Structural and functional organization of the photosystems in spinach chloroplasts. Antenna size,relative electron-transport capacity,and chlorophyll composition

The structural and functional organization of the spinach chloroplast photosystems (PS) I, II_α and II_β was investigated. Sensitive absorbance difference spectrophotometry in the ultraviolet (?A₃₂₀) and red (?A₇₀₀) regions of the spectrum provided information on the relative concentration of PS II and PS I reaction centers. The kinetic analysis of PS II and PS I photochemistry under continuous weak excitation provided information on the number (N) of chlorophyll (Chl) molecules transferring excitation energy to PS II_α, PS II_β and PS I. Spinach chloroplasts contained almost twice as many PS II reaction centers compared to PS I reaction centers. The number N_α of chlorophyll (Chl) molecules associated with PS II_α was 234, while N_β = 100 and N_{PS I} = 210. Thus, the functional photosynthetic unit size of PS II reaction centers was different from that of PS I reaction centers. The relative electron-transport capacity of PS II was significantly greater than that of PS I. Hence, under light-limiting green excitation when both Chl a and Chl b molecules are excited equally, the limiting factor in the overall electron-transfer reaction was the turnover of PS I. The Chl composition of PS I, PS II_α and PS II_β was analyzed on the basis of a core Chl a reaction center complex component and a Chl $\text{a}\text{b-}\text{LHC}$ component. There is a dissimilar Chl $\text{a}\text{b-}\text{LHC}$ composition in the three photosystems with 77% of total Chl b associated with PS II_α only. The results indicate that PS II_α, located in the membrane of the grana partition region, is poised to receive excitation from a wider spectral window than PS II_β and PS I.     

Identification of collagen alpha1(I) trimer and normal type I collagen in a polyoma virus-induced mouse tumor.

A bone- and cartilage-forming mouse tumor, induced by transforming salivary epithelial cells with polyoma virus, contained large quantities of collagen. Two types of collagen molecules were isolated which had different solubilities in salt. One was type I collagen with a chain composition [α1(I)]₂ α2 and the other was an unusual form of type I collagen with a chain composition [α1(I)]₃. This would appear to be the first in vivo demonstration of α1 type I trimer.     

Differently oriented chlorophylls in Mesotaenium caldariorum detected by microphotometrical dichroism measurements in vivo

The chloroplasts of individual cells of Mesotaenium caldariorum were examined microphotometrically under non-polarized and polarized measuring light. The measurement with non-polarized light showed different absorption bands of the thylakoids depending on the position of their surface with respect to the incident light beam: in the edge position, the absorption bands lie at 672 nm, in the face position at 678 nm. From this difference in absorption maxima, we conclude that the molecules related to the sub-bands at the two wavelengths are oriented differently. The Q_y transition of the molecules which absorb light at 678 nm must be oriented parallel to the face of the thylakoids (fraction I), while that of the molecules absorbing at 672 nm is oriented perpendicular to the face (fraction II). Measurement with polarized light leads to the same conclusion that two fractions of differently oriented chlorophylls exist: In the edge position, a very large difference between E_∥ and E_⊥ (dichroism) was found in red light, with a maximum of E_∥ lying at 675 nm and a maximum of E_⊥ at 670 nm, with a shoulder at 650 nm. In the blue region, especially in the Soret band zone, the chloroplast showed a negative dichroism in the edge position, which changes over to positive values when the wavelength exceeds 450 nm. In the face position no dichroism in red or blue light could be detected. Comparison of the ‘edge position dichroism’ in red light with that in blue light justifies the supposition that the chlorin planes of the chlorophyll molecules may be oriented perpendicular or parallel to the thylakoid face, in the case of perpendicular orientation with the Q_y transitions of fraction II and the x-transitions (B_x, Q_x) of fraction I projecting out of the plane, and for parallel orientation with all transition moments lying parallel to the plane (fraction I). The relative dichroism, $\text{(E}{}_{\mathrm{\parallel }}\text{? E}{}_{\mathrm{\perp }}\text{)}\text{(E}{}_{\mathrm{\parallel }}\text{+ E}{}_{\mathrm{\perp }}\text{)}$, measured at the edge position amounts to 0.34 (i.e., 34% of the total absorption) at 680 nm. These data probably do not reflect the total quantity of oriented chlorophyll because from the opposite orientations of the Q_y transition moments of fraction I and II pigment a partial quenching of the measurable dichroism results. The red light absorption bands of the two chlorophylls oriented in an opposite manner (fractions I and II) correspond to the known bands of Photosystem I and II.     

