Specificity of the interaction between lambda cro repressor protein and operator DNA fragments

Cro repressor protein is known to interact with specific sites in the operator DNA. The cro protein of lambda phage was isolated and the mode of its interaction with three different DNA fragment, lambda-OR3 17mer, phi 80-OR2 19mer and CAP binding site 22-mer, were examined by the use of proton NMR. Some of the imino proton resonances of lambda-OR3 shifted and were broadened remarkably on addition of lambda-cro protein, which indicated the induction of conformational change with complexation. In the spectrum of phi 80-OR2 which has a six base pair sequence common to lambda-OR3 the signals of the common base pairs revealed slight shifts on addition of lambda-cro protein. The imino proton signals of the CAP site DNA, however, did not show any change at all on mixing with lambda-cro. Combining the data of photo CIDNP of lambda-cro, we could postulate the mode of interaction between lambda-cro repressor and operator DNA.     

Specificity and kinetics defining the interaction between a murine monoclonal autoantibody and DNA

Interactions between a murine monoclonal anti-DNA autoantibody (BV17-45) and DNA were examined by direct binding and competitive radioimmunoassays. Binding isotherms constructed by titration of purified BV17-45 with a series of distinct 32P-labeled double-stranded DNA ([32P]dsDNA) fragments were super-impossible, suggesting: 1) BV17-45/[32P]dsDNA binding is independent of dsDNA size using fragments greater than or equal to 192 base pairs in length, and 2) BV17-45 does not exhibit stringent sequence specificity. Single-stranded DNA-specific monoclonal antibody BV04-01 did not react with [32P]dsDNA, confirming its duplex character. In competition experiments, BV17-45 cross-reacted with phage (phi X174, M13) RF AND VIRION DNAS AT PICOMOLAR concentrations. Selectivity for B-form DNA was suggested by the ability of poly(dA) . poly(dT), but not other helical duplex forms, to block BV17-45/[32P] dsDNA binding. Among the four deoxyribohomopolymers, only deoxyadenylic acid polymers completely inhibited BV17-45/[32P]dsDNA complex formation. [32P]dsDNA binding was relatively insensitive to ionic strength, suggesting minimal contribution of electrostatic forces to the binding free energy. Measured BV17-45/[32P]dsDNA association and dissociation rate constants (4 degrees C) were 7.4 X 10(6) M-1 s-1 and 9.2 X 10(-5) s-1, respectively, yielding a functional affinity of 8 X 10(10) M-1. Results are discussed in terms of the relative contribution of B-DNA structural and substructural determinants to the mechanism of BV17-45 recognition.     

Specificity of an ant-lycaenid interaction

Summary Many lycaenid butterflies are believed to be mutualists of ants — the butterfly larvae secrete sugars and amino acids as rewards for the ants, and the ants protect the larvae from predation or parasitism. We examined the specificity of the relationship between the lycaenid Plebejus argus and ants in the genus Lasius. Eggs were not attractive to Lasius ants until the emerging larvae had broken through the chorion. First instar larvae were palpated and picked up by Lasius workers and taken to the nest. First instars were mostly ignored by Myrmica sabuleti ants and they were rarely detected by Formica fusca. Older larvae were more attractive to Lasius than to the other ant genera. Pupae were very attractive to Lasius, moderately so to Myrmica, and were ignored by Formica fusca. Teneral adults were palpated by Lasius, but were attacked by Myrmica and Formica workers. We conclude that P. argus is a specialist associate of Lasius ants. Two populations of Plebejus argus were compared: one is naturally associated with Lasius niger, and the other with Lasius alienus. In reciprocal trials, larvae were slightly more attractive to their natural host ant species. Since test larvae were reared on a single host plant species in captivity, this differentiation probably has a genetic basis.     

