8-OxodGuo and Fapy•dG Mutagenicity in Escherichia coli Increases Significantly when They Are Part of a Tandem Lesion with 5-Formyl-2'-deoxyuridine.

Tandem lesions, which are defined by two or more contiguously damaged nucleotides, are a hallmark of ionizing radiation. Recently, tandem lesions containing 5-formyl-2'-deoxyuridine (5-fdU) flanked by a 5'-8-OxodGuo or Fapy•dG were discovered, and they are more mutagenic in human cells than the isolated lesions. In the current study, we examined replication of these tandem lesions in Escherichia coli. Bypass efficiency of both tandem lesions was reduced by 30-40% compared to the isolated lesions. Mutation frequencies (MFs) of isolated 8-OxodGuo and Fapy•dG were low, and no mutants were isolated from replication of a 5-fdU construct. The types of mutations from 8-OxodGuo were targeted G → T transversion, whereas Fapy•dG predominantly gave G → T and G deletion. 5'-8-OxodGuo-5-fdU also gave exclusively G → T mutation, which was 3-fold and 11-fold greater, without and with SOS induction, respectively, compared to that of an isolated 8-OxodGuo. In mutY/mutM cells, the MF of 8-OxodGuo and 5'-8-OxodGuo-5-fdU increased 13-fold and 7-fold, respectively. The MF of 5'-8-OxodGuo-5-fdU increased 2-fold and 3-fold in Pol II- and Pol IV-deficient cells, respectively, suggesting that these polymerases carry out largely error-free bypass. The MF of 5'- Fapy•dG-5-fdU was similar without (13 ± 1%) and with (16 ± 2%) SOS induction. Unlike the complex mutation spectrum reported earlier in human cells for 5'- Fapy•dG-5-fdU, with G → T as the major type of errors, in E. coli, the mutations were predominantly from deletion of 5-fdU. We postulate that removal of adenine-incorporated opposite 8-OxodGuo by Fpg and MutY repair proteins is partially impaired in the tandem 5'-8-OxodGuo-5-fdU, resulting in an increase in the G → T mutations, whereas a slippage mechanism may be operating in the 5'- Fapy•dG-5-fdU mutagenesis. This study showed that not only are these tandem lesions more mutagenic than the isolated lesions but they may also exhibit different types of mutations in different organisms.

7-Deazapurine and Pyrimidine Nucleoside and Oligonucleotide Cycloadducts Formed by Inverse Diels-Alder Reactions with 3,6-Di(pyrid-2-yl)-1,2,4,5-tetrazine: Ethynylated and Vinylated Nucleobases for Functionalization and Impact of Pyridazine Adducts on DNA Base Pair Stability and Mismatch Discrimination.

The manuscript reports on 7-deazapurine and pyrimidine nucleoside and oligonucleotide cycloadducts formed by the inverse electron demand Diels-Alder (iEDDA) reaction with 3,6-di(pyrid-2-yl)-1,2,4,5-tetrazine. Cycloadducts were constructed from ethynylated and vinylated nucleobases. Oligonucleotides were synthesized containing iEDDA modifications, and the impact on duplex stability was investigated. iEDDA reactions were performed on nucleoside triple bond side chains. Oxidation was not required in these cases as dihydropyridazine intermediates are not formed. In contrast, oxidation is necessary for reactions performed on alkenyl compounds. This was verified on 5-vinyl-2'-deoxyuridine. A diastereomeric mixture of 1,2-dihydropyridazine cycloadduct intermediates was isolated, characterized, and later oxidized. 12-mer oligonucleotides containing 1,2-pyridazine inverse Diels-Alder cycloadducts and their precursors were hybridized to short DNA duplexes. For that, a series of phosphoramidites was prepared. DNA duplexes with 7-functionalized 7-deazaadenines and 5-functionalized pyrimidines display high duplex stability when spacer units are present between nucleobases and pyridazine cycloadducts. A direct connectivity of the pyridazine moiety to nucleobases as reported for metabolic labeling of vinyl nucleosides reduced duplex stability strongly. Oligonucleotides bearing linkers with and without pyridazine cycloadducts attached to the 7-deazaadenine nucleobase significantly reduced mismatch formation with dC and dG.

Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase ß.

N6-(2-deoxy-α,ß-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase ß (Pol ß), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol ß incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.

Biochemical and Structural Characterization of Fapy•dG Replication by Human DNA Polymerase ß.

N6-(2-deoxy-α,ß-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase ß (Pol ß), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol ß incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3'-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.

Control of Charge-Spin Interconversion in van der Waals Heterostructures with Chiral Charge Density Waves.

A charge density wave (CDW) represents an exotic state in which electrons are arranged in a long-range ordered pattern in low-dimensional materials. Although the understanding of the fundamental character of CDW is enriched after extensive studies, its practical application remains limited. Here, an unprecedented demonstration of a tunable charge-spin interconversion (CSI) in graphene/1T-TaS2 van der Waals heterostructures is shown by manipulating the distinct CDW phases in 1T-TaS2. Whereas CSI from spins polarized in all three directions is observed in the heterostructure when the CDW phase does not show commensurability, the output of one of the components disappears, and the other two are enhanced when the CDW phase becomes commensurate. The experimental observation is supported by first-principles calculations, which evidence that chiral CDW multidomains in the heterostructure are at the origin of the switching of CSI. The results uncover a new approach for on-demand CSI in low-dimensional systems, paving the way for advanced spin-orbitronic devices.

Global transcontinental power pools for low-carbon electricity.

The transition to low-carbon electricity is crucial for meeting global climate goals. However, given the uneven spatial distribution and temporal variability of renewable resources, balancing the supply and demand of electricity will be challenging when relying on close to 100% shares of renewable energy. Here, we use an electricity planning model with hourly supply-demand projections and high-resolution renewable resource maps, to examine whether transcontinental power pools reliably meet the growing global demand for renewable electricity and reduce the system cost. If all suitable sites for renewable energy are available for development, transcontinental trade in electricity reduces the annual system cost of electricity in 2050 by 5-52% across six transcontinental power pools compared to no electricity trade. Under land constraints, if only the global top 10% of suitable renewable energy sites are available, then without international trade, renewables are unable to meet 12% of global demand in 2050. Introducing transcontinental power pools with the same land constraints, however, enables renewables to meet 100% of future electricity demand, while also reducing costs by up to 23% across power pools. Our results highlight the benefits of expanding regional transmission networks in highly decarbonized but land-constrained future electricity systems.

Local control of superconductivity in a NbSe2/CrSBr van der Waals heterostructure.

Two-dimensional magnets and superconductors are emerging as tunable building-blocks for quantum computing and superconducting spintronic devices, and have been used to fabricate all two-dimensional versions of traditional devices, such as Josephson junctions. However, novel devices enabled by unique features of two-dimensional materials have not yet been demonstrated. Here, we present NbSe2/CrSBr van der Waals superconducting spin valves that exhibit infinite magnetoresistance and nonreciprocal charge transport. These responses arise from a unique metamagnetic transition in CrSBr, which controls the presence of localized stray fields suitably oriented to suppress the NbSe2 superconductivity in nanoscale regions and to break time reversal symmetry. Moreover, by integrating different CrSBr crystals in a lateral heterostructure, we demonstrate a superconductive spin valve characterized by multiple stable resistance states. Our results show how the unique physical properties of layered materials enable the realization of high-performance quantum devices based on novel working principles.

Synergistic effects on mutagenicity of tandem lesions containing 8-oxo-7,8-dihydro-2'-deoxyguanosine or Fapy•dG flanked by a 3' 5-formyl-2'-deoxyuridine in human cells.