Dicyanoimidazole complexes of Cu(I): a carbonyl assisted alcoholysis of nitrile

We describe a series of compounds which result from the reaction of Cu(I) with 4,5-dicyanoimidazole. This ligand is far more acidic than imidazole and in all cases forms complexes as the anion. The presence of carbon monoxide with Cu(I) assists in the rapid alcoholysis of one of the nitrile groups. The resulting imino-ester remains coordinated to the copper in the phosphine derivative as confirmed by X-ray crystallography. The composition CuC₄₂H₃₅N₄P₂ crystallizes in the space group Pbca with a= 14.140(4), b=21.466(7), c=24.577(8) Å and Z=8 molecules per cell. The copper is four coordinate and the bidentate imino-ester imidazole is nearly planar.     

Visual observation of G-quadruplex DNA with the label-free fluorescent probe silole with aggregation-induced emission

AIE molecule silole 1 could be used to detect G-quadruplex formation using an exonuclease I hydrolysis assay. This visual observation of G-quadruplexes has been successfully used in investigating multiple G-quadruplexes, including the one-stranded telomeric, c-myc, c-kit, VEGF G-quadruplexes, and a d(G₄T₄G₄) inter-molecular G-quadruplex. The detection of G-quadruplex can be also applied to G-quadruplex isomers induced by small molecules.     

The crystallochemistry of tetracyanocomplexes. The crystal and molecular structures of tris(1,2-diaminoethane)zinc(II) tetracyanoniccolate(II) monohydrate and tris(1,2-diaminoethane)zinc(II) tetracyanoniccolate(II)

C₁₀H₂₆N₁₀ONiZn, tris(1,2-diaminoethane) zinc(II) tetrakis(cyano)niccolate(II) monohydrate (I), orthorhombic, Pbca, a = 1.1680(4), b = 1.5844(3), c = 1.9981(6) nm, Z = 8 d(meas) = 1.54, d(calc) = 1.53 g cm^?3. C₁₀H₂₄N₁₀NiZn, tris(1,2-diaminoethane) zinc(II) terakis(cyano)niccolate(II), (II), monoclinic, P2₁/n, a = 0.7957(2), b = 1.5170(5), c = 1.4932(4) nm, β = 96.41(2)°, Z = 4, d(meas) = 1.49, d(calc) = 1.51 g cm^?3. Both the structures (I) and (II) have been solved by the heavy atom method and refined by full-matrix least-squares to R(I) = 0.086 for 1890 independent reflections and R(II) = 0.058 for 1689 independent reflections, respectively. In the case of (II) the superlattice structure problem was solved. The crystal structure of (I) consists of [Zn(en)₃]²⁺ cations, [Ni(CN)₄]^2? anions and water molecules. Two of the cyano groups in trans positions are bonded to water molecules by hydrogen bonds, the distances CN?O being 0.289 and 0.291 nm, respectively. The crystal structure of (II) is constituted by [Zn(en)₃]²⁺ cations and [Ni(CN)₄]^2? anions.     

Characterization and directed evolution of propionyl-CoA carboxylase and its application in succinate biosynthetic pathway with two CO2 fixation reactions

Propionyl-CoA carboxylase (PCC) is a promising enzyme in the fields of biological CO₂ utilization, synthesis of natrual products, and so on. The activity and substrate specificity of PCC are dependent on its key subunit carboxyltransferase (CT). To obtain PCC with high enzyme activity, seven pccB genes encoding CT subunit from diverse microorganisms were expressed in recombinant E. coli, and PccB from Bacillus subtilis showed the highest activity in vitro. To further optimize this protein using directed evolution, a genetic screening system based on oxaloacetate availability was designed to enrich the active variants of PccB_Bs. Four amino acid substitutions (D46G, L97Q, N220I and I391T) proved of great assistance in PccB_Bs activity improvement, and a double mutant of PccB_Bs (N220I/I391T) showed a 94-fold increase of overall catalytic efficiency indicated by k_cat/K_m. Moreover, this PccB_Bs double mutant was applied in construction of new succinate biosynthetic pathway. This new pathway produces succinate from acetyl-CoA with fixation of two CO₂ molecules, which was confirmed by isotope labeling experiment with NaH¹³CO₃. Compared with previous succinate production based on carboxylation of phosphoenolpyruvate or pyruvate, this new pathway showed some advantages including higher CO₂ fixation potentiality and availability under aerobic conditions. In summary, this study developed a PCC with high enzyme activity which can be widely used in biotechnology field, and also demonstrated the feasibility of new succinate biosynthetic pathway with two CO₂ fixation reactions.     

