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The 8-nitroguanine lesion in DNA is increasingly associated with inflammation-related carcinogenesis, whereas the same modification on guanosine 3',5'-cyclic monophosphate generates a second messenger in NO-mediated signal transduction. Very little is known about the chemistry of 8-nitroguanine nucleotides, despite the fact that their biological effects are closely linked to their chemical properties. To this end, a selection of chemical reactions have been performed on 8-nitroguanine nucleosides and oligodeoxynucleotides. Reactions with alkylating reagents reveal how the 8-nitro substituent affects the reactivity of the purine ring, by significantly decreasing the reactivity of the N2 position, whilst the relative reactivity at N1 appears to be enhanced. Interestingly, the displacement of the nitro group with thiols results in an efficient and specific method of labelling this lesion and is demonstrated in oligodeoxynucleotides. Additionally, the repair of this lesion is also shown to be a chemically feasible reaction through a reductive denitration with a hydride source.

Rapid and sensitive methods to detect DNA lesions are essential in order to understand their role in carcinogenesis and for potential diagnosis of cancers. The 8-nitroguanine DNA lesion, which is closely associated with inflammation-induced cancers, has been characterised for the first time by surface-enhanced Raman spectroscopy (SERS). This lesion has been studied as the free base, as well as part of a dinucleotide and oligodeoxynucleotides (ODNs) at 5 different excitation wavelengths in the range 785-488 nm. All nitrated samples produced distinctly different spectra from their control guanine counterparts, with nitro bands being assigned by DFT calculations. Additional resonance enhancement was observed at the shorter excitation wavelengths, these SERRS measurements allowed the detection of one nitrated guanine in over 1,300 bases. In addition, SER(R)S can be used to detect whether the unstable lesion is covalently attached to the ODN or has been released by hydrolytic depurination.

Triplexes formed from oligonucleic acids are key to an umber of biological processes. They have attracted at- tention as molecular biology tools and as ar esult of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson-Crick (W-C) base-paired DNA duplexes and aH oogs- teen base-paired RNA strand, are reported to be more ther- modynamically stable than those in which the third strand is DNA. Consequently ,s ynthetic efforts have been focused on developing TFOs with RNA-like structura lp roperties. Here, the structura la nd stability studies of such aT FO, composed of deoxynucleic acids, bu tw ith 3'-S-phosphorothiolate (3'- SP) linkages at two sites is described. The modification re- sults in an increase in triplex meltin gt emperature as deter- mined by UV absorption measurements. 1 HN MR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altere db yt he major groove binding of either TFO. However ,t he triplex involving the 3'- SP modifications is more compact. The 3'-SP modification was previously shown to stabilis eG -quadruplex and i-motif structures and therefore is now proposed as ag eneric solu- tion to stabilising multi-stranded DNA structures.

The efficient digestion of nanoparticle assemblies connected by DNA linkers is demonstrated using a number of complementary methods (enzymatic cleavage with EcoRI is shown in the scheme). The efficiency of digestion is dependent on the design of the DNA linker. The ability to manipulate DNA enzymatically is important in the development of hierarchical chemical methods of nanoscale assembly.

NMR spectroscopy has been used to investigate the conformational effects of single and two consecutive 3'-S-phosphorothiolate modifications within a deoxythymidine trinucleotide. The presence of a single 3'-phosphorothioate modification shifts the conformation of the sugar ring it is attached to, from a mainly south to north pucker; this effect is also transmitted to the 3'-neighbour deoxyribose. This transmission is thought to be caused by favourable stacking of the heterocyclic bases. Similar observations have been made previously by this group. When two adjacent modifications are present, the conformations of the attached deoxyribose rings are again shifted almost completely to the north, however, there is no transmission to the 3' deoxyribose ring. Base proton chemical shift analysis and molecular modelling have been used to aid elucidation of the origin of this feature. The observation for the dimodified sequence is consistent with our previously reported results for a related system in which spaced modifications are more thermodynamically stable than consecutive ones.