Modified nucleotides often hinder and/or decrease the fidelity of DNA polymerases. Tandem lesions, which are comprised of DNA modifications at two contiguous nucleotide positions, can be even more detrimental to genome stability. Recently, tandem lesions containing 5-formyl-2'-deoxyuridine (5fdU) flanked at the 5'-position by 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodGuo) or N-(2-deoxy-α,ß-D-erythropentofuranosyl)-N-(2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy•dG) were discovered. We examined the replication of 5'- 8-OxodGuo-5fdU and 5'-Fapy•dG-5fdU tandem lesions in HEK 293T cells and several polymerase deficient variants by transfecting single-stranded vectors containing them. The local sequence of the tandem lesions encompasses the 273 codon of the p53 gene, a mutational hot-spot. The bypass efficiency and mutation spectra of the tandem lesions were compared to those of the isolated lesions. Replication of weakly mutagenic 5-fdU is little changed when part of the 5'- 8-OxodGuo-5fdU tandem lesion. G → T transversions attributable to 8-OxodGuo increase > 10-fold when the tandem lesion is bypassed. 5'-Fapy•dG-5fdU has a synergistic effect on the error-prone bypass of both lesions. The mutation frequency (MF) of 5'-Fapy•dG-5fdU increases 3-fold compared to isolated Fapy•dG. In addition, a 5'-adjacent Fapy•dG significantly increases the MF of 5fdU. The major mutation, G → T transversions, decrease by almost a third in hPol κ- cells, which is the opposite effect when isolated Fapy•dG in the same sequence context is replicated in HEK 293T cells in the same sequence. Steady-state kinetics indicate that hPol κ contributes to greater G → T transversions by decreasing the specificity constant for dCTP compared to an isolated Fapy•dG. The greater conformational freedom of Fapy•dG compared to 8-OxodGuo and its unusual ability to epimerize at the anomeric center is believed to be the source of the complex effects of 5'-Fapy•dG-5fdU on replication.

Gate-Tunable Spin Hall Effect in an All-Light-Element Heterostructure: Graphene with Copper Oxide.

Graphene is a light material for long-distance spin transport due to its low spin-orbit coupling, which at the same time is the main drawback for exhibiting a sizable spin Hall effect. Decoration by light atoms has been predicted to enhance the spin Hall angle in graphene while retaining a long spin diffusion length. Here, we combine a light metal oxide (oxidized Cu) with graphene to induce the spin Hall effect. Its efficiency, given by the product of the spin Hall angle and the spin diffusion length, can be tuned with the Fermi level position, exhibiting a maximum (1.8 ± 0.6 nm at 100 K) around the charge neutrality point. This all-light-element heterostructure shows a larger efficiency than conventional spin Hall materials. The gate-tunable spin Hall effect is observed up to room temperature. Our experimental demonstration provides an efficient spin-to-charge conversion system free from heavy metals and compatible with large-scale fabrication.

8-Oxo-2'-deoxyguanosine Replication in Mutational Hot Spot Sequences of the p53 Gene in Human Cells Is Less Mutagenic than That of the Corresponding Formamidopyrimidine.

7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo) is a ubiquitous DNA damage formed by oxidation of 2'-deoxyguanosine. In this study, plasmid DNA containing 8-OxodGuo located in three mutational hot spots of human cancers, codons 248, 249, and 273 of the Tp53 tumor suppressor gene, was replicated in HEK 293T cells. 8-OxodGuo was only a weak block of replication, and the bypass was largely error-free. The mutations (1-5%) were primarily G → T transversions, and the mutation frequency was generally lower than that of the chemically related Fapy·dG. A unique 8-OxodGuo mutation spectrum was observed at each site, as reflected by replication in translesion synthesis (TLS) polymerase- or hPol λ-deficient cells. In codon 248 (CG*G) and 249 (AG*G), where G* denotes 8-OxodGuo, hPol η and hPol ζ carried out largely error-free bypass of the lesion, whereas hPol κ and hPol ι were involved mostly in error-prone TLS, resulting in G → T mutations. 8-OxodGuo bypass in codon 273 (CG*T) was unlike the other two sites, as hPol κ participated in the mostly error-free bypass of the lesion. Yet, in all three sites, including codon 273, simultaneous deficiency of hpol κ and hPol ι resulted in reduction of G → T transversions. This indicates a convincing role of these two TLS polymerases in error-prone bypass of 8-OxodGuo. Although the dominant mutation was G → T in each site, in codon 249, and to a lesser extent in codon 248, significant semi-targeted single-base deletions also occurred, which suggests that 8-OxodGuo can initiate slippage of a base near the lesion site. This study underscores the importance of sequence context in 8-OxodGuo mutagenesis in human cells. It also provides a more comprehensive comparison between 8-OxodGuo and the sister lesion, Fapy·dG. The greater mutagenicity of the latter in the same sequence contexts indicates that Fapy·dG is a biologically significant lesion and biomarker on par with 8-OxodGuo.