Intracellular events during infection by Haemophilus influenzae phage and transfection by its DNA

Intracellular events following infection of competent Haemophilus influenzae by HPlcl phage, or transfection by DNA from the phage, were examined. Physical separation of a large fraction of the intracellular phage DNA from the bulk of the host DNA was achieved by lysis of infected or transfected cells with digitonin, followed by low-speed centrifugation. The small amount of bacterial DNA remaining with the phage DNA in the supernatants could be distinguished from phage DNA by its ability to yield transformants. After infection by whole phage, three forms of intracellular phage DNA were observable by sedimentation velocity analysis: form III, the slowest-sedimenting one; form II, which sedimented 1.1 times faster than III, and form I, which sedimented 1.6 times faster than III. It was shown by electron microscopy, velocity sedimentation in alkali, and equilibrium sedimentation with ethidium bromide, that forms I, II and III are twisted circles, open circles, and linear duplexes, respectively.After the entry of phage DNA into wild-type cells in transfection, the DNA is degraded at early times, but later some of the fragments are reassembled, resulting in molecules that sediment faster than the monomer length of phage DNA. Some of the fast-sedimenting molecules are presumably concatemers and are generated by recombination. In strain rec₁^? the fast-sedimenting molecules do not appear and degradation of phage DNA is even more pronounced than in wild-type cells. In strain rec₂^? there is little degradation of phage DNA, and the proportion of fast-sedimenting molecules is much smaller than in wild-type cells. Since rec₁^? and rec₂^? are transfected with much lower efficiency than wild type, our hypothesis is that both fragmentation and generation of fast-sedimenting phage DNA by recombination are required for more efficient transfection.     

On the mutual orientation of pigments in Photosystem I particles from green plants

The mutual orientation of pigments in Photosystem I reaction centers from spinach is evaluated by polarized photochemistry. The photoinduced linear dichroism of the absorption changes of chlorophyll a₁ at 701 nm is studied as function of the excitation wavelength. The Photosystem I reaction center particles contain about 100 and if depleted about 40 chlorophylls, respectively. To prevent their rapid Brownian rotation they were immobilized on DEAE-Sephadex.The excitation spectrum of the linear dichroism reveals a high degree of order between the long axis of β-carotene and the Q_y transition moments of those chlorophyll a molecules absorbing at the red end of the spectrum. The latter are the most endangered ones for destructive oxidation via their triplet state. Hence, the location of β-carotene in close proximity to and in parallel with these chlorophylls seems to be most favourable for the protective role of β-carotene within the antennae system I. It is observed that the dichroic ratio of the absorption changes of chlorophyll a₁ does not exceed a figure of $\text{4}\text{3}$, which characterizes a circularly degenerate system, even at far red excitation (724 nm). This will hit selectively those few chlorophyll a molecules with their peak absorption at about 700 nm (including the photooxidizable dimer). We conclude, if the dimer is the only species peaking at 700 nm then the two chlorophyll a within the dimer have their y-axes oriented perpendicular to each other. If there are some antennae in addition to the dimer, the y-axes of all chlorophyll-a peaking at 700 nm form a star which accounts for the circular degeneracy of absorption.     

Chlorophyll composition of Photosystems IIα, IIβ and I in tobacco chloroplasts

The antenna composition of the Photosystems II_α, II_β and I was studied in tobacco chloroplasts. Absorbance spectra, recorded at 4 K, were analyzed for the wild type and the mutants Su/su and Su/su var. Aurea, containing higher concentrations of the photosystems. With chloroplasts of Su/su we measured the action spectra of the three photosystems from 625 to 690 nm. Above 675 nm absorption by Photosystem I dominated. This sytem had a maximum at 678 nm and a shoulder at 660 nm. Of the long-wavelength chlorophyll a forms, absorbing at 690, 697 and 705 nm at 4 K, which are generally assigned to Photosystem I, the 697 nm form occurred in an amount of four molecules per reaction center of Photosystem I in each type of chloroplast. The Photosystem II_α spectrum was characterized by maxima at 650 and 672 nm, showing clearly the participation of the chlorophyll a and b containing light-harvesting complex. In the mutants the light-harvesting complex has a chlorophyll a to chlorophyll b ratio of more than 1; the amount of the 672 nm chlorophyll a was normal, whereas the amount of chlorophyll b was markedly decreased in the mutants relative to the wild type. The Photosystem II_β spectrum mainly consisted of a band at 683 nm.     

