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.
The bacterial second messenger c-di-GMP: probing interactions with protein and RNA binding partners using cyclic dinucleotide analogs
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.
Tuning and assembling metal
nanostructures with DNA
Here, we highlight the strategies for the synthesis and tuning of a variety of metal nanostructures and nanoassemblies with oligonucleotides and their applications.
Expansion of the aptamer library from a “natural soup” to an “unnatural soup”
Extension of aptamer selection from natural components to from unnatural components realizes the creation of new functional molecules.
Nucleic acid aptamers: an emerging frontier in cancer therapy
The development and application of nucleic acid aptamers for targeted cancer therapy and cancer biomarker identification were reviewed.
The number of
amino acids in a genetic code
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.
DNA glycoclusters and DNA-based carbohydrate microarrays: From design to applications
This article covers glycoclusters prepared by DNA automated synthesis and click chemistry to their interactions with lectins studied with a DNA-based microarray
pyrene “click”-type modification of DNA affects solubilisation and photoluminescence of single-walled carbon nanotubes
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.
Synthesis and enzymatic incorporation of norbornene-modified nucleoside triphosphates for Diels–Alder bioconjugation
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.
Transfer of a
protein pattern from self-assembled DNA origami to a functionalized substrate
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.
nanostructure serum stability: greater than the sum of its parts
A combination of end-modifications and 3D topology is shown to stabilize DNA triangular prisms in fetal bovine serum up to 62 hours.
Oligo switches: photoresponsive
oligonucleotide conjugates by solid-supported click chemistry
Site-specific incorporation of photoswitches with tuneable thermal stability.
A G-quadruplex-selective luminescent switch-on probe for the detection of sub-nanomolar human neutrophil elastase
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.
Structural stabilization of DNA-templated
nanostructures: crosslinking with 2,5-bis(2-thienyl)pyrrole monomers
Ordered 2,5-bis(2-thienyl)pyrrole (SNS) zipper arrays are formed by hybridization of complementary DNA oligomers each containing covalently bound SNS monomers.
Hydrogen-bonding controlled rigidity of an isoindoline-derived nitroxide
spin label for nucleic acids
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 luminescent G-quadruplex switch-on probe for the highly selective and tunable detection of
cysteine and glutathione
A G-quadruplex-selective luminescent iridium(III) switch-on probe has been developed for the detection of cysteine (Cys) in aqueous solution.
An invasive DNA approach toward a general method for portable quantification of metal ions using a personal
A general method has been developed using personal glucose meters to quantify different metal ions through an invasive DNA approach.
Polyelectrolyte-assisted transconformation of a stem-loop DNA
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 clocked finite state machine built from DNA
A finite state machine built from DNA with transitions between states triggered by a clock signal.
RNA-templated molecule release induced
protein expression in bacterial cells
RNA templated molecular releasing reaction is applied to the protein expression in bacterial cells.
Construction of ratiometric fluorescent sensors by ribonucleopeptides
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.
DNA cohesion through bubble–bubble recognition
This communication reports a novel intermolecular interaction for structural DNA nanotechnology.
ferrocene nucleic acid oligomer as an organometallic structural mimic of DNA
A synthetic and organometallic nucleic acid analogue can be prepared by replacing repeating dinucleotide units in DNA with ferrocene units.
Synthesis and hybridization properties of
oligonucleotides modified with 5-(1-aryl-1,2,3-triazol-4-yl)-2′-deoxyuridines
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.
biotin labelled cap analogue – incorporable into mRNA transcripts and promoting cap-dependent translation
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.
In vitro selection of a photo-responsive
peptide aptamer using ribosome display
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
Reduction of metal ions by boranephosphonate DNA via a novel reaction pathway producing nanoparticles and phosphate diesters or triesters is described.
Mercury–thymine interaction with a chair type G-quadruplex architecture
The T–Hg–T bond was utilized to cross-link two lateral loops of chair-type G-quadruplex DNA (G4-DNA) structures.
