The application of DNA and RNA G-quadruplexes to therapeutic medicines

The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).     

Sequence-structure relationships in DNA oligomers: a computational approach

A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA.     

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.     

Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline

RNA plays critical roles in numerous biological processes and constitutes valuable therapeutic targets. RNA is significant not only for its roles in transmitting the genetic code but also for its enzymatic functions in ribozymes and in peptide bond formation in ribosomes. Recent studies have shown that RNAs containing as few as 22 nucleotides can be key elements in cellular functions. This suggests the possibility of using short RNAs as regulatory elements. Here, we show that ligand recognition and selectivity by RNA molecules can occur with only the presence of a binding pocket and as few as six additional scaffolding nucleotides holding the binding pocket in place. A 13-mer RNA truncation of a 33-mer aptamer for theophylline preserves the ability to bind to theophylline and to discriminate against the structurally similar compound caffeine. The truncated aptamer retains nearly all of the same structural elements in its binding site as those present in the original aptamer. This is the first demonstration of selective ligand binding by a 13-mer RNA.     

Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

Sequence-dependent bending of DNA induced by cisplatin: NMR structures of an A.T-rich 14-mer duplex

The NMR solution structure of the A.T rich DNA 14-mer duplex d(ATACATGGTACATA).d(TATGTACCATGTAT) is reported. This is compared with the NMR structure of the same duplex intrastrand cross-linked at the d(G*pG*) site by cis-(Pt(NH3)2?2+, derived from the anticancer drug cisplatin. The unmodified duplex has B-DNA geometry, but there is a large positive base-pair roll (roll angle 24 +/- 2 degrees) at the T9-A10 step on the 3' side of the central GG site. Platination of the DNA duplex causes the adjacent guanine bases to roll toward one another (roll angle 44 +/- 4 degrees), leading to an overall helix bend of 52 +/- 9 degrees. The platinum atom is displaced from the planes of the coordinated G7* and G8* by 0.8 A and 0.3 A, respectively. The minor groove opposite the platinum lesion is widened and flattened, with geometric parameters similar to those of A-form DNA. The unwinding of the helix at the platination site is 26 degrees. Platination causes the DNA duplex to bend toward the 3'-end (with respect to the G*G* strand), in contrast to G C-rich structures reported previously, which bend toward the 5'-end. This difference can be attributed to the predisposition of the A.T rich duplex toward bending in this region. Protein recognition of bent platinated G*G* lesions may therefore exhibit a strong dependence on the local DNA structure.     

GnRH binding RNA and DNA Spiegelmers: a novel approach toward GnRH antagonism

Mirror-image oligonucleotide ligands (Spiegelmers) that bind to the pharmacologically relevant target gonadotropin-releasing hormone I (GnRH) with high affinity and high specificity have been identified using the Spiegelmer technology. GnRH is a decapeptide that plays an important role in mammalian reproduction and sexual maturation and is associated with several benign and malignant diseases. First, aptamers that bind to D-GnRH with dissociation constants of 50-100 nM were isolated out of RNA and DNA libraries. The respective enantiomers of the DNA and RNA aptamers were synthesized, and their binding to L-GnRH was shown. These Spiegelmers bind to L-GnRH with similar affinity to that of the corresponding aptamers that bind to D-GnRH. We further demonstrated dose-dependent inhibition of GnRH-induced Ca(2+) release in Chinese hamster ovary cells that were stably transfected with the human GnRH receptor.     

Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review

Bioluminescence (BL) is an amazing natural phenomenon whose visible light is produced by living organisms. BL phenomenon is quite pervasive and has been observed in 17 phyla of 4 kingdoms. This fascinating natural phenomenon has unceasingly attracted people’s curiosity from ancient era to today. For a very long time, we can only receive some sporadic and static information from experimental observations, the mechanism of most BL remains is unclear. How the chemical reaction of BL process is initiated? Where the energy for light emission comes from? How does the light emitter produce? What is the light emitter for a wild bioluminescent organism? How to regain luciferin for next bioluminescence when it is used up? The luciferin is utilized forthwith or stored and release for subsequent light emission? What factors affect the color and strength of a bioluminescence? How to artificially tune the bioluminescence for special application? Computational BL plays unreplaceable role in answering these mechanistic questions. In contrast with experimental BL, computational BL came very late. In the past two decades, computational BL has touched nearly all the bioluminescent systems with chemical bases via the method of multiscale simulation. In this review, the author firstly introduced the history, types and general chemical process of BL. Then, the computational scheme on BL was briefly epitomized. Using firefly BL as a paradigmatic case, the author summarized theoretical investigation on the six stages of general chemical process in a BL cycle: luciferin oxidation, peroxide thermolysis, light emission, luciferin regeneration, luciferin storage and luciferin release. At each stage, the available theoretical studies of other bioluminescent organisms are briefly introduced and compared with the firefly system. Basing on the mechanistic understanding, the author reviewed the up-to-date theoretical design on bioluminescent systems. Again, the firefly was mainly focused on, and the other possible systems were just briefly introduced. This review summarized the theoretical studies to date on BL and addressed the status, critical challenges and future prospects of computational BL.     

