A Mismatch-Selective Bifunctional Rhodium−Oregon Green Conjugate: A Fluorescent Probe for Mismatched DNA

Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes

Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.

Mitochondria-targeting single-layered graphene quantum dots with dual recognition sites for ATP imaging in living cells

As a molecular unit of intracellular energy transfer, adenosine triphosphate (ATP) is significant for maintaining the energy balance in living cells and thus monitoring cellular ATP is important to assess cellular physiological functions. However, effective monitoring of cellular ATP still faces challenges owing to the similarity of ATP to other nucleoside polyphosphates. Herein, yellow emissive single-layered graphene quantum dots (s-GQDs) with dual recognition sites including π-conjugated single sheets and positively charged sites were developed. The s-GQDs exhibit a good mitochondria targeting ability and respond only to purine nucleotides and show good selectivity in discriminating tri-, di- and monophosphate nucleotides. The good selectivity should be attributed to the concurrent effect of π-π stacking and electrostatic interactions between filmy layered positive s-GQDs and negative purine nucleotides. Owing to the mitochondria targeting ability and dual recognition sites of the s-GQDs, the mitochondrial ATP fluctuation resulting from the activation and suppression of ATP in living cells has been successfully monitored.

A Family of Rhodium Complexes with Selective Toxicity toward Mismatch Repair-Deficient Cancers

Rhodium metalloinsertors are a unique set of metal complexes that bind specifically to DNA base pair mismatches in vitro and kill mismatch repair (MMR)-deficient cells at lower concentrations than their MMR-proficient counterparts. A family of metalloinsertors containing rhodium-oxygen ligand coordination, termed "Rh-O" metalloinsertors, has been prepared and shown to have a significant increase in both overall potency and selectivity toward MMR-deficient cells regardless of structural changes in the ancillary ligands. Here we describe DNA-binding and cellular studies with the second generation of Rh-O metalloinsertors in which an ancillary ligand is varied in both steric bulk and lipophilicity. These complexes, of the form [Rh(L)(chrysi)(PPO)]²⁺, all include the O-containing PPO ligand (PPO = 2-(pyridine-2-yl)propan-2-ol) and the aromatic inserting ligand chrysi (5,6-chrysene quinone diimine) but differ in the identity of their ancillary ligand L, where L is a phenanthroline or bipyridyl derivative. The Rh-O metalloinsertors in this family all show micromolar binding affinities for a 29-mer DNA hairpin containing a single CC mismatch. The complexes display comparable lipophilic tendencies and p K_a values of 8.1-9.1 for dissociation of an imine proton on the chrysi ligand. In cellular proliferation and cytotoxicity assays with MMR-deficient cells (HCT116O) and MMR-proficient cells (HCT116N), the complexes containing the phenanthroline-derived ligands show highly selective cytotoxic preference for the MMR-deficient cells at nanomolar concentrations. Using mass spectral analyses, it is shown that the complexes are taken into cells through a passive mechanism and exhibit low accumulation in mitochondria, an off-target organelle that, when targeted by parent metalloinsertors, can lead to nonselective cytotoxicity. Overall, these Rh-O metalloinsertors have distinct and improved behavior compared to previous generations of parent metalloinsertors, making them ideal candidates for further therapeutic assessment.

Luminescent platinum(II) complexes with functionalized N-heterocyclic carbene or diphosphine selectively probe mismatched and abasic DNA

The selective targeting of mismatched DNA overexpressed in cancer cells is an appealing strategy in designing cancer diagnosis and therapy protocols. Few luminescent probes that specifically detect intracellular mismatched DNA have been reported. Here we used Pt(II) complexes with luminescence sensitive to subtle changes in the local environment and report several Pt(II) complexes that selectively bind to and identify DNA mismatches. We evaluated the complexes' DNA-binding characteristics by ultraviolet/visible absorption titration, isothermal titration calorimetry, nuclear magnetic resonance and quantum mechanics/molecular mechanics calculations. These Pt(II) complexes show up to 15-fold higher emission intensities upon binding to mismatched DNA over matched DNA and can be utilized for both detecting DNA abasic sites and identifying cancer cells and human tissue samples with different levels of mismatch repair. Our work highlights the potential of luminescent Pt(II) complexes to differentiate between normal cells and cancer cells which generally possess more aberrant DNA structures.