The programmed self-assembly of nanostructures from well-defined units is an important aim in nanoscience.[1], [2] The use of gold nanoparticles stabilized by thiol-modified DNA is a promising approach towards this goal.[3]-[8] The specificity of DNA base-pairing provides a precise means of programming interactions between particles by hybridization with specifically designed linker strands. To introduce an additional level of control, we have developed a general method by which the reactivity of initially latent DNA linking sites can be switched on deliberately. We have adapted well-developed methods of molecular biology to produce a nanoscale analogue of protecting groups. We show that linking sites can be protected by hybridization with complementary strands and deprotected by cleaving these double strands at predetermined sites with restriction enzymes. This results in cohesive ends of single-stranded DNA, which can bind by hybridization to complementary sequences present in the system. In a second enzymatic step the DNA phosphodiester backbones at the hybridization sites are covalently joined using a DNA ligase. This approach represents a generic protocol that will enable multistep nanostructure syntheses.

Artemisinin-based combination therapies (ACTs) are currently the recommended treatment for uncomplicated and severe cases of malaria.[1] Additionally, artemisinins, as well as a number of other sesquiterpene lactones (SLs), are currently in phase I–II clinical trials against breast, colorectal and nonsmall-cell lung cancers.[2] As outlined by the iron-dependent activation hypothesis,[3] the activity of artemisinin (ART) is dependent on the endoperoxide bridge.[4] The peroxide is cleaved by endogenous sources of FeII to generate highly reactive carbon-centred radicals (CCRs), which are believed to react with critical cellular targets.[3] ART demonstrates selectivity towards rapidly proliferating cancer cell lines that possess a high intracellular iron content required to sustain their characteristic high rates of multiplication.[5] Iron activation links this particular potency of ART towards rapidly proliferating cancer cell lines; differentiation between healthy and cancerous cells by variation of iron concentration provides a strategy for selective cytotoxicity by ART and its derivatives.[4] The mechanism by which ART exerts its cytotoxic activity still remains elusive. ART acts by disruption of proliferation,[6, 7] oxidative stress,[8] anti-angiogenesis,[9] NF-kB signalling,[10] apoptosis[4] and interfering with iron uptake and metabolism.[6] ART also induces DNA breakage,[11] and it has been reported that artesunate-mediated DNA damage contributes to its therapeutic efficacy.

Since the first unequivocal description of RNA interference (RNAi) in 1998, it has remained one of the hottest topics under investigation, culminating in the award of a Nobel Prize to its discoverers in 2006. Excitement over this technique derives from the ease with which it can be used to switch-off a specific gene in almost any organism, thereby allowing the role of that gene to be identified. More importantly, it offers the potential to treat certain diseases by switching-off the causative genes. Key to the RNAi pathway are the small-interfering RNAs (siRNAs), which at 21–23 nucleotides in length are very amenable to analogue development by chemists. However in comparison to the use of oligonucleotides as antisense agents, an area where many chemists first developed an interest in nucleic acids, the RNAi pathway is exceedingly complex. The literature is also complicated by the fact that the phenomenon has been studied in a wide range of organisms. In this tutorial review we have presented the subject from a more chemical perspective, incorporating a glossary to give a clear explanation of the specialist terms. However, the coverage of the biology remains sufficiently detailed to give the reader the necessary insight that we believe will be essential for the successful design of chemically modified siRNA.

The incorporation of 6-N-(2-aminoethyl)-2′-deoxyadenosine 1 into 6-N-(2-aminoethyl)-2′-deoxyadenylyl-(3′-5′)-thymidine 2 using a phosphoramidite intermediate is described. The trifluoroacetyl group is demonstrated to be an ideal protecting group for the amino function whilst the 4,4′-dimethoxytrityl group is utilised to block the 5′-hydroxy function. This study serves as a model investigation for the incorporation of compound 1 into oligodeoxynucleotides to investigate their potential for forming sequency specific interstrand cross-links.

2′-Deoxy-3′-thio-5′-O-(4-monomethoxytrityl)-6-N-benzoyladenosine ( 1a ) has been prepared from adenosine in seven steps and, following conversion of to a 3′-S-phosphorothioamidite, used to synthesize a dinucleoside 3′-S-phosphorothiolate containing 2′-deoxy-3′-thioadenosine. The procedure is compatible with automated methods of DNA synthesis and extends the potential of the recently developed phosphorothiolate method for strand specific cleavage of DNA.

Efficient procedures are described for the synthesis of dinucleoside phosphorothiolates using either a Michaelis-Arbusov-type reaction or a phosphotriester approach.

