Modes of Interaction

One should first distinguish two very different types of monocation-quadruplex interaction the first is based on central ions which are specifically sandwiched between quartets while the second is based on external ions which contribute to partial charge screening of the quadruplex. The central ions interact with a quadruplex in a specific fashion. X-ray crystallography provided definitive evidence of dehydrated cation coordination by G-quartets along the central 

Cations are also important for the self-assembly of nueleotides. Wong and Wu have found that the eation-induced stability of a 5 -GMP structure is determined by the affinity of monovalent cations for the channel site (with the order NH4 Rb Na Cs Li ). Polycations such as spermine also interact with quadruplex structures/ but their effects on the thermodynamics of the quadruplex are still not completely understood. 

Some cations may actively disrupt quadruplexes stabilization of quadruplex structure by is specifically counteracted by low concentrations of Mn , Co or When the quadruplex and monovalent cation concen- 

The two best-studied ions are Na and K . The preference of quadruplex central cavity for potassium over sodium ions is the result of two opposite effects from one side the free energy of Na binding to a quadruplex is more favourable than that of K, but from the other side this effect is more than compensated by the much greater cost of Na dehydration. The net result is a free energy change in favour of the potassium form. The number of released ions upon melting of the human telomeric quadruplex can be estimated by melting experiments as 5 in the presence of NaCl and 6 in the presence of KCl. Note that this value should not be interpreted as the number of ions bound in the quadruplex channel, as the total number of ions released on thermal denaturation includes the ions bound in the quadruplex channel, and the difference between the number of ions condensed on the quadruplex and on the random coil. In our hands, the dilfer-ences in thermal stability between the sodium and potassium forms of a quadruplex are very sequence dependent values (Tni(K+) — Ln(Na+)) are 

8 and 30°C for the human telomeric motif and the thrombin aptamer, respectively. Takenaka et alP found a 43,000-fold preference of the human telomeric intramolecular quadruplex for over Na . This value is surprisingly large, given the relatively small difference in thermal stability between the sodium and potassium forms of this quadruplex, corresponding to a AAG° of 2 kcal moL (L. Lacroix, unpublished). 

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A range of plasticizer molecule models and a model for PVC have been generated and energy minimized to observe their most stable conformations. Such models highlight the free volume iacrease caused by the mobiHty of the plasticizer alkyl chains. More detailed models have also been produced to concentrate on the polar region of the plasticizer and its possible mode of interaction with the polymer. These show the expected repulsion between areas on the polymer and plasticizer of like charge as weU as attraction between the negative portions of the plasticizer and positive portions of the PVC. 

This series of walls between the functional areas are eventually being broken down and replaced with new alliances and modes of interaction. This has been accomplished by (Russell and Taylor, 1995) ... 

The precise mode of interaction between the casein and the formaldehyde has not been fully elucidated but the following reactions are believed to occur ... 

The electrostatic solvait effects discussed in the preceding paragraphs are not the only possible modes of interaction of solvent with reactants and transition states. Specific structural effects may cause either the reactants or the transition state to be particularly stroi ly solvated. Figure 4.12 shows how such solvation can affect the relative energies of the ground state and transition state and cause rate variations from solvent to solvent. 

FIGURE 2.3. Modes of Interacting with the World (Reason, 1990). 

By structural complementarity, dicationic l,4-diazabicyclo[2.2.2]octane (VII) provides an appropriate recognition site for phosphate ions and two stearyl side chains attached to the amines add lipophilic properties 59,60). Such a carrier model can selectively extract nucleotides from aqueous solution to chloroform solution via lipophilic salt formation. The order of nucleotide affinity is ATP > ADP > AMP. The selectivity ratios were 45 for ADP/AMP and 7500 for ATP/AMP at pH 3. The relative transport rate was ATP > ADP > AMP. The ratios were 60 for ATP/AMP and 51 for ADP/AMP. The modes of interaction of ADP and ATP are proposed to be as shown in Fig. 6. 

For 7-ray energies below 1 MeV (the range of interest) there are two principal modes of interaction with matter — Compton scattering and photoelectron absorption. Compton scattering is the elastic scattering of the 7 photon by an orbital electron in which part of the incident 7-energy is imparted to the recoiling electron. 