Specificity of interaction of hexokinase isozyme II with mitochondrial membranes

Study on the mechanism of hexokinase isozyme II adsorption on mitochondrial membranes in the presence of 10 mM MgCl2 demonstrated that 0.16% of the total proteins of the soluble fraction and the total hexokinase pool are capable of reversible binding to the membrane. The plot for the dependence of the degree of enzyme adsorption on Mg2+ concentration is hyperbolic. Under these conditions, hexokinase competes favourably for the binding sites with lactate dehydrogenase and creatine kinase. Analysis of the adsorption capacity of natural and artificial phospholipid membranes showed that hexokinase isozyme II is adsorbed in much the same way on inner and outer mitochondrial membranes as well as on a mixture of membranes obtained from various sources and on lecithin liposomes. The adsorption properties of hexokinase isozyme II and of its functional analog--isozyme I--point to marked differences in the mechanism of their interaction with the membrane. In contrast with isozyme I, isozyme II of hexokinase undergoes kinetic alterations. Besides, it was found that mild autolysis of isozyme II is accompanied by a loss of the enzyme ability to bind to mitochondrial membranes. The data obtained suggest that the specificity of hexokinase isozyme II adsorption depends on the structural peculiarities of the protein but not on those of the mitochondrial membrane.     

Specificity in DNA interactions: an nmr investigation of the interaction of propidium with oligodeoxyribonucleotides containing normal and G-T base pairs

The interaction of propidium with three self-complementary oligodeoxyribonucleotides has been investigated by ¹H- (base-pair imino proton assigned by 1D NOE and saturation transfer methods) and ³¹P-nmr as a function of ratio of propidium to oligomer (from zero to saturation) and temperature. The three oligomers are dTATATGCGCATATA (1), dTATATGTGCATATA (2), which has the same sequence as 1 except for the mismatched base pair at position 7, and dTATGTGCATA (3), which is a shortened version of 2. The imino proton chemical-shift changes of 1 on titration with propidium can be explained by the effects of the ring-current anisotropy of propidium at intercalation (3.4 Å) and next-neighbor sites (6.8 Å). The results indicate that propidium binds with neighbor exclusion but with no significant specificity for any intercalation site in the sequence of 1. The addition of propidium to 1 results in general downfield shifts of all ³¹P signals, as expected for a nonspecific intercalator. Imino and ³¹P-nmr spectra for 2 indicate that this oligomer forms a hydrogen-bonded G · T base pair at position 7 with little change in base pairing and stacking of base pairs 1–6 compared to 1. The results for addition of propidium to 2 and 3 are quite different than with 1. At low ratio only secondary shifts (6.8 Å) are seen for the G and T imino protons of base-pair 7 on addition of propidium. At higher ratios of propidium, the signals for these G and T protons are lost in 2 and severely broadened in 3, even at low temperature. The other potential intercalation sites in 2 and 3 appear to bind propidium strongly and without significant specificity as with 1. ³¹P spectra of 2 in the presence of propidium show the expected downfield shifts and broadening. Thus, the minor differences in local helix geometry in 1, and in 2 and 3, away from the G · T base pair do not significantly affect propidium intercalation specificity. Having one or two G · T base pairs at a site, however, makes intercalation in the standard manner significantly less favorable.     

Specificity of the interaction between ubiquitin-associated domains and ubiquitin

Ubiquitin-associated (UBA) domains are found in a large number of proteins with diverse functions involved in ubiquitination, DNA repair, and signaling pathways. Recent studies have shown that several UBA domain proteins interact with ubiquitin (Ub), specifically p62, the phosphotyrosine-independent ligand of the SH2 domain of p56(lck); HHR23A, a human nucleotide excision repair protein; and DDI1, another damage-inducible protein. NMR chemical shift mapping reveals that Ub binds specifically but weakly to a conserved hydrophobic epitope on HHR23A UBA(1) and UBA(2) and that the UBA domains bind on the hydrophobic patch on the surface of the five-stranded beta-sheet of Ub. Models of the UBA(1)-Ub and UBA(2)-Ub complexes obtained from de novo docking reveal different orientations of the UBA domains on the Ub surface compared with those obtained by homology modeling with the related CUE domains, which also bind Ub. Our results suggest that UBA domains may interact with Ub as well as other proteins in more than one way while utilizing the same binding surface.     