Pt(II) compounds with sulfoxide ligands and crystal structures of complexes of the types I(R2SO)Pt(μ-I)2Pt(R2SO)I and trans-Pt(R2SO)(L)X2 (L = amine,pyridine and pyrimidine)

The crystal structures of several Pt(II) complexes containing sulfoxide ligands are described. The two iodo bridged dimers of the type I(R₂SO)Pt(μ-I)₂Pt(R₂SO)I (where R is ethyl or n-butyl) are twinned structures. The dinuclear species are the trans isomers. Two compounds of the type trans-Pt(DMSO)(amine)X₂ were studied by X-ray diffraction methods. The diiodo MeNH₂ compound forms H-bonded chains, formed by maximizing the H-bonds between the amine group with the O atom of DMSO and one iodo ligand. The H-bonding pattern is quite different in the dichloro t-BuNH₂ complex. In the latter crystal, there are two independent molecules which are H-bonded in pairs. The methyl groups of DMSO and the t-butyl group of the amine are oriented towards the outside of the pairs of molecules, while the H-bonds link the two independent molecules. Again, the amino group forms the maximum H-bonds with the O atom of DMSO and one chloro ligand. The crystal structures of trans-Pt(DMSO)(pyridine)I₂ and of trans-Pt(MeBzSO)(pyrimidine)I₂ (Bz = benzyl) were also studied. In the pyridine complex, the O atom of DMSO is in the Pt(II) plane by symmetry, while in the pyrimidine compound, the C atom of the –CH₃ group is in the Pt(II) plane. The pyridine and the pyrimidine ligands are perpendicular to the Pt(II) square plane. The trans influence of the different ligands is discussed.     

Demonstration of human platelet β-adrenergic receptors using 125I-labeled cyanopindolol and 125I-labeled hydroxybenzylpindolol

The radioiodinated pindolol analogs ¹²⁵I-labeled cyanopindolol ([¹²⁵I]CYP) and ¹²⁵I-labeled hydroxybenzylpindolol ([¹²⁵I]HBP) have been used to study binding to human platelet β-adrenergic receptors. [¹²⁵I]CYP binds to a saturable class of binding sites on platelet membranes with a dissociation constant (K_d) of 14±3 pM and maximal binding capacity (B_max) of 18±4 fmol/mg protein. Binding of [¹²⁵I]CYP is reversible and is characterized by forward and reverse rate constants of 1.8·10⁷ s^?1·M^?1 and 3.8·10^?4 s^?1, respectively. [¹²⁵I]HBP binds to a saturable class of platelet membrane sites with a K_d of 50±10 pM and B_max of 32±6 fmol/mg protein. [¹²⁵I]HBP also binds to a saturable class of sites on intact platelets with a K_d of 58±14 pM and B_max of 24±4 molecules per platelet. Binding of [¹²⁵I]CYP and [¹²⁵I]HBP is stereospecifically inhibited by propranolol and epinephrine; the (?) stereoisomers are at least 50-times more potent than the (+) stereoisomers. Binding of both radioligands is inhibited by adrenergic ligands with a potency order of propranolol ? isoproterenol > epinephrine > practolol > norepinephrine > phenylephrine. These observations indicate that [¹²⁵I]CYP and [¹²⁵I]HBP bind to platelet sites which have the pharmacological characteristics of β-adrenergic receptors but which are not typical of either the β₁ or β₂ sub-type.     

Computer simulation of plastocyanin interaction with cytochrome f and photosystem I in cyanobacterium Phormidium laminosum

The paper is devoted to computer simulation of complex formation of protein plastocyanin with transmembrane pigment-protein complex photosystem I and subunit f of cytochrome b ₆ f complex in the cyanobacterium Phormidium laminosum. The computer algorithm considers diffusion and electrostatic interactions of protein molecules. The computer models have shown that electrostatic interactions in the cyanobacterium play a less important role than in higher plants because of different electrostatic potentials created by charged amino acid residues on the protein surfaces.     