The strength of the adsorptive interaction as expressed in values of AG jj depends on the mode of interaction between the adsorbate molecule and the electrode surface. Weak adsorption (physisorption) is based mostly on van-der-Waals-interactions. It shows t5q)ically values of AG jj > - 20 kJ mol Stronger... 

Anchordoguy, T.J., Rudolph, A.S., Carpenter, J.F., Crowe, J.H. (1987). Modes of interaction of cryoprotectants with membrane phospholipids during freezing. Cryobiol. 24,324-331. 

An anticooperative mode of interactions was assumed in case of concave-shaped Scatchard plots, as alrea% proposed by other authors (Mattai Kwak, 1986 Gamier et al, 1994). A convexe curvature of the plots indicated a cooperative binding process (figure 4). 

The tveak and reversible binding of these complexes to calf-thymus DNA (ct DNA) suggests a dominant electrostatic mode of interaction nevertheless, relevant conformational distortions of the double helix are caused [50]. A multinuclear NMR study of the reactivity of [Au(en)Cl2]Cl and [Au(en)2]Cl3 vith guanosine 5 -monopho-sphate (5 -GMP) reveals that in an aqueous solution only [Au(en)Cl2]Cl binds very weakly to 5 -GMP via N(7) to give a 1 1 adduct [48]. 

Tomasz, M. Mercado, C. M. Olson, J. Chatteijie, N. The mode of interaction of mitomycin C with deoxyribonucleic acid and other polynucleotides in vitro. Biochemistry 1974, 13, 4878-4887. 

J. H. Crowe, J. F. Carpenter, L. M. Crowe, and T. J. Anchordoguy, Are freezing and dehydration similar stress vectors A comparison of modes of interaction of stabilizing solutes with biomolecules, Cryobiology, 27, 219 (1990). 

Among many examples of -orbital interaction, only the following two are selected to illustrate the feature of HO—LU conjugation. One is the cyclooctadiene-transition metal complex ">. The figure indicates the symmetry-favourable mode of interaction in a nickel complex. The electron configuration of nickel is (3d)8 (4s)2. The HO and LU of nickel can be provided from the partly occupied 3d shell from which symmetry-allowed occupied and unoccupied d orbitals for interaction with cyclo-octadiene orbitals are picked up. 

Also the a-n interaction in Diels-Alder additions, which occurs with sy -fashion with regard to both diene and dienophile, is explained (Fig. 7.38). For the first place, the p-a type interaction is allowed, by the selection rule already mentioned, between the jr-part of butadiene and the ji-part of ethylene. Once this weak p-a type interaction starts, the p AO part forms a six-electron system. The HO of this -part will come from HO of butadiene jr-part interacting with LU of ethylene jr-part will interact with er-LU s of both butadiene and ethylene. The mode of interaction is as indicated in Fig. 7.38. 

Douthwaite, S. and Champney, W.S. (2001) Structures of ketolides and macrolides determine their mode of interaction with the ribosomal target site. The Journal of Antimicrobial Chemotherapy, 48 (Suppl 2), 1. 

Portoghese PS. A new concept on the mode of interaction of narcotic analgesics with receptors. J Med Chem 1965 8 609-616. 

A completely different mode of interaction has been reported for Pt(en)2, which binds to double-stranded oligonucleotides in a noncova-lent manner. NMR studies have indicated that in the duplexes d(TCGGGATCCCGA)2 and d(CAATCCGGATTG)2 this square planar Pt(II) species selectively binds to the AT sequence in the minor groove [101]. It was suggested that the binding is stabilized by close van der Waals interactions as well as hydrogen bonds [101]. 

The isolation of diazobenzo[fr ]fluorenes as stable antitumor natural products raises several questions about their mode of action. The inability to cleave DNA by diazotization of 9-aminofluorene may imply that if the diazo functionality is involved in the mode of interaction of kinamycins with DNA, its conversion to diazonium and the ensuing reduction may seem to be of negligible importance. An additional possibility, which will be discussed later, is that 9-diazofluorene may not be the ideal model for these natural products. In exploring DNA cleavage as a possible route to the kinamycins role as a stable antitumor agent, which may supplement their speculative and as yet unconfirmed role as alkylating molecules [67], this early model seemed to suggest that the well-established activation of diazonium may not be relevant. 

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