The Health and Climate Benefits of Economic Dispatch in China's Power System.

China's power system is highly regulated and uses an "equal-share" dispatch approach. However, market mechanisms are being introduced to reduce generation costs and improve system reliability. Here, we quantify the climate and human health impacts brought about by this transition, modeling China's power system operations under economic dispatch. We find that significant reductions in mortality related to air pollution (11%) and CO2 emissions (3%) from the power sector can be attained by economic dispatch, relative to the equal-share approach, through more efficient coal-powered generation. Additional health and climate benefits can be achieved by incorporating emission externalities in electricity generation costs. However, the benefits of the transition to economic dispatch will be unevenly distributed across China and may lead to increased health damage in some regions. Our results show the potential of dispatch decision-making in electricity generation to mitigate the negative impacts of power plant emissions with existing facilities in China.

Helicity dependent photoresistance measurement vs. beam-shift thermal gradient.

Optical detection techniques are among the most powerful methods used to characterize spintronic phenomena. The spin orientation can affect the light polarization, which, by the reciprocal mechanism, can modify the spin density. Numerous recent experiments, report local changes in the spin density induced by a circularly polarized focused laser beam. These effects are typically probed electrically, by detecting the variations of the photoresistance or photocurrent associated to the reversal of the light helicity. Here we show that in general, when the light helicity is modified, the beam profile is slightly altered, and the barycenter of the laser spot is displaced. Consequently, the temperature gradients produced by the laser heating will be modulated, producing thermo-electric signals that alternate in phase with the light polarization. These unintended signals, having no connection with the electron spin, appear under the same experimental conditions and can be easily misinterpreted. We show how this contribution can be experimentally assessed and removed from the measured data. We find that even when the beam profile is optimized, this effect is large, and completely overshadows the spin related signals in all the materials and experimental conditions that we have tested.

All-Electrical Spin-to-Charge Conversion in Sputtered BixSe1-x.

One of the major obstacles to realizing spintronic devices such as MESO logic devices is the small signal magnitude used for magnetization readout, making it important to find materials with high spin-to-charge conversion efficiency. Although intermixing at the junction of two materials is a widely occurring phenomenon, its influence on material characterization and the estimation of spin-to-charge conversion efficiencies are easily neglected or underestimated. Here, we demonstrate all-electrical spin-to-charge conversion in BixSe1-x nanodevices and show how the conversion efficiency can be overestimated by tens of times depending on the adjacent metal used as a contact. We attribute this to the intermixing-induced compositional change and the properties of a polycrystal that lead to drastic changes in resistivity and spin Hall angle. Strategies to improve the spin-to-charge conversion signal in similar structures for functional devices are discussed.

The design and evaluation of bionic porous bone scaffolds in fluid flow characteristics and mechanical properties.