Modulation of the current signatures of DNA abasic site adducts in the α-hemolysin ion channel
The size, shape and rigidity of the amine adduct influence the electrical current through the nanopore providing characteristic signatures.
Clear-cut observation of PNA invasion using nanomechanical DNA origami devices
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 location and stability of DNA origami with a label-free fluorescent probe
Visualization of the intracellular distribution and stability of DNA origami was achieved with a label-free fluorescent cyanine molecule.
Synthesis of oligodeoxyribonucleotides containing a conformationally-locked anti analogue of
O6-methyl-2′-deoxyguanosine and their recognition by MGMT and Atl1
DNA containing the locked anti O6-alkylguanine analogue (right) is not repaired by MGMT, suggesting why O6-alkylguanines some are poor MGMT substrates.
Fast and efficient DNA crosslinking and multiple orthogonal
labelling by copper-free click chemistry
Oligonucleotides containing cyclooctyne-labelled thymidines have been used to efficiently crosslink DNA strands and to orthogonally label fluorescent genetic probes.
A DNA based five-state switch with programmed reversibility
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.
electron transfer dynamics in DNA hairpins conjugated with N,N-dimethylaminopyrene as a photosensitizing electron donor
It is revealed that the excess electron hopping rate between T's in DNA hairpins is faster than that of the hole.
guanosine phosphoramidite for click functionalization of RNA on the sugar edge
The effect of 5′-labeling on RNAi activity has been explored, by comparing a guanine sugar edge label to 5′-phosphate labeled siRNA.
Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry
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.
Screening mutant libraries of T7 RNA polymerase for candidates with increased acceptance of 2′-modified nucleotides
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.
pH-induced morphology-shifting of DNA-b-poly(propylene oxide) assemblies
A designed DNA-b-PPO copolymer can undergo in situ transition between diblock and triblock, and alter assembly morphologies accordingly upon pH changes.
Dehydration from conserved stem regions is fundamental for
ligand-dependent conformational transition of the adenine-specific riboswitch
Dehydration during conformational transition of the add-A riboswitch in response to a binding of ligand.
Triplex-directed covalent cross-linking of a DNA nanostructure
Triplex DNA recognition is utilized to direct inter-strand cross-linking reactions at precise locations within a pre-assembled DNA nanostructure.
Hybridization and reaction-based fluorogenic nucleic acid probes
We developed fluorogenic probes, which are photoactivated in the presence of specific nucleic acid templates with the release of fluorescent dyes.
A highly selective G-quadruplex-based luminescent switch-on probe for the detection of gene deletion
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.
Interstrand disulfide crosslinking of DNA bases supports a double
nucleotide unpairing mechanism for flap endonucleases
Reversible disulfide crosslinks between thionucleosides in DNA substrates demonstrate double nucleotide unpairing is required for structure-sensing nuclease specificity.
Efficient synthesis of 2′-C-α-aminomethyl-2′-deoxynucleosides
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.
Interactions of non-polar and “Click-able” nucleotides in the confines of a DNA polymerase active site
Modified nucleotides play a paramount role in many cutting-edge biomolecular techniques.
Templated chemistry for monitoring damage and repair directly in duplex DNA
Designed DNA bases and fluorogenic templated chemistry have been used to detect enzymatic removal of damaged bases in double-stranded DNA.
Fully automated sequential solid phase approach towards viral RNA-nucleopeptides
Preparation of ribonucleoprotein fragments of unprecedented complexity comprising solid-phase peptide and reverse RNA synthesis on a single solid support.
Synthetic mammalian riboswitches based on
Guanine-responsive allosteric ribozymes were designed and used to control mammalian gene expression via two mechanisms.
Folding super-sized DNA origami with scaffold strands from long-range PCR
A 26 kilobase ssDNA obtained from long-range PCR amplification was folded into a super-sized DNA origami nanostructure with 792 staple strands.
Interstrand interactions on DNA duplexes modified by TTF units at the 3′ or 5′-ends
Short DNA duplexes carrying TTF units at the same termini exhibit a high increase in melting temperature.
Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove
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.
Ligand assembly and chirality transfer guided by DNA modified with enantiomerically pure [2.2]paracyclophanes
Enantiomerically pure (Rp)- and (Sp)-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.
Accurate prediction of 1H chemical shifts in interstrand cross-linked DNA
Proton chemical shifts in modified DNA oligonucleotides are accurately predicted using DFT-NMR calculations during MD simulations in a (QM/)MM framework.
oligonucleotide mediated knockdown of HOXC13 affects cell growth and induces apoptosis in tumor cells and over expression of HOXC13 induces 3D-colony formation
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.
templated self-assembly of discrete length single wall carbon nanotubes
A convenient, versatile method to organize discrete length single-walled carbon nanotubes (SWNT) into complex geometries using 2D DNA origami structures is developed here.
Design of synthetic oligoribonucleotide-based
agonists of Toll-like receptor 3 and their immune response profiles in vitro and in vivo
Double-stranded synthetic oligoribonucleotides (dsORNs) of 50-mer length show potent TLR3 activation in vitro and in vivo in mice and non-human primates.
purines as metal-ion-binding surrogate nucleobases that enhance hybridization with unmodified 2′-O-methyl oligoribonucleotides
Terminal Cu2+-mediated base pairs dramatically stabilize short oligonucleotide duplexes, without compromising sequence-selectivity.
Thermal stabilisation of RNA·RNA duplexes and G-quadruplexes by phosphorothiolate linkages
Phosphorothiolate linkages are now shown to stabilise RNA·RNA duplexes and G-quadruplex structures.
nucleosides and dNTPs bearing oligopyridine ligands linked through an octadiyne tether, their incorporation into DNA and complexation with transition metal cations
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.
Synthesis and structural studies of S-type/N-type-locked/frozen
nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2′–5′ linked oligonucleotides
Locking/freezing the sugar conformation in the S-type geometry in 2′–5′ DNA would improve the strength of RNA binding through entropic advantage.
Light up G-quadruplex DNA with a [2.2.2]heptamethinecyanine
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 nucleic acid probe labeled with desmethyl thiazole orange: a new type of hybridization-sensitive fluorescent
oligonucleotide for live-cell RNA imaging
A nucleoside with desmethyl thiazole orange dyes has been developed for live-cell RNA imaging.
Synthesis and duplex-forming ability of
oligonucleotides containing 4′-carboxythymidine analogs
Oligonucleotides containing 4′-carboxythymidine had an increased binding affinity to RNA complements compared to a natural oligonucleotide.
Concise and efficient syntheses of preQ1 base, Q base, and (ent)-Q base
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.
oligonucleotides with “clickable” m3G-CAPs
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.
photon excitation of the fluorescent nucleobase analogues 2-AP and tC
Two-photon excitation of fluorescent nucleobase analogues is a promising approach to the sensitive detection and imaging of nucleic acids.
Easy introduction of
maleimides at different positions of oligonucleotide chains for conjugation purposes
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.
Quick regulation of mRNA functions by a few seconds of photoirradiation
By the use of oligodeoxyribonucleotides containing 3-cyanovinylcarbazole nucleoside (CNVK) as antisense oligonucleotides, quick and selective photo-regulation of the mRNA functions was achieved.
Synthesis and properties of novel L-isonucleoside modified
oligonucleotides and siRNAs
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.
About this collection
This joint ChemComm-OBC-RSC Advances web-based themed issue highlights recent achievements in nucleic acids research and applications in emerging areas. Some of the work presented in this virtual collection is also 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.
The guest editors for this issue are:
Mike Gait (Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK)
Makoto Komiyama (University of Tsukuba, Japan)
David Liu (Harvard University, USA)
Jason Micklefield (University of Manchester, UK)
Ned Seeman (New York University, USA)
Oliver Seitz (Humboldt-Universität zu Berlin, Germany)
Articles in this web themed issue will be added below as soon as possible after they are published. Please return to this page frequently to see the collection grow.