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Langmuir : the ACS Journal of Surfaces... Jun 2022As one of the natural nucleobases, guanine has attracted increasing interest in molecular self-assembly science because of its abundant interaction sites and high... (Review)
Review
As one of the natural nucleobases, guanine has attracted increasing interest in molecular self-assembly science because of its abundant interaction sites and high electron cloud density. Guanines, guanine derivatives, and guanine-rich DNA sequence are able to self-assemble into versatile aggregate structures by the means of hydrogen bonds and π-π, ion-dipole, solvophobic, and electrostatic interactions. Recent advances have shown that many guanine analogue-based (G-based) luminescent aggregates exhibit promising applications for fluorescent and chemiluminescent sensing and circularly polarized luminescence (CPL). This perspective summarizes the state-of-art strategies for constructing G-based assemblies and presents representative examples for luminescence functions. Finally, the inspirations are provided for exploiting unique G-based systems and luminescent G-based assemblies.
Topics: Guanine; Luminescence
PubMed: 35648843
DOI: 10.1021/acs.langmuir.2c00705 -
International Journal of Molecular... Oct 2020Among the natural bases, guanine is the most oxidizable base. The damage caused by oxidation of guanine, commonly referred to as oxidative guanine damage, results in the... (Review)
Review
Among the natural bases, guanine is the most oxidizable base. The damage caused by oxidation of guanine, commonly referred to as oxidative guanine damage, results in the formation of several products, including 2,5-diamino-4-imidazol-4-one (Iz), 2,2,4-triamino-5(2)-oxazolone (Oz), guanidinoformimine (Gf), guanidinohydantoin/iminoallantoin (Gh/Ia), spiroiminodihydantoin (Sp), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), urea (Ua), 5-guanidino-4-nitroimidazole (NI), spirodi(iminohydantoin) (5-Si and 8-Si), triazine, the M+7 product, other products by peroxynitrite, alkylated guanines, and 8,5'-cyclo-2'-deoxyguanosine (cG). Herein, we summarize the present knowledge about base pairs containing the products of oxidative guanine damage and guanine. Of these products, Iz is involved in G-C transversions. Oz, Gh/Ia, and Sp form preferably Oz:G, Gh/Ia:G, and Sp:G base pairs in some cases. An involvement of Gf, 2Ih, