Electrostatic contribution to the energy of binding of aromatic ligands with DNA

The method of solution of the nonlinear Poisson-Boltzmann equation was used to calculate electrostatic energy of binding of various aromatic ligands with DNA oligomers of different length. Analysis of the electrostatic contribution was made in terms of a two-step DNA binding process: formation of the intercalation cavity and insertion of the ligand. The total electrostatic energy was also partitioned into components: the energy of atom-atom coulombic interactions and the energy of interaction with surrounding water. The results indicate that electrostatic interactions are, as a whole, unfavorable to the intercalation process and that a correct analysis of structure-energy interrelation for Ligand-DNA interactions should only be accomplished at the level of the components rather than at the level of total electrostatic energy.     

Transverse dipoles added to DNA chains by drug binding can induce inversion of the long-range chirality of DNA condensates

The addition of poly(ethylene glycol) (PEG) to a DNA solution induces phase separation of droplets of condensed DNA. These droplets possess liquid crystalline properties and their ordering is cholesteric. It was recently proved that daunomycin, by binding to DNA chains, inverts the long-range chirality of their tertiary packing into aggregates. The present paper suggests one possible mechanism by which this inversion can take place. Daunomycin bears a cationic group in its sugar residue. Its intercalation adds a helicoidal distribution of transverse dipoles to DNA chains. By this mechanism, in favourable cases, ionic or strongly polar groups in drugs which bind DNA can induce handedness inversion of the cholesteric ordering of its condensates. This inversion mechanism was tested experimentally using several, charged and uncharged, homologues of daunomycin. All those bearing the cationic ammonium group inverted the long-range chirality of the PEG-induced DNA mesomorphic state. The effects of the uncharged desamino homologues could not be evaluated because of their lower solubility and binding affinity for DNA.     

Emergence of molecular chirality due to chiral interactions in a biological environment

We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and thus preserve the initial chiral state. At the strong-coupling limit, considering the memory effects of the environment, Markovian behavior is observed at long times.     

Lamellar cationic lipid‐DNA complexes from lipids with a strong preference for planar geometry: A Minimal Electrostatic Model

We formulate and analyze a minimal model, based on condensation theory, of the lamellar cationic lipid (CL)‐DNA complex of alternately charged lipid bilayers and DNA monolayers in a salt solution. Each lipid bilayer, composed by a random mixture of cationic and neutral lipids, is assumed to be a rigid uniformly charged plane. Each DNA monolayer, located between two lipid bilayers, is formed by the same number of parallel DNAs with a uniform separation distance. For the electrostatic calculation, the model lipoplex is collapsed to a single plane with charge density equal to the net lipid and DNA charge. The free energy difference between the lamellar lipoplex and a reference state of the same number of free lipid bilayers and free DNAs, is calculated as a function of the fraction of CLs, of the ratio of the number of CL charges to the number of negative charges of the DNA phosphates, and of the total number of planes. At the isoelectric point the free energy difference is minimal. The complex formation, already favoured by the decrease of the electrostatic charging free energy, is driven further by the free energy gain due to the release of counterions from the DNAs and from the lipid bilayers, if strongly charged. This minimal model compares well with experiment for lipids having a strong preference for planar geometry and with major features of more detailed models of the lipoplex. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1114–1128, 2014.     

Effect of Different Z‐Inducers on the Stabilization of Z Portion in BZ‐DNA Sequence: Correlation Between Experimental and Simulation Data

In this study we show the outstanding agreement between simulation and experimental data concerning the efficient stabilization effect by NaCl of Z conformation. We demonstrate by circular dichroism (CD) experiments that Na⁺ not only is able to induce a B to Z form transition in a short (GC)₃ alternated portion of a sequence having 17 basis, but also is the best stabilizer in comparison with other Z inducers used (spermine and NiCl₂). This result was confirmed by free energy calculations. Chirality 27:773–778, 2015. © 2015 Wiley Periodicals, Inc.     

Interactions of polyamines with the DNA octamers d(m5CG)4 and d(GGAATTCC): A 1H‐NMR investigation

The interaction of two DNA octamers, d(m⁵CG)₄ and d(GGAATTCC), with the polyamines spermine⁴⁺ and spermidine³⁺, has been studied by means of ¹H‐nmr nuclear Overhauser effect (NOE) difference measurements. The experiments were performed at 10°C and for a polyamine charge to DNA charge (i.e., phosphate) ratio of 0.4, where the solution of d(m⁵CG)₄ contains about 50% Z‐form of the DNA. The results show that the polyamine intramolecular NOEs for the protons on the propyl chains are similarly negative with the two oligonucleotides, while those on the butyl chain show slightly more negative NOE with d(m⁵CG)₄ than with d(GGAATTCC). The fully N‐methylated analogues of spermine (Me₁₀Spn⁴⁺) and spermidine (Me₈Spd³⁺) as well as the diamines 1,3‐diaminopropane (DAP²⁺) and 1,4‐diaminobutane (putrescine²⁺) have been studied for the ability to transform d(m⁵CG)₄ from the B‐ to the Z‐form. ¹H‐nmr spectra showed the order spermine⁴⁺ > spermidine³⁺ > Me₁₀Spn⁴⁺ > Me₈Spd³⁺ > 1,3‐diaminopropane²⁺ > putrescine²⁺, with spermine showing the largest relative amount of Z‐DNA. ¹H‐nmr pulsed‐gradient self‐diffusion measurements of the triamines showed a large difference in the interaction of Spd and Me₈Spd with the two different duplexes. With the same duplex (either of the two), however, no difference between Spd and Me₈Spd can be seen. Within a two‐state model this is interpreted as a larger fraction of bound polyamines with d(m⁵CG)₄ than with d(GGAATTCC). © 1999 John Wiley & Sons, Inc. Biopoly 49: 41–53, 1999     

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.     

Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure

We analyzed structural features of 11,038 direct atomic contacts (either electrostatic, H-bonds, hydrophobic, or other van der Waals interactions) extracted from 139 protein-DNA and 49 protein-RNA nonhomologous complexes from the Protein Data Bank (PDB). Globally, H-bonds are the most frequent interactions (approximately 50%), followed by van der Waals, hydrophobic, and electrostatic interactions. From the protein viewpoint, hydrophilic amino acids are over-represented in the interaction databases: Positively charged amino acids mainly contact nucleic acid phosphate groups but can also interact with base edges. From the nucleotide point of view, DNA and RNA behave differently: Most protein-DNA interactions involve phosphate atoms, while protein-RNA interactions involve more frequently base edge and ribose atoms. The increased participation of DNA phosphate involves H-bonds rather than salt bridges. A statistical analysis was performed to find the occurrence of amino acid-nucleotide pairs most different from chance. These pairs were analyzed individually. Finally, we studied the conformation of DNA in the interaction sites. Despite the prevalence of B-DNA in the database, our results suggest that A-DNA is favored in the interaction sites.     

The chirality selectivity in the uptake of platinum (II) complexes with 1,2-cyclohexanediamine isomers as carrier ligand by human erythrocytes

The uptake kinetics of cisplatin analogs of 1,2-cyclohexanediamine(dach) isomers with various leaving groups, by human erythrocytes in plasma isotonic buffer, were studied. The experimental results showed that the uptake rate constants (k values) decrease with the change of leaving group in the sequence: chloride (Cl) > squaric acid (SA) > oxalate (OX) > demethylcantharic acid (DA), with the same dach isomer as carrier group. It is noteworthy that for the platinum (II) complexes with the same leaving group, the k values always reduce as: 1R, 2R-dach > 1R, 2S-dach > 1S, 2S-dach. This result reflects the chirality selectivity. No differences in reactivity to protein thiols and effects on membrane permeability were found for the R,R-, R,S-, S,S-isomeric complexes. It is proposed that the chirality selectivity in uptake is due to the recognition of the chirality of the platinum complexes by the erythrocyte membrane. The interactions between the chiral platinum complexes and the head groups of the membrane phospholipid molecules are probably involved.     

Enhanced recognition of cystic fibrosis W1282X DNA point mutation by chiral peptide nucleic acid probes by a surface plasmon resonance biosensor

Peptide nucleic acids (PNAs) containing an insert of three chiral monomers based on D-lysine ('chiral box') were synthesized and used as probes in Biospecific Interaction Analysis (BIA) for the recognition of DNA containing the W1282X point mutation of the cystic fibrosis gene. Hybridization experiments carried out in solution showed enhanced mismatch recognition when compared with the analogous achiral PNAs and oligonucleotides. The signal intensity was lower, but the selectivity of the Biacore response was found to be much higher than that observed with achiral PNAs. The newly designed chiral PNA probes were also found to hybridize with a 1:1 mixture of normal (N-W1282X) and mutated (M-W1282X) DNA oligomers immobilized on the biosensor, thus allowing discrimination not only between a normal and a mutated sequence (healthy/homozygous), but also between homo- and heterozygous individuals. These results suggest that 'chiral box' PNAs are potential powerful tools for the analysis of single point mutations of biological/biomedical relevance.     

The development of biphasic chiral recognition in chiral separation

In chiral separation, enantioseparation factor is an important parameter which influences the resolution of enantiomers. In this current overview, a biphasic chiral recognition method is introduced to the readers. This method can significantly improve the enantioseparation factor in two‐phase solvent through adding lipophilic and hydrophilic chiral selectors which have opposite chiral recognition ability to organic and aqueous phases, respectively. This overview presents the development and applications of biphasic chiral recognition in liquid‐liquid extraction and counter current chromatography. It mainly focuses on the topics of mechanism, advantages and limitations, applications, and key factors of biphasic chiral recognition. In addition, the future outlook on development of biphasic chiral recognition also has been discussed in this overview.     

Interaction of aromatic ionen oligomers with DNA

A novel polycationic ionen was synthesized and fractionated on carboxymethyl-Sephadex using a salt gradient in 7M urea. A series of oligomers of discrete length were characterised by ultraviolet spectra. The ultraviolet spectra of oligomers revealed a new band centred at 232.5 nm which was probably due to exciton splitting. Thermal denaturation studies indicated both stabilization of the helix conformation and a higher degree of cooperativity in the melting of DNA (oligomers)n complex as compared to native calf thymus DNA. Ionen oligomers exhibited large extrinsic Cotton effect at 232.5 nm which could be attributed to exciton interaction.     