Mechanism of primary and secondary ion-radical pair formation in photosystem I complexes

The mechanisms of the ultrafast charge separation in reaction centers of photosystem I (PS I) complexes are discussed. A kinetic model of the primary reactions in PS I complexes is presented. The model takes into account previously calculated values of redox potentials of cofactors, reorganization energies of the primary P700⁺A ₀ ^- and secondary P700⁺A ₁ ^- ion-radical pairs formation, and the possibility of electron transfer via both symmetric branches A and B of redox-cofactors. The model assumes that the primary electron acceptor A₀ in PS I is represented by a dimer of chlorophyll molecules Chl2A/Chl3A and Chl2B/Chl3B in branches A and B of the cofactors. The characteristic times of formation of P700⁺A ₀ ^- and P700⁺A ₁ ^- calculated on the basis of the model are close to the experimental values obtained by pump-probe femtosecond absorption spectroscopy. It is demonstrated that a small difference in the values of redox potentials between the primary electron acceptors A_0A and A_0B in branches A and B leads to asymmetry of the electron transfer in a ratio of 70: 30 in favor of branch A. The secondary charge separation is thermodynamically irreversible in the submicrosecond range and is accompanied by additional increase in asymmetry between the branches of cofactors of PS I.     

Synthesis and characterization of the 1:1 adducts of copper(I) halides with bidentate N,N′-bis(benzophenone)-1,2-diiminoethane Schiff base: Crystal structures of [Cu(bz2en)2][CuX2] (X = Br, I) complexes

1:1 adducts of N,N′-bis(benzophenone)-1,2-diiminoethane (bz₂en) with copper(I) chloride, bromide and iodide, [Cu(bz₂en)₂][CuX₂] (X = Cl, Br, and I), have been synthesized and the structures of the solid bromide and iodide adducts were determined by X-ray crystallography from single-crystal data. The solid-state structure reveals ionic complexes containing a cation of copper(I) ion coordinated to four nitrogen atoms of two bz₂en molecules (distorted tetrahedron) and a linear dibromocuprate(I) and a di-μ-iodo-diiododicuprate(I) anion for the bromo and iodo adducts, respectively. The bromo adduct structure contains CH?Br intermolecular hydrogen bonds. The complexes are very stable towards atmospheric oxygen in the solid state. The spectral properties of the above complexes are also discussed.     

Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein which bridges DNA

Genetic evidence suggests that the Bacillus subtilis lrpC gene product participates in cell growth and sporulation. The purified LrpC protein, which has a predicted molecular mass of 16.4 kDa, is a tetramer in solution. LrpC binds with higher affinity (K_app ~ 80 nM) to intrinsically curved DNA than to non-curved DNA (K_app ~ 700 nM). DNase I footprinting and the supercoiling of relaxed circular plasmid DNA in the presence of topoisomerase I revealed that LrpC induces DNA bending and constrains DNA supercoils in vitro. The LrpC protein cooperatively increases DNA binding of the bona fide DNA-binding and DNA-bending protein Hbsu. LrpC forms inter- and intramolecular bridges on linear and supercoiled DNA molecules, resulting in a large network and DNA compactation. Collectively, these findings suggest that LrpC is an architectural protein and that its activities could provide a means to modulate DNA transactions.     

Identification of extracellular haemoglobin as the major high molecular weight cadmium-binding protein of the polychaete annelid Nereis diversicolor

1. A high molecular weight cadmium-binding protein called MP I was isolated from Nereis diversicolor exposed to 20 ppm of cadmium (CdCl₂) for 4 days via sea water.2. The protein had a molecular weight comprising between 20 × 10⁶ and 1.5 × 10⁶ Da. It shows high absorptions at 280 and 415 nm and contained iron in addition to cadmium.3. Two dimensional SDS-PAGE of unreduced and reduced MP I revealed a dissociation pattern similar to that of extracellular haemoglobins of polychaetes and oligochaetes.4. Furthermore, negatively stained MP I molecules examined by conventional transmission electron microscopy showed the common appearance of extracellular haemoglobins of annelids.5. Evidence of the extracellular haemoglobin nature for the MP I was found by the identical Chromatographie behaviour of MP I with the main Nereis blood component and, by the labelling of blood vessel content with ¹⁰⁹Cd visualized by autoradiography on paraffin-embedded sections of exposed Nereis.     