Specificity and mutual dependency of the orchid-euglossine bee interaction

Seasonal and geographic relationships, and host pollinator specificities are examined for indications of interdependency in the orchid-euglossine bee interaction. The orchids are dependent on the bees for pollination, and their flowering seasonality corresponds well with peak activity of their pollinators. However, there is little evidence that the bees are dependent on these fragrance hosts. The orchids tap the majority of euglossine species and individuals for pollinator services during any given season, but most of those bee species that temporarily lack orchid fragrance hosts persist in the area, continually emerge from nests, and seek floral fragrance compounds. Pollinator specificity occurs in less than half of the orchids, and host specificity is rare. Geographic distributions of nearly all orchid-pollinator pairs are not mutually inclusive. Moreover, nearly a third of the local male euglossine bee species censused are not pollinators of any fragrance orchids in the area. Local alternative fragrance sources occur. The orchid-male euglossine bee interaction does not appear to represent a mutually obligatory relationship. The orchids may have exploited a preexisting behavioural phenomenon of the bees, and reciprocal evolutionary responses may not have occurred.     

Specificity in the interaction of non intercalative groove binding ligands with nucleic acids

This paper presents results of theoretical computations on the interaction energies and geometries for the binding to nucleic acids of a number of representative groove binding non intercalating drugs: netropsin, distamycin A, SN 18071, etc. The computations account for the specificity of binding in all cases and demonstrate that the formation of hydrogen bonds is not necessary neither for binding nor for the preference for the minor groove of AT sequences of B-DNA. It appears that if a relatively good steric fit can be obtained in the minor groove, the interaction will be preferentially stabilized there by the favorable electrostatic potential generated in this groove by the AT sequences. The computation of the interaction energies in free space does not reproduce, however, the order of affinities of the ligands studied and yields too great values of the binding energies. The introduction of the solvent effect, through the computation of the hydration and cavitation effects, confirms the specificity, improves the ordering and brings the values of the energies close to the experimental ones. The theoretical account of the “surprising” effect of netrospin binding to the major groove of theTψC stem of tRNA^Phe confirms the decisive significance of the distribution of the molecular electrostatic potential for the selection of the binding site. The inclusion in the computations of the flexibility of DNA enables to predict correctly the main features of the macromolecular deformation upon the binding of the ligand.     

Specificity of DNA lesion bypass by the yeast DNA polymerase eta

DNA polymerase eta (Pol(eta), xeroderma pigmentosum variant, or Rad30) plays an important role in an error-free response to unrepaired UV damage during replication. It faithfully synthesizes DNA opposite a thymine-thymine cis-syn-cyclobutane dimer. We have purified the yeast Pol(eta) and studied its lesion bypass activity in vitro with various types of DNA damage. The yeast Pol(eta) lacked a nuclease or a proofreading activity. It efficiently bypassed 8-oxoguanine, incorporating C, A, and G opposite the lesion with a relative efficiency of approximately 100:56:14, respectively. The yeast Pol(eta) efficiently incorporated a C opposite an acetylaminofluorene-modified G, and efficiently inserted a G or less frequently an A opposite an apurinic/apyrimidinic (AP) site but was unable to extend the DNA synthesis further in both cases. However, some continued DNA synthesis was observed in the presence of the yeast Pol(zeta) following the Pol(eta) action opposite an AP site, achieving true lesion bypass. In contrast, the yeast Pol(alpha) was able to bypass efficiently a template AP site, predominantly incorporating an A residue opposite the lesion. These results suggest that other than UV damage, Pol(eta) may also play a role in bypassing additional DNA lesions, some of which can be error-prone.     

