Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

Background

Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase.

Results

We have cloned and purified SSB from Bacillus anthracis (SSB_BA). In the absence of DNA, at concentrations ??100 ??g/ml, SSB_BA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB_BA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)₇₀ binding suggested that SSB_BA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure.

Conclusions

Unlike other prokaryotic SSB proteins, SSB_BA from Bacillus anthracis appeared to be monomeric at concentrations ??100 ??g/ml as determined by SE-HPLC. SSB_BA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB_BA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB_BA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.     

Programmable conformational regulation of porphyrin dimers on geometric scaffold of duplex DNA

DNA-porphyrin conjugates were designed and synthesized in which free-base and Zn-coordinated porphyrins were introduced to the N⁶-position of the internal adenosine. Conformations of the porphyrin dimer in the major groove of duplex DNA were controlled by changing the orientation and the distance between the two porphyrin moieties. The porphyrin dimers formed a thermally favorable face-to-face conformation on the duplex DNA. In the disadvantageous geometry for porphyrin dimer formation on the duplex, the porphyrins induced the DNA duplex structures to the Z-form conformation. These results indicate that the interaction of the two porphyrins and the conformation of duplex DNA are controlled by the program of DNA sequences.     

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (K_b = 2–7 × 10⁵ M⁻¹) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φ_fl < 0.01) that increases significantly upon binding to G4-DNA (Φ_fl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φ_fl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.     

Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA

One of the important determinants in the efficiency of a molecular interaction is the necessity for conformational changes in host and/or guest molecules upon binding. In small‐molecule interactions with nucleic acids, conformational changes on both molecules are often involved, especially in intercalating binding. Mismatch binding ligands (MBLs) we described here consist of two heterocycles that predominantly exist in one conformation, so it is of interest to determine if such molecules can bind to any DNA and RNA structures. One molecule, 1 ‐NHR, which predominantly exists as the unstacked conformation in aqueous solvent, has been successfully synthesized and characterized. Compound 1 ‐NHR did not efficiently bind to GX/Y DNA and RNA sequences, but the binding pattern is different from that of authentic MBL naphthyridine carbamate dimer. In vitro selection of RNA that specifically binds to 1 ‐NHR was performed from pre‐miR‐29a loop library RNA, and one RNA, to which 1 ‐NHR bound with high affinity, has been successfully identified. Although it was anticipated that 1 ‐NHR, with a predominantly unstacked conformation, would show entropy‐driven binding, isothermal titration calorimetry analysis suggested that the binding of 1 ‐NHR to RNA was enthalpy driven with an apparent K _d of about 100 nm .     

Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms

Thymine DNA Glycosylase (TDG) is an enzyme of the base excision repair mechanism and removes damaged or mispaired bases from DNA via hydrolysis of the glycosidic bond. Specificity is of high importance for such a glycosylase, so as to avoid the damage of intact DNA. Among the substrates reported for TDG are mispaired uracil and thymine but also formyl-cytosine and carboxyl-cytosine. Methyl-cytosine and hydroxylmethyl-cytosine are, in contrast, not processed by the TDG enzyme. We have in this work employed molecular dynamics simulations to explore the conformational dynamics of DNA carrying a formyl-cytosine or carboxyl-cytosine and compared those to DNA with the non-cognate bases methyl-cytosine and hydroxylmethyl-cytosine, as amino and imino tautomers. Whereas for the mispairs a wobble conformation is likely decisive for recognition, all amino tautomers of formyl-cytosine and carboxyl-cytosine exhibit the same Watson–Crick conformation, but all imino tautomers indeed form wobble pairs. The conformational dynamics of the amino tautomers in free DNA do not exhibit differences that could be exploited for recognition, and also complexation to the TDG enzyme does not induce any alteration that would indicate preferable binding to one or the other oxidised methyl-cytosine. The imino tautomers, in contrast, undergo a shift in the equilibrium between a closed and a more open, partially flipped state, towards the more open form upon complexation to the TDG enzyme. This stabilisation of the more open conformation is most pronounced for the non-cognate bases methyl-cytosine and hydroxyl-cytosine and is thus not a likely mode for recognition. Moreover, calculated binding affinities for the different forms indicate the imino forms to be less likely in the complexed DNA. These findings, together with the low probability of imino tautomers in free DNA and the indifference of the complexed amino tautomers, suggest that discrimination of the oxidised methyl-cytosines does not take place in the initial complex formation.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Photocontrolled release and uptake of a porphyrin guest by dithienylethene-tethered beta-cyclodextrin host dimers