Structure of a classical MHC class I molecule that binds "non-classical" ligands

Chicken YF1 genes share a close sequence relationship with classical MHC class I loci but map outside of the core MHC region. To obtain insights into their function, we determined the structure of the YF1*7.1/β₂-microgloblin complex by X-ray crystallography at 1.3 Å resolution. It exhibits the architecture typical of classical MHC class I molecules but possesses a hydrophobic binding groove that contains a non-peptidic ligand. This finding prompted us to reconstitute YF1*7.1 also with various self-lipids. Seven additional YF1*7.1 structures were solved, but only polyethyleneglycol molecules could be modeled into the electron density within the binding groove. However, an assessment of YF1*7.1 by native isoelectric focusing indicated that the molecules were also able to bind nonself-lipids. The ability of YF1*7.1 to interact with hydrophobic ligands is unprecedented among classical MHC class I proteins and might aid the chicken immune system to recognize a diverse ligand repertoire with a minimal number of MHC class I molecules.     

Origin of the sarcosine molecules of actinomycins

1. Streptomyces V–187 produces on minimal medium a mixture composed mainly of actinomycin C₁ (actinomycin D) and actinomycin A₁ (actinomycin I). If sarcosine is added to the medium, the micro-organism produces, in addition to actinomycins C₁ and A₁, actinomycin F₈ (actinomycin II) and actinomycin F₉ (actinomycin (III), characterized by the substitution by sarcosine of one or both the proline molecules present in actinomycin C₁. 2. Exogenous sarcosine seems to be incorporated as such by Streptomyces V–187 only in the sarcosine molecule(s) that replace proline in the actinomycins of the F group, whereas, for the synthesis of the other sarcosine molecules, the amino acid is first demethylated to glycine. 3. The incorporation of sarcosine and glycine into actinomycin by Streptomyces antibioticus appears to follow a similar pattern, except that a portion of the methyl group produced in the degradation of sarcosine is utilized as a source of the methyl groups of the antibiotic. This explains the previously reported lack of cross-dilution between glycine and sarcosine observed in the incorporation of these amino acids into actinomycin.     

Binding and Incision Activities of UvrABC Excinuclease on Slipped DNA Intermediates that Generate Frameshift Mutations

Previousin vivostudies involving sequence 5′-CCCG₁G₂G₃-3′ (SmaI site) have demonstrated that adducts ofN-2-acetylaminofluorene (AAF) to any of the three guanine residues of theSmaI sequence induce, with different efficiencies, two classes of −1 frameshift events, namely −G and −C mutations, referred to as targeted and semitargeted mutations, respectively. It has been proposed that both events occur during replication as a consequence of slippage events involving slipped mutagenic intermediates (SMIs). In order to evaluate the potential role of the UvrABC excinuclease in frameshift mutagenesis, we have studied the interaction of this enzyme with DNA molecules mimicking SMIsin vitro.In all of our constructions, when present, the AAF adduct was located on the third guanine residue of theSmaI site (5′-CCCG₁G₂G₃-3′). This strand was referred to as the top strand, the complementary strand being the bottom strand. Double-stranded heteroduplexes mimicking the targeted and semitargeted SMIs contained a deletion of a C and a G within theSmaI sequence in the bottom strand and were designated ΔC/3 and ΔG/3 when modified with the AAF on the third guanine residue in the top strand or ΔC/O and ΔG/O when unmodified. The modified homoduplex was designatedSmaI/3.ΔC/O and ΔG/O were weakly recognized by UvrA₂B, but not incised. All three AAF-modified substrates were recognized with similar efficiency and much more efficiently than unmodified heteroduplexes. With AAF-monomodified substrates, dissociation of UvrA₂from the UvrA₂B- DNA complex occurred more readily in heteroduplexes than in the homoduplex.SmaI/3 and ΔC/3 were incised with equal efficiency, while ΔG/3 was less incised. The position of the AAF lesion dictated the position of the incised phosphodiester bonds, suggesting that the presence of a bulge can modulate the yield but not the incision pattern of AAF-modified substrates. The finding that UvrABC excinuclease acts on substrates that mimic SMIs suggests that the nucleotide excision repair pathway may help in fixing frameshift mutations before the following round of replication.