Deep-hole transfer leads to ultrafast charge migration in DNA hairpins.

Charge transport through the DNA double helix is of fundamental interest in chemistry and biochemistry, but also has potential technological applications such as for DNA-based nanoelectronics. For the latter, it is of considerable interest to explore ways to influence or enhance charge transfer. In this Article we demonstrate a new mechanism for DNA charge transport, namely 'deep-hole transfer', which involves long-range migration of a hole through low-lying electronic states of the nucleobases.

Conformationally Gated Charge Transfer in DNA Three-Way Junctions.

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes.

Charge Transport across DNA-Based Three-Way Junctions.

DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations.

Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins.

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here.

Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins.

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data.

DNA base pair stacks with high electric conductance: a systematic structural search.

We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes.

Exponential distance dependence of photoinitiated stepwise electron transfer in donor-bridge-acceptor molecules: implications for wirelike behavior.

Donor-bridge-acceptor (D-B-A) systems in which a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) chromophore and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked by oligomeric 2,7-fluorenone (FN(n)) bridges (n = 1-3) have been synthesized. Selective photoexcitation of DMJ-An quantitatively produces DMJ(+•)-An(-•), and An(-•) acts as a high-potential electron donor. Femtosecond transient absorption spectroscopy in the visible and mid-IR regions showed that electron transfer occurs quantitatively in the sequence: DMJ(+•)-An(-•)-FN(n)-NI → DMJ(+•)-An-FN(n)(-•)-NI → DMJ(+•)-An-FN(n)-NI(-•).

Effects of various halogen anions and cations of alkali metals on energetics of excess charge recombination in stilbene donor-acceptor capped DNA hairpins.

DNA hairpin conjugates with a stilbenedicarboxamide (Sa) hole donor and a stilbenediether (Sd) hole acceptor are considered as model systems for studying charge recombination (CR) of excess charges in DNA. Using the method of thermodynamic integration, we estimated the relative free energies of this process in hairpins with three adenine:thymine pairs between Sa and Sd surrounded by 1 M aqueous solutions of ionic compounds M(+)Cl(-) (M = Li, Na, K) and Na(+)X(-) (X = F, Cl, Br, I). The values of this quantity were calculated with respect to the free energy for the same hairpin in the 1 M NaCl aqueous solution.

Effect of electrostatic interactions and dynamic disorder on the distance dependence of charge transfer in donor-bridge-acceptor systems.

Using a tight-binding model of charge transport in systems with static and dynamic disorder, we present a theoretical study of the positive charge transfer in molecular assemblies that involve a hole donor and an acceptor connected by fluorene and phenyl bridges. Two parameters that determine the rate of charge transfer within the proposed model are the charge transfer integral between neighboring units and the site energies. Fluctuations in the values of the charge transfer integral and the energy landscape for hole transport were calculated by taking into account variations of the dihedral angle between neighboring units and electrostatic interaction of positive charge moving along the bridge and the negative charge that remains on the hole donor.

Effect of GC base pairs on charge transfer through DNA hairpins: the importance of electrostatic interactions.

DNA hairpins in which an electron donor and an electron acceptor are attached to the ends are excellent model systems for the study of charge transfer in weakly coupled pi-stacked systems. In this communication we report on a computational study of the effect of the base pair sequence in these DNA hairpins on the kinetics of charge transfer. We show that the rate of charge transfer strongly depends on the actual position of a GC base pair in a sequence that otherwise only contains AT base pairs.

Effect of structural dynamics on charge transfer in DNA hairpins.

We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studied by a combination of molecular dynamics simulations of the structural dynamics and density functional theory calculations of charge transfer integrals and orbital energies.

Absolute rates of hole transfer in DNA.

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclassical superexchange model. Site energies and charge-transfer integrals were calculated directly as the diagonal and off-diagonal matrix elements of the Kohn-Sham Hamiltonian, respectively, for all possible combinations of nucleobases.

Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli.

In bacterial expression systems, translation initiation is usually the rate limiting and the least predictable stage of protein synthesis. Efficiency of a translation initiation site can vary dramatically depending on the sequence context. This is why many standard expression vectors provide very poor expression levels of some genes.

DNA splicing by directed ligation (SDL).

Splicing by directed ligation (SDL) is a method of in-phase joining of PCR-generated DNA fragments that is based on a pre-designed combination of class IIS restriction endonuclease recognition and cleavage sites. Since these enzymes cleave outside of their recognition sites, the resulting sticky end can have any desired sequence, and the site itself can be removed and does not appear in the final spliced DNA product. SDL is based on the addition of class IIS recognition sites onto primers used to amplify DNA sequences.

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G.

Probing accessible sites for ribozymes on human acetylcholinesterase RNA.

In order to design ribozymes for the efficient cleavage of a human acetylcholinesterase (AChE) in vitro transcript, a completely randomized decadeoxyribonucleotide (dN10) was used in conjunction with RNase H to identify suitable sites for annealing. Based on the observed cleavage pattern, ribozymes were designed to cleave the transcript at these positions. Five ribozymes so designed proved to be efficient in the transcript cleavage (k(react)/Km ranged from 0.

A high-level prokaryotic expression system: synthesis of human interleukin 1 alpha and its receptor antagonist.

Synthetic intronless genes, coding for human interleukin 1 alpha (IL 1 alpha) and interleukin 1 receptor antagonist (IL1ra), have been expressed efficiently in a specially designed prokaryotic vector, pGMCE (a pGEM1 derivative), where the target gene forms the second part of a two-cistron system. The first part of the system is a translation enhancer-containing mini-cistron, whose termination codon overlaps the start codon of the target gene. In the case of the IL1 alpha gene, the high expression level is largely due to the direct efficient translation initiation at the second cistron, whereas with the IL1ra gene in the same system, the proximal translation initiation region (TIR) provides a high level of coupled expression of the target gene.

Reagent for introducing pyrene residues in oligonucleotides.

A novel pyrenyl-containing phosphoramidite reagent, N-[4-(1-pyrenyl)butyryl]-O1-(4,4'-dimethoxytrityl)-O2- [(diisopropylamino)(2-cyanoethoxy)phosphino]-3-amino-1 ,2-propanediol (5), has been synthesized from 4-(1-pyrenyl)butanoic acid in four steps with the 52% overall yield and used to incorporate pyrene residue(s) into oligonucleotides. Oligonucleotides 6 and 7, bearing one or two pyrenes at the 5'-terminus, have been prepared by means of that reagent, characterized with fluorescence spectra, and successfully used as primers in a polymerase chain reaction.

On inherited fertility in biological systems: a model of correlated fluctuations in the stochastic branching process.

A new evolutionary model with hereditary modes considered as correlated fluctuations of fertility has been proposed. It has been demonstrated that the model allows the global statistical properties of the system to be evaluated, e.g.

A modified approach to identification of the sickle cell anemia mutation by means of allele-specific polymerase chain reaction.

The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.

Site-specificity of abnormal excision: the mechanism of formation of a specialized transducing bacteriophage lambda plac5.

Molecular mechanism of the specialized transducing bacteriophage lambda plac5 formation has been studied. Phage-bacterial DNA junctions in lambda plac5 DNA are localized and primary structure of regions of the abnormal excisional recombination leading to the phage formation is elucidated; the crossover region proved to be comparable with the central part of attP and attB sites (the core and the adjacent tetranucleotide) in length and degree of homology. Bacterial insert in lambda plac5 DNA is shown to end immediately after Z-Y spacer, the DNA not containing lacY gene segments.