Diels-Alder ribozyme catalysis: a computational approach

A computational comparison of the Diels-Alder reaction of a maleimide and an anthracene in water and the active site of the ribozyme Diels-Alderase is reported. During the course of the catalyzed reaction, the maleimide is held in the hydrophobic pocket while the anthracene approaches to the maleimide through the back passage of the active site. The active site is so narrow that the anthracene has to adopt a tilted approach angle toward maleimide. The conformation of the active site changes marginally at different states of the reaction. Active site dynamics contribution to catalysis has been ruled out. The active site stabilizes the product more than the transition state (TS). The reaction coordinates of the ribozyme reaction in TS, RC1-CD1 and RC4-CD2, are 2.35 and 2.33 A, respectively, compared to 2.37 and 2.36 A in water. The approach angle of anthracene toward maleimide is twisted by 18 degrees in the TS structure of ribozyme reaction while no twisted angle is found in TS of the reaction in water. The free energy barriers for reactions in both ribozyme and water were obtained by umbrella sampling combined with SCCDFTB/MM. The calculated free energy barriers for the ribozyme and water reactions are in good agreement with the experimental values. As expected, Mulliken charges of the atoms involved in the ribozyme reaction change in a similar manner as that of the reaction in water. The proficiency of the Diels-Alder ribozyme reaction originates from the active site holding the two reactants in reactive conformations, in which the reacting atoms are brought together in van der Waals distances and reactants approach to each other at an appropriate angle.     

Combustion-generated nanoparticles produced in a benzene flame: a multiscale approach

This paper details the multiscale methodology developed to analyze the formation of nanoparticles in a manner that makes it possible to follow the evolution of the structures in a chemically specific way. The atomistic model for particle inception code that combines the strengths of kinetic Monte Carlo and molecular dynamics is used to study the chemical and physical properties of nanoparticles generated in a premixed fuel-rich benzene flame, providing atomistic scale structures (bonds, bond angles, dihedral angles) as soot precursors evolve into a three-dimensional structure. Morphology, density, porosity, and other physical properties are computed. Two heights corresponding to two different times in the benzene flame, experimentally studied by Bittner and Howard [Proc. Combust. Inst. 18, 1105 (1981)], were chosen to examine the influence of different environments on structural properties of the particles formed.     

Synthesis and characterization of a fluorescent adenosine derivative for detection of intermolecular RNA G-quadruplexes

We synthesized a fluorescent adenosine derivative, rA^py, as a probe to study RNA structural transitions, in particular the intermolecular G-quadruplex formation. rA^py was incorporated into the dangling positions of guanine-rich oligonucleotides, which under physiological conditions undergo π-stacking on top of each other exhibiting a strong emission signal in their G-quadruplex conformation, but not in their single-stranded state.     

Tetra-end-linked oligonucleotides forming DNA G-quadruplexes: a new class of aptamers showing anti-HIV activity

The biophysical and biological properties of unprecedented anti-HIV aptamers are presented. The most active aptamer (1L) shows a significant affinity to the HIV protein gp120.     