BACKGROUND AND OBJECTIVE: At present, there is a lack of efficient modeling methods for bionic artificial bone scaffolds, and the tissue fluid/nutrient mass transport characteristics of bone scaffolds has not been evaluated sufficiently. This study aims to explore an effective and efficient modeling method for biomimetic porous bone scaffolds for biological three-dimensional printing based on the imitation of the histomorphological characteristics of human vertebral cancellous bone. The fluid mass transport and mechanical characteristics of the porous scaffolds were evaluated and compared with those of a human cancellous bone,and the relationship between the geometric parameters (e.g., the size, number, shape of pores and porosity) and the performence of biomimetic porous bone scaffolds are revealed. METHODS: The bionic modeling design method proposed in this study considers the biological characteristics of vertebral cancellous tissue and performs imitation and design of vertebrae-like two-dimensional slices images.It then reconstructs the slices layer-by-layer to form porous scaffolds with a three-dimensional reconstruction method, similar to computed tomography image reconstruction. By controlling the design parameters, this method can easily realize the formation of plate-like (femoral cancellous bone-like) or rod-like (vertebral cancellous bone-like) porous scaffolds. The flow characterization of porous structures was performed using the computational fluid simulation method. RESULTS: The flow characterization results showed that the permeability of the porous scaffolds and human bone was 10-8∼10-9m2,and when the porosity of the porous scaffolds was higher than 70%, the permeability was higher than that of human vertebrae with a porosity of 82%. The maximum shear stress of the designed porous scaffolds and human vertebra were less than 0.8Mpa, which was conducive to cell adhesion, cell migration, and cell differentiation. The results of 3D printing and mechanical testing showed good printability and reflected the relationship between the mechanical properties and design parameters. CONCLUSIONS: The design method proposed in this study has many controllable parameters, which can be adjusted to generate diversified functional porous structures to meet specific needs, increase the potential of bone scaffold design, and leave room for meeting the new requirements for bone scaffold characteristics in the future.

Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.

N6-(2-Deoxy-α,ß-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido pyrimidine (Fapy•dG) is a prevalent form of genomic DNA damage. Fapy•dG is formed in greater amounts under anoxic conditions than the well-studied, chemically related 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodGuo). Fapy•dG is more mutagenic in mammalian cells than 8-oxodGuo. A distinctive property of Fapy•dG is facile epimerization, but prior works with Fapy•dG analogues have precluded determining its effect on chemistry. We present crystallographic characterization of natural Fapy•dG in duplex DNA and as the template base for DNA polymerase ß (Pol ß). Fapy•dG adopts the ß-anomer when base paired with cytosine but exists as a mixture of α- and ß-anomers when promutagenically base paired with adenine. Rotation about the bond between the glycosidic nitrogen atom and the pyrimidine ring is also affected by the opposing nucleotide. Sodium cyanoborohydride soaking experiments trap the ring-opened Fapy•dG, demonstrating that ring opening and epimerization occur in the crystalline state. Ring opening and epimerization are facilitated by propitious water molecules that are observed in the structures. Determination of Fapy•dG mutagenicity in wild type and Pol ß knockdown HEK 293T cells indicates that Pol ß contributes to G → T transversions but also suppresses G → A transitions. Complementary kinetic studies have determined that Fapy•dG promotes mutagenesis by decreasing the catalytic efficiency of dCMP insertion opposite Fapy•dG, thus reducing polymerase fidelity. Kinetic studies have determined that dCMP incorporation opposite the ß-anomer is ∼90 times faster than the α-anomer. This research identifies the importance of anomer dynamics, a feature unique to formamidopyrimidines, when considering the incorporation of nucleotides opposite Fapy•dG and potentially the repair of this structurally unusual lesion.

Effect of Chiral Damping on the dynamics of chiral domain walls and skyrmions.

Friction plays an essential role in most physical processes that we experience in our everyday life. Examples range from our ability to walk or swim, to setting boundaries of speed and fuel efficiency of moving vehicles. In magnetic systems, the displacement of chiral domain walls (DW) and skyrmions (SK) by Spin Orbit Torques (SOT), is also prone to friction. Chiral damping (αc), the dissipative counterpart of the Dzyaloshinskii Moriya Interaction (DMI), plays a central role in these dynamics. Despite experimental observation, and numerous theoretical studies confirming its existence, the influence of chiral damping on DW and SK dynamics has remained elusive due to the difficulty of discriminating from DMI. Here we unveil the effect that αc has on the flow motion of DWs and SKs driven by current and magnetic field. We use a static in-plane field to lift the chiral degeneracy. As the in-plane field is increased, the chiral asymmetry changes sign. When considered separately, neither DMI nor αc can explain the sign reversal of the asymmetry, which we prove to be the result of their competing effects. Finally, numerical modelling unveils the non-linear nature of chiral dissipation and its critical role for the stabilization of moving SKs.

Gate-tuneable and chirality-dependent charge-to-spin conversion in tellurium nanowires.