DNA pairing defects such as mismatched and abasic DNA are prevalent in cancer cells. Here, the authors present luminescent platinum based probes capable of preferentially binding to mismatched and abasic DNA, and reporting this by a significant luminescence enhancement

Zinc complexes as fluorescent chemosensors for nucleic acids: new perspectives for a "boring" element

Zinc(II) complexes are effective and selective nucleic acid-binders and strongly fluorescent molecules in the low energy range, from the visible to the near infrared. These two properties have often been exploited to quantitatively detect nucleic acids in biological samples, in both in vitro and in vivo models. In particular, the fluorescent emission of several zinc(II) complexes is drastically enhanced or quenched by the binding to nucleic acids and/or upon visible light exposure, in a different fashion in bulk solution and when bound to DNA. The twofold objective of this perspective is (1) to review recent utilisations of zinc(II) complexes as selective fluorescent probes for nucleic acids and (2) to highlight their novel potential applications as diagnostic tools based on their photophysical properties.

Luminescent properties of ruthenium(II) complexes with sterically expansive ligands bound to DNA defects

A new family of ruthenium(II) complexes with sterically expansive ligands for targeting DNA defects was prepared, and their luminescent responses to base pair mismatches and/or abasic sites were investigated. Design of the complexes sought to combine the mismatch specificity of sterically expansive metalloinsertors, such as [Rh(bpy)2(chrysi)](3+) (chrysi = chrysene-5,6-quinone diimine), and the light switch behavior of [Ru(bpy)2(dppz)](2+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine). In one approach, complexes bearing analogues of chrysi incorporating hydrogen-bonding functionality similar to dppz were synthesized. While the complexes show luminescence only at low temperatures (77 K), competition experiments with [Ru(bpy)2(dppz)](2+) at ambient temperatures reveal that the chrysi derivatives preferentially bind DNA mismatches. In another approach, various substituents were introduced onto the dppz ligand to increase its steric bulk for mismatch binding while maintaining planarity. Steady state luminescence and luminescence lifetime measurements reveal that these dppz derivative complexes behave as DNA "light switches" but that the selectivity in binding and luminescence with mismatched/abasic versus well-matched DNA is not high. In all cases, luminescence depends sensitively upon structural perturbations to the dppz ligand.

A selective luminescent probe for the direct time-gated detection of adenosine triphosphate

A molecular probe for the luminescent detection of adenosine nucleotides is presented. The probe, Tb-DOTAm-Phen, readily distinguishes among the three adenosine nucleotides in buffered aqueous conditions at neutral pH, a requirement for the direct monitoring of enzymatic reactions converting adenosine triphosphate (ATP) to adenosine diphosphate or adenosine monophosphate. The probe is most efficient under millimolar concentrations of ATP which are relevant to intracellular conditions. Moreover, the long luminescence lifetime of the probe readily enables time-gating experiments.

DNA-hosted copper nanoclusters for fluorescent identification of single nucleotide polymorphisms

Metal nanoclusters have received considerable interest due to their unique properties and potential applications in numerous fields. Particularly, newly emerging Cu nanoclusters offer excellent potential as functional biological probes. In this work, we for the first time report that the fluorescence of DNA-hosted Cu nanoclusters is very sensitive to base type located in the major groove. This intriguing finding provides a sensitive fluorimetric diagnostic of the mismatch type in a specific DNA sequence, which is difficult to achieve by traditional methods. Furthermore, the research results have shed some light on the luminescent mechanism of Cu nanoclusters. Owing to its high specificity and easy operation without rigorously controlled temperature and arduous probe DNA design, it is expected that the proposed procedure can provide a tool for early diagnosis and risk assessment of malignancy.