Two photoswitchable dithienylethene-tethered beta-cyclodextrin dimers were synthesized to function as host molecules with an externally controllable binding affinity. The cyclodextrin cavities of these dimers are linked through their secondary sides by a photochromic dithienylethene unit that is connected to the secondary rim either directly (4) or through propyl spacers (9). Irradiation with light switches these dimers between a relatively flexible (open) and a rigid (closed) form. The binding properties of the dimers depend on the configuration of the dithienylethene spacer, as is shown by microcalorimetry performed with tetrakis-sulfonatophenyl porphyrin (TSPP) as a guest molecule. The differences in binding properties are most pronounced for the more rigid dimer 4, which binds TSPP 35 times more strongly in the open form (4 a) than in the closed form (4 b). The values found for the enthalpy of binding (deltaH degrees ) indicate that this difference in binding is due to the loss of cooperativity between the two beta-cyclodextrin cavities in the closed form. Molecular modeling shows that 4 b is not able to bind TSPP effectively in both cyclodextrin cavities. The open and closed forms of the more flexible dimer 9 show no substantial difference in their binding of TSPP. Thermodynamic values indicative of strong binding of TSPP by two beta-cyclodextrin cavities were measured for both forms of the dimer, and molecular modeling confirms that both are flexible enough to tightly bind TSPP. The binding differences between the forms of dimer 4 allow the photocontrolled release and uptake of TSPP, which renders control of the ratio of complexed to free TSPP in solution possible.     

Multi-State Second-Order Nonlinear Optical Switches Incorporating One to Three Benzazolo-Oxazolidine Units: A Quantum Chemistry Investigation

This contribution employs quantum chemistry methods to describe the variations of the second nonlinear optical responses of molecular switches based on benzazolo-oxazolidine (BOX) units, connected by π-linkers, along their successive opening/closing. Under the fully closed forms, all of them display negligible first hyperpolarizability (β) values. When one BOX is opened, which is sketched as C→O, a push–pull π-conjugated segment is formed, having the potential to enhance β and to set the depolarization ratio (DR) to its one-dimensional-like value (DR = 5). This is observed when only one BOX is open, either for the monoBOX species (C→O) or for the diBOX (CC→CO) and triBOX (CCC→CCO) compounds, i.e., when the remaining BOXs stay closed. The next BOX openings have much different effects. For the diBOXs, the second opening (CO→OO) is associated with a decrease of β, and this decrease is tuned by controlling the conformation of the π-linker, i.e., the centrosymmetry of the whole compound because β vanishes in centrosymmetric compounds. For the triBOXs, the second opening gives rise to a Λ-shape compound, with a negligible change of β, but a decrease of the DR whereas, along the third opening, β remains similar and the DR decreases to the typical value of octupolar systems (DR = 1.5).     

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA–ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

We present the rational design of photoswitchable DNA glue to trigger the reversible formation of duplex DNA by light. The supramolecular assembly shows a mutual interaction between ligand and DNA, which induces a preferred helicity in the switch.     

Synthesis and structural and electronic properties of the diacetylene- and ethylene-groups connected octaethylporphyrin(Ni) tetramer

The tetramer of octaethylporphyrin nickel complex [OEP(Ni)], connected with diacetylene and ethylene linkages, was synthesized. Its structural and electronic properties were studied, proving that two constituents of the diacetylene-group connected OEP(Ni) dimer face to each other in s-cis conformation about the ethylene linkage but not so closely as to induce a transannular π-electronic interaction between them.     

Bis(phenylthienyl)ethene-tethered beta-cyclodextrin dimers as photoswitchable hosts

Two beta-cyclodextrin dimers tethered by photoswitchable bis(phenylthienyl)ethene moieties were synthesized as potentially tunable receptor molecules. The cyclodextrin cavities of these dimers were linked via their secondary sides, with the photochromic bis(phenylthienyl)ethene unit either directly connected to the secondary rim (7) or via propyl spacers (10). By irradiation with light the dimers were reversibly switched between a relatively flexible (open) form and a rigid (closed) form. The photostationary states for both dimers consisted of 92% of the open and 8% of the closed form, enabling the nearly complete conversion between the two forms. The binding properties of the open and closed forms of dimers 7 and 10 were assessed by complexation studies with meso-tetrakis(4-sulfonatophenyl)porphyrin (TSPP) using isothermal titration calorimetry. For the rigidly tethered dimer 7, a factor 8 difference in binding affinity between the open and closed form of the dimer was found. This difference in binding affinity reflects the difference in enthalpy of binding for the two dimers, indicating that the beta-cyclodextrin cavities of the closed dimer 7b are spaced too far apart from each other by the rigid closed bis(phenylthienyl)ethene tether to cooperatively bind TSPP. The difference in binding affinity was sufficient to enable the phototriggered release of TSPP from dimer. The thermodynamic parameters obtained for dimer 10 suggested that the closed tether substantially contributes to the binding of TSPP. The open and closed form of dimer 10 bound TSPP with similar association constants, although the enthalpy of binding for the complexation of TSPP by the closed form of dimer 10 was more favorable than that found for the open form of the dimer.     