Chiral materials are an ideal playground for exploring the relation between symmetry, relativistic effects and electronic transport. For instance, chiral organic molecules have been intensively studied to electrically generate spin-polarized currents in the last decade, but their poor electronic conductivity limits their potential for applications. Conversely, chiral inorganic materials such as tellurium have excellent electrical conductivity, but their potential for enabling the electrical control of spin polarization in devices remains unclear. Here, we demonstrate the all-electrical generation, manipulation and detection of spin polarization in chiral single-crystalline tellurium nanowires. By recording a large (up to 7%) and chirality-dependent unidirectional magnetoresistance, we show that the orientation of the electrically generated spin polarization is determined by the nanowire handedness and uniquely follows the current direction, while its magnitude can be manipulated by an electrostatic gate. Our results pave the way for the development of magnet-free chirality-based spintronic devices.

Economic disparity among generations under the Paris Agreement.

The costs and benefits of climate change mitigation are known to be distributed unevenly across time and space, while their intergenerational distribution across nations has not been evaluated. Here, we analyze the lifetime costs and benefits of climate change mitigation by age cohorts across countries under the Paris Agreement. Our results show that the age cohorts born prior to 1960 generally experience a net reduction in lifetime gross domestic product per capita. Age cohorts born after 1990 will gain net benefits from climate change mitigation in most lower income countries. However, no age cohorts enjoy net benefits regardless of the birth year in many higher income countries. Furthermore, the cost-benefit disparity among old and young age cohorts is expected to widen over time. Particularly, lower income countries are expected to have much larger cost-benefit disparity between the young and the old. Our findings highlight the challenges in building consensus for equitable climate policy among nations and generations.

Sequence context effects of replication of Fapy•dG in three mutational hot spot sequences of the p53 gene in human cells.

Fapy•dG and 8-OxodGuo are formed in DNA from a common N7-dG radical intermediate by reaction with hydroxyl radical. Although cellular levels of Fapy•dG are often greater, its effects on replication are less well understood than those of 8-OxodGuo. In this study plasmid DNA containing Fapy•dG in three mutational hotspots of human cancers, codons 248, 249, and 273 of the p53 tumor suppressor gene, was replicated in HEK 293T cells. TLS efficiencies for the Fapy•dG containing plasmids varied from 72 to 89%, and were further reduced in polymerase-deficient cells. The mutation frequency (MF) of Fapy•dG ranged from 7.3 to 11.6%, with G→T and G→A as major mutations in codons 248 and 249 compared to primarily G→T in codon 273. Increased MF in hPol ι-, hPol κ-, and hPol ζ-deficient cells suggested that these polymerases more frequently insert the correct nucleotide dC opposite Fapy•dG, whereas decreased G→A in codons 248 and 249 and reduction of all mutations in codon 273 in hPol λ-deficient cells indicated hPol λ's involvement in Fapy•dG mutagenesis. In vitro kinetic analysis using isolated translesion synthesis polymerases and hPol λ incompletely corroborated the mutagenesis experiments, indicating codependence on other proteins in the cellular milieu. In conclusion, Fapy•dG mutagenesis is dependent on the DNA sequence context, but its bypass by the TLS polymerases is largely error-free.

Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space.

Small ribozymes such as Oryza sativa twister spontaneously cleave their own RNA when the ribozyme folds into its active conformation. The coupling between twister folding and self-cleavage has been difficult to study, however, because the active ribozyme rapidly converts to product. Here, we describe the synthesis of a photocaged nucleotide that releases guanosine within microseconds upon photosolvolysis with blue light. Application of this tool to O. sativa twister achieved the spatial (75 µm) and temporal (≤30 ms) control required to resolve folding and self-cleavage events when combined with single-molecule fluorescence detection of the ribozyme folding pathway. Real-time observation of single ribozymes after photo-deprotection showed that the precleaved folded state is unstable and quickly unfolds if the RNA does not react. Kinetic analysis showed that Mg2+ and Mn2+ ions increase ribozyme efficiency by making transitions to the high energy active conformation more probable, rather than by stabilizing the folded ground state or the cleaved product. This tool for light-controlled single RNA folding should offer precise and rapid control of other nucleic acid systems.