An intramolecular Michaelis–Arbusov reaction taking place between a 5′-phosphite and a 3′-S-disulfide can be used to prepare nucleoside 3′-S,5′-O-cyclic phosphorothiolate triesters.

A general procedure for the preparation of S -nucleosidyl S -aryl disulfides from the corresponding thioesters is described. This procedure has been used for the preparation of a ribonucleoside disulphide ( 8d ), a key intermediate for the synthesis of oligoribonucleotides containing 3′- S -phosphorothiolate linkages. The regioselectivity of the Arbusov reaction of 8d with phosphites has been examined. The X-ray structure of 3′-deoxy-3′- S -(2-nitrophenyldisulfanyl)thymidine ( 9b ) is also reported.

Four functionalized 2‘-deoxy-2‘-α-C-branched nucleosides, namely, 2‘-deoxy-2‘-α-C-(carboxymethyl)uridine, 2‘-deoxy-2‘-α-C-acetamidouridine, 2‘-deoxy-2‘-α-C-(hydroxyethyl)uridine, and 2‘-deoxy-2‘-α-...

The synthesis of two dinucleoside monophosphate analogues is described in which the 3′-O-P-O-5′ phosphodiester linkage is replaced by either an isosteric 3′-C-S-S-5′ or a shorter 3′-S-S-5′ linkage. In both cases the -S-S- bond was formed through a disulfide exchange reaction using an activated S -nucleosidyl S -aryl disulfide and a suitably protected derivative of 5′-thiothymidine. © 1997 Elsevier Science Ltd.

The novel 2′,3′-cyclic phosphate (1) derived from 2′-homouridine has been prepared by phosphorylation with 2-cyanoethylN,N,N′,N′-tetraisopropylphosphorodiamidite.

A novel stereo-controlled process is described which enables the uracil base on a 2′-deoxy-2′-α-C-carboxymethyluridine nucleoside to be exchanged for either a purine or another pyrimidine base, via the intermediacy of an isolable pentofuranosyl butyrolactone.

For the first time a fully automated procedure has been developed for the incorporation of a 3'-S-phosphorothiolate linkage into DNA, using phosphorothioamidite monomers. Coupling yields with either of the activators 5-ethylthiotetrazole or 4,5-dicyanoimidazole were in the range of 80-90%. Coupling yields were equally good when performed on either a 0.2 or 1 mumole reaction column, thus facilitating large scale synthesis.

The synthesis of uridine monomers containing either a 2′-deoxy-2′-C-methy- lcyano or ethylcyano group is described. These monomers are intended for incorporation into oligonucleotides to investigate a proposed duplex-stabilising effect exerted by 2′-tethered amide groups.

A novel nucleoside-derived macrocycle formed from three thymidine 5'-carboxylic acid monomer units is described.

3′-S-Phosphorothiolate (3′-SP) linkages have been incorporated into the DNA strand of both a DNA·RNA duplex and a DNA·DNA duplex. Thermal melting (Tm) studies established that this modification significantly stabilises the DNA·RNA duplex with an average increase in Tm of about 1.4 °C per modification. For two or three modifications, the increase in Tm was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on Tm. In contrast to the DNA·RNA duplex, the 3′-S-phosphorothiolate linkage destabilised the DNA·DNA duplex, irrespective of the arrangement of the 3′-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA·DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.

A series of di-(adenosin-N6-yl) alkanes (1b) - (1l) has been prepared by reaction of the appropriate diaminoalkanes with 6-chloro-9-β-D-(2,3,5-tri-O-acetyl)-ribofuranosyl-purine (2) followed by ammonolysis. Alternatively, an analogous reaction with 6-chloro-9-β-D-(2,3-O-isopropylidene)-ribofuranosylpurine (3) produced an intermediate which could be phosphorylated at the 5'-position prior to hydrolytic removal of the isopropylidene group. 4-(1,2,4-Triazolo)-1-(β-D-2,3,5-tri-O-acetyl ribofuranosyl)-2(1H)-pyrimidone (7) was an effective intermediate for the preparation of di-(cytidin-N4-yl) alkanes (8a), (8b), and (8c) from the appropriate diaminoalkanes. The longer chain di-(adenosin-N6-yl) alkanes are very effective inhibitors of adenosine kinase. In addition an approach to the di-(adenosin-N6-yl) alkanes is described which should allow tritium labelling of the alkyl chain.