Preparation of a chiral ferrocenyl derivative containing a biphenyl unit via nickel-mediated homocoupling

Ferrocenyl derivative 2, which possesses a biphenyl unit, was prepared by nickel(0)-mediated homocoupling of a chiral ferrocenyloxazoline. Compound 2 exists as an equilibrium mixture of two diastereomers, in a ratio dependent on temperature and solvent, due to the partially hindered rotation around biaryl bond. Upon complexation with Cu(I) or Zn(II), complete fixation of the stereogenic axis was obtained and a single stable atropoisomer was formed, whose absolute configuration was assigned on the basis of its NOESY spectrum. The 2-Cu(I) complex was used as catalyst in the cyclopropanation of styrene.     

Selective distortion of the planar group CαC'(O)O to a chiral flat tetrahedron in the amino acid alanine

Based on a Cambridge Structural Database (CSD) search, a meta‐analysis of 116 structures of alanine H₃NC_αH(CH₃)C′(O)O and its derivatives H₃NC_αH(CH₃)C′(O)O(H/R/M), protonated, esterified, or coordinated at the carboxylic group, shows that in the first step of a chirality chain, the L configuration at C_α induces (M) and (P) conformations with respect to rotation around the central C′─C_α bond. In the second step, the (M) and (P) conformations selectively distort the planar carboxylic group C_αC'(O_cis)O_trans to asymmetric flat (R) and (S) tetrahedra. High diastereoselectivities are caused by the two players attraction N…O_cis and repulsion O_trans…C_Me, which work together in (L,M,R) configurations but against each other in (L,P,S) configurations.     

Absorption, fluorescence, and cd spectroscopic study of chiral recognition by a binaphthyl-derived chromogenic calixcrown host

The (R)- and (S)-enantiomers of a binaphthyl-appended calix[4]crown-6 ether with two 2,4-dinitrophenylazo chromophore units ((R)-1 and (S)-1) as chiral hosts were tested in their reactions with the enantiomers of alpha-methylbenzylamine ((R)-MBA, (S)-MBA)) and phenylglycinol ((R)-PGL, (S)-PGL) as chiral guests. The visible absorption spectra indicate a two-step process: the first is a nonenantioselective proton transfer from the host to the guest, which is followed by the enantioselective real complexation. In the visible range of the CD spectra a positive/negative band belongs to the absorption of pure (R)-1/(S)-1, and a negative/positive exciton couplet to the absorption of (R)-1-(S)-MBA/(S)-1-(R)-MBA complexes. The latter phenomenon suggests that the complexation of amines is accompanied by a chiral arrangement of the two chromophore units in the hosts. The UV fluorescence of (R)-1/(S)-1 arising from the binaphthyl moiety is quenched by K+ ions, but not by the amine guests, showing that the interaction between the binaphthyl group and the complexed amines is weak.     

Electrostatic interactions with histone tails may bend linker DNA in chromatin

Is linker DNA bent in the 30‐nm chromatin fiber at physiological conditions? We show here that electrostatic interactions between linker DNA and histone tails including salt condensation and release may bend linker DNA, thus affecting the higher order organization of chromatin. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 20–28, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Metal-induced supramolecular chirality in optically active polymers of oxazoline-substituted N-phenylmaleimides

Polymerization of N-phenylmaleimide derivatives bearing a chiral oxazoline substituent at ortho-position on the phenyl group (namely, N-[o-(4,5-dihydro-1,3-oxazol-2-yl)phenyl]maleimides, OPMI) was carried out with diethylzinc (Et2Zn) as an initiator. The resulting polymers exhibited a quite high specific rotation and a unique split-type circular dichroism. Furthermore, an induced Cotton effect was observed in the pi-pi* transition region of the chromophores upon complexation of these polymers with copper(II) salt in tetrahydrofuran solution, indicating the formation of chiral supramolecular aggregates. The induced supramolecular chirality was found to be dependent on the absolute configuration of monomer units, that is, the polymers with (R)-configurational oxazolinyl chromophores tended to form chiral aggregates with levorotatory handedness, while polymers obtained from the (S)-monomer offered dextrogyrate one upon the addition of Cu(II) salt.     

Self-assembling protein arrays on DNA chips by auto-labeling fusion proteins with a single DNA address

The high-throughput deposition of recombinant proteins on chips, beads or biosensor devices would be greatly facilitated by the implementation of self-assembly concepts. DNA-directed immobilization via conjugation of proteins to an oligonucleotide would be preeminently suited for this purpose. Here, we present a unique method to attach a single DNA address to proteins in one step during the purification from the E. coli lysate by fusion to human O6-alkylguanine-DNA-alkyltransferase (SNAP-tag) and the Avitag. Use of the conjugates in converting a DNA chip into a protein chip by self assembly is demonstrated.