Polyomavirus interaction with the DNA damage response

Viruses are obligate intracellular parasites that subvert cellular metabolism and pathways to mediate their own replication—normally at the expense of the host cell. Polyomaviruses are a group of small DNA viruses, which have long been studied as a model for eukaryotic DNA replication. Polyomaviruses manipulate host replication proteins, as well as proteins involved in DNA maintenance and repair, to serve as essential cofactors for productive infection. Moreover, evidence suggests that polyomavirus infection poses a unique genotoxic threat to the host cell. In response to any source of DNA damage, cells must initiate an effective DNA damage response(DDR) to maintain genomic integrity, wherein two protein kinases, ataxia telangiectasia mutated(ATM) and ATM- and Rad3-related(ATR), are major regulators of DNA damage recognition and repair. Recent investigation suggests that these essential DDR proteins are required for productive polyomavirus infection. This review will focus on polyomaviruses and their interaction with ATMand ATR-mediated DNA damage responses and the effect of this interaction on host genomic stability.     

DNA interaction with the antitumor agent thiophosphamide

DNA interaction with an alkylating antitumor drug N,N',N"-triethylenethiophosphoramide (thiotepa) in water-salt solutions at 37 degrees C has been studied by UV-spectroscopy, heat denaturation and electron microscopy methods. Changes of the DNA melting curve parameters provide information on the kinetics of alkylation. The dependence of the alkylation rate on DNA and thiotepa concentrations shows that the alkylation reaction is biomolecular. The increase of sodium chloride concentration from 10(-3) to 10(-1) M is accompanied by a drastic decrease of the alkylation rate. Thiotepa binding results in destabilization of the DNA secondary structure and formation of cross-links. An increased amount of bounded thiotepa results in DNA denaturation; prolonged alkylation causes breaks in the sugar-phosphate backbone. The results of the work are discussed in connection with the literature data on DNA interaction with thiotepa in vivo.     

DNA interaction with the bifunctional acridine dye

The comparative studies of the formation of DNA-complexes with the acridines containing one and two chromophores were accomplished. It was shown that both of acridines were bonded with DNA by means of intercalation irrespective of the ionic strength of medium (mu). When mu = 0.1 the diacridine (1,6-bis(9-acridylamino)-hexan) behaves as an mono-intercalator. Under these conditions both of the ligands exert equal influence of the molecular parameters of DNA. When mu = 0.001 the binding mode of the diacridine with DNA depends on its concentration in a complex. If a number of diacridine molecules on a pair of nucleotides (r) falls in a region 0 less than r less than 0.2 its binding with DNA is accomplished via the bis-intercalation mode and accompanied by the structure distortion of the monomer remnant of the macromolecule. As r increases from 0.2 to 0.4 the gradual change of the binding mode of the diacridine with DNA from bis-intercalation to mono-intercalation takes place. Moreover the structure of nucleotides is reduced. When mu = 0.001 the behaviour of DNA complexes with mono-acridine is analogous to the observed one when mu = 0.1.     

Thermodynamics of the interaction of daunomycin with DNA

The association constant for the interaction of daunomycin with DNA was determined as a function of temperature (using [³H] daunomycin in conventional equilibrium dialysis cells) and ionic strength (using a spectrophotometric titration method). The association constant varied between 3.1 × 10⁶ M^?1 (4°C) and 3.9 × 10⁵ M^?1 (65°C). The free energy change was ?8.2 to ?8.8 $\text{kcal}\text{mol}$, the enthalpy change ?5.3 $\text{kcal}\text{mol}$ and the entropy change +10 to +11 eu, all values being consistent with that expected of an intercalation process. The apparent number of intercalation sites detected (0.15 to 0.16 per nucleotide) was independent of temperature. The large positive entropy change accompanying the interaction appeals to be due to extensive release of water from the DNA and daunomycin. The apparent number of binding sites increased dramatically with decrease of ionic strength, although the apparent association constant remained largely unaffected by ionic strength.