Synthesis of hybrid calix[6]arenes having both methylene and epithio bridging groups

Mono-, tri-, and tetra-thiacalix[6]arene were obtained by acid-catalyzed condensation of the corresponding tetramer and dimer derivatives of p-tert-butylphenol bridged by methylene or sulfur. Replacement of CH₂ by sulfur has significant effect on the properties of calix[6]arene such as the strength of intramolecular hydrogen bonding, inclusion ability toward organic molecules, and conformation properties.     

Photochromic Properties of β-Cyclodextrin Dimer Linked by Dithienylethene

A fi-cyclodextrin dimer tethered by photoswitchable dithienylethene moieties was synthesized as a potentially tunable receptor. The dimer exhibits pronounced photochromic properties. Irradiation of the dimer in open form with UV light at 254 nm resulted in immediate photocyclization to the pink closed form; the colorless open form could be regenerated by irradiation with visible light of wavelength >460 nm. The reaction kinetics of the forward photoprocess were also studied. To investigate the binding ability of the dimer in open and closed forms, a fluorescence titration was performed. It was found that the stability constant for the binding of TSPP (meso-tetrakis (4-sulfonatophenyl)porphyrin) by the closed form of the dimer is a factor of 5 higher than that of the open form.     

NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone‐like DNA binding protein of Helicobacter pylori

Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone‐like DNA binding protein (Hup), which in its homo‐dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti‐H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup‐dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti‐H. pylori agents employing structure‐based‐rational drug discovery approach.     

Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH

In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.     

Chemically induced hairpin formation in DNA monolayers

A naphthyridine dimer that binds specifically to G-G mismatches has been used to induce hairpin formation in oligonucleotides immobilized onto chemically modified gold surfaces. Surface plasmon resonance (SPR) imaging measurements of DNA microarrays were used to demonstrate that binding of the naphthyridine dimer to G-G mismatches within the stem portion of an immobilized 42-mer oligonucleotide could be used to induce hairpin formation that prevented hybridization of DNA complementary to the loop sequence. In addition, the selectivity of the naphthyridine dimer for G-G mismatches was verified through SPR imaging measurements of the hybridization adsorption of an 11-mer oligonucleotide to a four-component DNA array of zero- and single-base mismatch sequences.     

Arene Ru(II) Complexes Acted as Potential KRAS G-Quadruplex DNA Stabilizer Induced DNA Damage Mediated Apoptosis to Inhibit Breast Cancer Progress

A series of arene Ru(II) complexes, [(η⁶-MeC₆H₅)Ru(L)Cl]Cl, (L=o-ClPIP, 1; m-ClPIP, 2 and p-ClPIP, 3) (o-ClPIP=2-(2-chlorophenyl)imidazo[4,5-f][1,10]phenanthroline; m-ClPIP=2-(3-chlorophenyl)imidazo[4,5-f][1,10]phenanthroline; p-ClPIP=2-(4-chlorophenyl)imidazo[4,5-f][1,10]phenanthroline) was synthesized and investigated as a potential apoptosis inducer in chemotherapy. Spectroscopy and molecular docking simulations show that 1 exhibits moderated binding affinity to KRAS G-quadruplex DNA by groove mode. Further, in vitro studies reveal that 1 displays inhibitory activity against MCF-7 growth with IC₅₀ = 3.7 ± 0.2 μM. Flow cytometric analysis, comet assay, and immunofluorescence confirm that 1 can induce the apoptosis of MCF-7 cells and G0/G1 phase arrest through DNA damage. In summary, the prepared arene Ru(II) complexes can be developed as a promising candidate for targeting G-quadruplex structure to induce the apoptosis of breast cancer cells via binding and stabilizing KRAS G-quadruplex conformation on oncogene promoter.