Recognition of a C-C mismatch in a DNA duplex using a fluorescent small molecule with application for "off-on" discrimination of C/G mutation

The fluorescent small molecule 2-amino-7-methyl-1,8-naphthyridine (AMND) can selectively bind to a cytosine (C) at a C-C mismatch in double-stranded DNA (dsDNA). The interactions between AMND and C-C mismatch-containing dsDNA were investigated by measuring ultraviolet (UV) absorption as a function of temperature to obtain melting curves as well as circular dichroism and fluorescence spectra. Results show that AMND strongly stabilizes C-C mismatch-containing dsDNA, whereas fully matched duplexes are not stabilized under the same conditions. The fluorescence of AMND was efficiently quenched when it was bound to a C-C mismatch in dsDNA. Binding constants (K(11)), obtained by fluorescence titration, were 1.2 × 10(5) M(-1). Although sensing functions depend on the sequences flanking the mismatch site, the change in AMND fluorescence intensity can be utilized to detect the C-C mismatch-containing dsDNA. Accordingly, discrimination of the C/G mutation in the model sequence (PGR gene rs1255998) was achieved by visualizing fluorescence of AMND. A probe DNA molecule was designed to contain a C opposite the C/G base in the target DNA, and this probe was used to hybridize the target DNA. The fluorescence of AMND was "on" for a C-G match, while the fluorescence was "off" for a C-C mismatch. This assay is simple and does not require DNA labeling.

DNA-binding and photocleavage studies of ruthenium(II) complexes containing asymmetric intercalative ligand

A novel asymmetric ligand 2-(pyridine-2-yl)-1-H-imidazo[4,5-i]dibenzo[2,3-a:2',3'-c]phenazine (pidbp) and its ruthenium complexes [Ru(L)(2)(pidbp)](2+) (L=bpy (2, 2'- bipyridine), phen (1, 10 - phenanthroline)), have been synthesized and characterized by elemental analysis, ES-MS, (1)H NMR. Various methods support the conclusion that both Ru(II) complexes can intercalate into DNA base pairs. Complex [Ru(bpy)(2)(pidbp)](2+)4 exhibits its DNA "molecular light switch" properties. Furthermore, the two complexes are efficient DNA-photocleavers under irradiation at 365 nm, and complex 5 exhibits a stronger DNA-photocleavage efficiency than complex 4. The mechanism of DNA cleavage is an oxidative process by generating singlet oxygen.

Metal Complexes for DNA-Mediated Charge Transport

In all organisms, oxidation threatens the integrity of the genome. DNA-mediated charge transport (CT) may play an important role in the generation and repair of this oxidative damage. In studies involving long-range CT from intercalating Ru and Rh complexes to 5'-GG-3' sites, we have examined the efficiency of CT as a function of distance, temperature, and the electronic coupling of metal oxidants bound to the base stack. Most striking is the shallow distance dependence and the sensitivity of DNA CT to how the metal complexes are stacked in the helix. Experiments with cyclopropylamine-modified bases have revealed that charge occupation occurs at all sites along the bridge. Using Ir complexes, we have seen that the process of DNA-mediated reduction is very similar to that of DNA-mediated oxidation. Studies involving metalloproteins have, furthermore, shown that their redox activity is DNA-dependent and can be DNA-mediated. Long range DNA-mediated CT can facilitate the oxidation of DNA-bound base excision repair proteins to initiate a redox-active search for DNA lesions. DNA CT can also activate the transcription factor SoxR, triggering a cellular response to oxidative stress. Indeed, these studies show that within the cell, redox-active proteins may utilize the same chemistry as that of synthetic metal complexes in vitro, and these proteins may harness DNA-mediated CT to reduce damage to the genome and regulate cellular processes.

pH- and DNA-induced dual molecular light switches based on a novel ruthenium(II) complex

A novel Ru(II) complex, [Ru(bpy)(2)(btppz)]Cl(2), where bpy=2,2'-bipyridine and btppz=benzo[h]tripyrido[3,2-a:2',3'-c:2'',3''-j]phenazine, has been synthesized and characterized. The pH effects on UV-visible (UV-vis) absorption and emission spectra of the complex have been studied and ground- and excited-state ionization constants of the complex have been derived. The calf thymus DNA (ct-DNA) binding properties of the complex were investigated with UV-vis absorption and luminescence spectrophotometric titrations, steady-state emission quenching by [Fe(CN)(6)](4-), DNA competitive binding with ethidium bromide, DNA melting experiments, reverse salt titrations and viscosity measurements. The complex was demonstrated to act as dual molecular switches: pH-induced "on-off" emission switch with an on-off intensity ratio of approximately 54 which is favorably compared with those reported for structurally analogous Ru(II) complexes, and a DNA molecular light switch with a luminescence enhancement factor of 22 as it intercalatively bound to the DNA.

