with an activated triple bond partner allows efficient formation of oligonucleotide m₃G-CAP conjugates.

Two-photon excitation of fluorescent nucleobase analogues is a promising approach to the sensitive detection and imaging of nucleic acids.

New derivatives incorporating protected maleimides allow easy access to oligonucleotides with a maleimide linked to either the 3′-end or to internal positions, from which a variety of conjugates can be prepared.

By the use of oligodeoxyribonucleotides containing 3-cyanovinylcarbazole nucleoside (^CNVK) as antisense oligonucleotides, quick and selective photo-regulation of the mRNA functions was achieved.

A novel isonucleoside 5 containing a 5′-CH₂ extended chain at the sugar moiety was synthesized. In siRNA, passenger strand modified with isonucleoside (5a/b) at 3′ or 5′ terminal can retain the silencing activity and minimize the passenger strand specific off-target effect.