Conformations and charge transport characteristics of biphenyldithiol self-assembled-monolayer molecular electronic devices: a multiscale computational study

We report a computational study of conformations and charge transport characteristics of biphenyldithiol (BPDT) monolayers in the (sqrt.3 x sqrt.3)R30 degrees packing ratio sandwiched between Au(111) electrodes. From force-field molecular-dynamics and annealing simulations of BPDT self-assembled monolayers (SAMs) with up to 100 molecules on a Au(111) substrate, we identify an energetically favorable herringbone-type SAM packing configuration and a less-stable parallel packing configuration. Both SAMs are described by the (2sqrt.3 x sqrt.3)R30 degrees unit cell including two molecules. With subsequent density-functional theory calculations of one unit cell of the (i) herringbone SAM with the molecular tilt angle theta approximately 15 degrees , (ii) herringbone SAM with theta approximately 30 degrees , and (iii) parallel SAM with theta approximately 30 degrees, we confirm that the herringbone packing configuration is more stable than the parallel one but find that the energy variation with respect to the molecule tilting within the herringbone packing is very small. Next, by capping these SAMs with the top Au(111) electrode, we prepare three molecular electronic device models and calculate their coherent charge transport properties within the matrix Green's function approach. Current-voltage (I-V) curves are then obtained via the Landauer-Buttiker formula. We find that at low-bias voltages (|V| < or = 0.2 V) the I-V characteristics of models (ii) and (iii) are similar and the current in model (i) is smaller than that in (ii) and (iii). On the other hand, at higher-bias voltages (|V| > or 0.5 V), the I-V characteristics of the three models show noticeable differences due to different phenyl band structures. We thus conclude that the BPDT SAM I-V characteristics in the low-bias voltage region are mainly determined by the -Au [corrected] interaction within the individual molecule-electrode contact, while both intramolecular conformation and intermolecular interaction can affect the BPDT SAM I-V characteristics in the high-bias voltage region.     

Interactions of the 5-fluorouracil anticancer drug with DNA pyrimidine bases: a detailed computational approach

The H-bonded complexes formed from interaction between 5-fluorouracil (FU) and DNA pyrimidine bases have been investigated by B3LYP method using 6-311++G** basis set in the gas phase and the water solution. Vibrational frequencies and physical properties such as dipole moment, chemical potential, and chemical hardness of these compounds have been systematically explored. The natural bond orbital analysis and the Bader’s quantum theory of atoms in molecules are also used to elucidate the interaction characteristics of the investigated complexes. The aromaticity is measured using several well-established indices of aromaticity such as NICS, HOMA, PDI, ATI, and FLU. The MEP is given the visual representation of the chemically active sites and comparative reactivity of atoms. Furthermore, the effects of interactions on NMR data have been used for further investigation of the studied compounds.     

Interaction of divalent metal cations and nucleotides: A computational study

In this study, the anionic phosphate group of nucleotides was found to be the best site to bind the divalent metal cations Be²⁺, Mg²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ to form the most stable complexes. Molecular orbital calculations at the semiempirical level were performed on nucleotidemetal cation complexes to report energies of complexation reactions, geometrical parameters of complexes and charge distributions on the complexes. In the discussion, complexational preferences of divalent metal cations, the charge transfer involved in the binding of the metal cations to the phosphate anion of the nucleotides and their conformational effects are included.     

Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity

Changes in RNA conformation can alter gene expression. The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K(+) ions. Changes in the conformation of this motif could be especially important in regulating gene expression in plants because intracellular K(+) concentrations often increase during drought stress. Little is known about the folding thermodynamics of RNA GQS. We show here that RNA GQS with tracts containing three G's [e.g., (GGGxx)(4)] have a modest dependence on the K(+) concentration, folding with no or even negative cooperativity (Hill coefficients ≤1), and are associated with populated folding intermediates. In contrast, GQS with tracts containing just two G's [e.g., (GGxx)(4)] have a steep dependence on the K(+) concentration and fold with positive cooperativity (Hill coefficients of 1.7-2.7) without significantly populating intermediate states. We postulate that in plants, the more stable G3 sequences are largely folded even under unstressed conditions, while the less stable G2 sequences fold only at the higher K(+) concentrations associated with cellular stress, wherein they respond sharply to changing K(+) concentrations. Given the binary nature of their folding, G2 sequences may find application in computation with DNA and in engineering of genetic circuits.     

Kinetically grafting G-quadruplexes onto DNA nanostructures for structure and function encoding via a DNA machine

Kinetically grafting G-quadruplexes onto one-dimensional DNA nanostructures with precise positioning was realized in this study. The programs hold great promise for label-free and enzyme-free detection of various targets as a result of signal amplification from G-quadruplexes, and building DNA nanostructures as scaffolds due to the molecular recognition capacity of G-quadruplex aptamers.