A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode

Two crystal structures of Delta-Rh(bpy)(2)(chrysi)(3+) (chrysi is 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5'-CGGAAATTACCG-3' containing two adenosine-adenosine mismatches (italics) through metalloinsertion were determined. Diffraction quality crystals with two different space groups (P3(2)21 and P4(3)2(1)2) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2'-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5'-AT-3' step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Delta-Rh(bpy)(2)(chrysi)(3+) bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single-base mismatches. These results underscore the generality of metalloinsertion as a new mode of noncovalent binding by small molecules with a DNA duplex.

Sensitivity of Ru(bpy)2dppz2+ luminescence to DNA defects

The luminescent characteristics of Ru(bpy)(2)dppz(2+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine), a DNA light switch, were investigated in the presence of oligonucleotides containing single base mismatches or an abasic site. In water, the ruthenium luminescence is quenched, but, bound to well matched duplex DNA, the Ru complex luminesces. Here we show that with DNAs containing a defect, rac-, Delta-, and Lambda-Ru(bpy)(2)dppz(2+) exhibit significant luminescent enhancements above that with well matched DNA. In the presence of a single base mismatch, large luminescent enhancements are evident for the Delta-Ru isomer; the Lambda-isomer shows particularly high luminescence bound to an oligonucleotide containing an abasic site. Similar increases are not evident with two common DNA-binding organic fluorophores, ethidium bromide and TO-PRO-3. Titrations with hairpin oligonucleotides containing a variable mismatch site show correlation between the level of luminescent enhancement and the thermodynamic destabilization associated with the mismatch. This correlation is reminiscent of that found earlier for a bulky rhodium complex that binds mismatched DNA sites through metalloinsertion, where the complex binds the DNA from the minor groove side, ejecting the mismatched bases into the major groove. Differential quenching studies with minor and major groove quenchers and time-resolved emission studies support this metalloinsertion mode for the dppz complex at the defect site. Certainly these data underscore the utility of Ru(bpy)(2)dppz(2+) as a sensitive luminescent reporter of DNA and its defects.

Structure-specific binding of [Co(phen)(2)(HPIP)](3+) to a DNA duplex containing sheared G:A mismatch base pairs

The binding of a Co(III) complex to the decanucleotide d(CCGAATGAGG)(2) containing two pairs of G:A mismatches was studied by 2D-NMR, UV absorption, and molecular modeling. NMR investigations indicate that racemic [Co(phen)(2)(HPIP)]Cl(3) [HPIP=2-(2-hydroxyphenyl) imidazo [4,5-f][1,10] phenanthroline] binds the decanucleotide by intercalation: the HPIP ligand selectively inserts between the stacked bases from the minor groove at the terminal regions and from the major groove at the sheared region. Further, molecular modeling revealed that the recognition shows strong enantioselectivity: the Lambda-isomer preferentially intercalates into the T(6)G(7):A(5)A(4) region from the DNA major groove, while Delta-isomer favors the terminal C(1)C(2):G(10)G(9) region and intercalates from the minor groove. Detailed energy analysis suggests that the steric interaction, especially the electrostatic effect, is the primary determinants of the recognition event. Melting experiments indicate that binding stabilizes the DNA duplex and increases the melting temperature by 9.5 degrees C. The intrinsic binding constant of the complex to the mismatched duplex was determined to be 3.5x105M(-1).

Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators

Binding of three macrocyclic bis-intercalators, derivatives of acridine and naphthalene, and two acyclic model compounds to mismatch-containing and matched duplex oligodeoxynucleotides was analyzed by thermal denaturation experiments, electrospray ionization mass spectrometry studies (ESI-MS) and fluorescent intercalator displacement (FID) titrations. The macrocyclic bis-intercalators bind to duplexes containing mismatched thymine bases with high selectivity over the fully matched ones, whereas the acyclic model compounds are much less selective and strongly bind to the matched DNA. Moreover, the results from thermal denaturation experiments are in very good agreement with the binding affinities obtained by ESI-MS and FID measurements. The FID results also demonstrate that the macrocyclic naphthalene derivative BisNP preferentially binds to pyrimidine–pyrimidine mismatches compared to all other possible base mismatches. This ligand also efficiently competes with a DNA enzyme (M.TaqI) for binding to a duplex with a TT-mismatch, as shown by competitive fluorescence titrations. Altogether, our results demonstrate that macrocyclic distance-constrained bis-intercalators are efficient and selective mismatch-binding ligands that can interfere with mismatch-binding enzymes.

Binding of Ru(bpy)2(eilatin)2+ to matched and mismatched DNA

The DNA-binding properties of Ru(bpy)2(eilatin)(2+) have been investigated to determine if the sterically expansive eilatin ligand confers specificity for destabilized single-base mismatches in DNA. Competitive DNA photocleavage experiments employing a sequence-neutral metallointercalator, Rh(bpy)2(phi)(3+) (phi = 9,10-phenanthrenequinonediimine), and a mismatch-specific metalloinsertor, Rh(bpy)2(chrysi)(3+) (chrysi = chrysene-5,6-quinonediimine), reveal that the eilatin complex binds to a CC mismatched site with an apparent binding constant of 2.2(2) x 10(6) M(-1). Nonetheless, the selectivity in binding mismatched DNA is not high: competitive titrations with Rh(bpy)2(phi)(3+) show that the complex binds also to well-matched B-form sites. Thus, Ru(bpy)2(eilatin)(2+), despite containing the extremely expansive eilatin ligand, displays lower selectivity for the mismatch than does Rh(bpy)2(chrysi)(3+), a metalloinsertor containing the smaller, though still bulky, chrysene-5,6-quinonediimine ligand. In summary, the size and shape of the eilatin ligand allow stacking with both well-matched and mismatched DNA.

Targeting abasic sites and single base bulges in DNA with metalloinsertors

The site-specific recognition of abasic sites and single base bulges in duplex DNA by sterically expansive rhodium metalloinsertors has been investigated. Through DNA photocleavage experiments, Rh(bpy)2(chrysi)3+ is shown to bind both abasic sites and single base bulges site-specifically and, upon irradiation, to cleave the backbone of the defect-containing DNA. Photocleavage titrations reveal that the metal complex binds DNA containing an abasic site with high affinity (2.6(5) x 106 M-1), comparably to the metalloinsertor and a CC mismatch. The complex binds single base bulge sites with lower affinity (approximately 105 M-1). Analysis of cleavage products and the correlation of affinities with helix destabilization suggest that Rh(bpy)2(chrysi)3+ binds both lesions via metalloinsertion, as observed for Rh binding at mismatched sites, a binding mode in which the mismatched or unpaired bases are extruded from the helix and replaced in the base stack by the sterically expansive ligand of the metalloinsertor.

Metallo-intercalators and metallo-insertors

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion.

DNA strand cleavage near a CC mismatch directed by a metalloinsertor

Reagents for recognition and efficient cleavage of mismatched DNA without photoactivation were designed. They contain a combination of a mismatch-directing metalloinsertor, [Rh(bpy)2(chrysi)]3+ (bpy=2,2'-bipyridyl, chrysi=5,6-chrysenequinone diimine), and an oxidative cleavage functionality, [Cu(phen)2]+ (Cu). Both unconjugated (Rh+Cu) and conjugated (Rh-Cu) frameworks of the Rh insertor and Cu were prepared. Compared to Cu, both constructs Rh+Cu and Rh-Cu exhibit efficient site-specific DNA scission only with mismatched DNA, confirmed by experiments with 32P-labeled oligonucleotides. Furthermore, these studies indicate that DNA cleavage occurs near the mismatch in the minor groove and on both strands. Interestingly, the order of reactivity of the three systems with a CC mismatch is Rh+Cu>Rh-Cu>>Cu. Rh binding appears to direct Cu reactivity with or without tethering. These results illustrate advantages and disadvantages in bifunctional conjugation.

Insertion of a bulky rhodium complex into a DNA cytosine-cytosine mismatch: an NMR solution study

The bulky octahedral complex Rh(bpy)2chrysi3+ (chrysi = 5,6-chrysenequinonediimine) binds single-base mismatches in a DNA duplex with micromolar binding affinities and high selectivity. Here we present an NMR solution study to characterize the binding mode of this bulky metal complex with its target CC mismatch in the oligonucleotide duplex (5'-CGGACTCCG-3')2. Both NOESY and COSY studies indicate that Rh(bpy)2chrysi3+ inserts deeply in the DNA at the mismatch site via the minor groove and with ejection of both destabilized cytosines into the opposite major groove. The insertion only minimally distorts the conformation of the oligonucleotide local to the binding site. Both flanking, well-matched base pairs remain tightly hydrogen-bonded to each other, and 2D DQF-COSY experiments indicate that all sugars maintain their original C2'-endo conformation. Remarkably, 31P NMR reveals that opening of the phosphate angles from a BI to a BII conformation is sufficient for insertion of the bulky metal complex. These results corroborate those obtained crystallographically and, importantly, provide structural evidence for this specific insertion mode in solution.

DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications

This protocol describes the syntheses and applications of two metallointercalators, Rh(bpy)2(chrysi)3+ and Rh(bpy)2(phzi)3+, that target single base mismatches in DNA. The complexes bind mismatched DNA sites specifically and, upon photoactivation, promote strand scission neighboring the mismatch. Owing to their high specificity and sequence context independence, targeting mismatches with these complexes offers an attractive alternative to current mismatch- and SNP-detection methodologies. This protocol also describes the synthesis of these complexes and their use in marking mismatched sites. Irradiation of 32P-labeled duplex DNA with either intercalator followed by denaturing PAGE allows the detection of mismatches in oligonucleotides. The protocol also outlines a method for efficient detection of single nucleotide polymorphisms (SNPs) in larger genes or plasmids. Pooled genes are denatured and re-annealed to form heteroduplexes; they are then incubated with either complex, irradiated and analyzed using capillary electrophoresis to probe for mismatches (SNP sites). The synthesis of the metallointercalators requires approximately 5-7 d. The mismatch- and SNP-detection experiments each require approximately 3 d.

Targeting DNA Mismatches with Rhodium Intercalators Functionalized with a Cell-Penetrating Peptide†

Cell-penetrating peptides are widely used to deliver cargo molecules into cells. Here we describe the synthesis, characterization, DNA binding, and cellular uptake studies of a series of metal-peptide conjugates containing oligoarginine as a cell-penetrating peptide. d-Octaarginine units are appended onto a rhodium intercalator containing the sterically expansive chrysenequinone diimine (chrysi) ligand to form Rh(chrysi)(phen)(bpy)(3+)-tethered oligoarginine conjugates, where the peptide is attached to the ancillary bpy ligand; some conjugates also include a fluorescein or thiazole orange tag. These complexes bind and with photoactivation selectively cleave DNA neighboring single-base mismatches. The presence of the oligoarginines is found to increase the nonspecific binding affinity of the complexes for both matched and mismatched DNA, but for these conjugates, photocleavage remains selective for the mismatched site, as assayed using both gel electrophoresis and mass spectrometry experiments. Significantly, the rhodium complex does not interfere with the delivery properties of the cell-penetrating peptide. Confocal microscopy experiments show rapid nuclear localization of the metal-peptide conjugates containing the tethered fluorescein. Mass spectrometry experiments confirm the association of the rhodium with the HeLa cells. These results provide a strategy for targeting mismatch-selective metal complexes inside cell nuclei.

Detection of a single DNA base-pair mismatch using an anthracene-tagged fluorescent probe

A novel anthracene-tagged oligonucleotide can discriminate between a fully-matched DNA target sequence and one with a single mismatching base-pair through a remarkable difference in fluorescence emission intensity upon duplex formation.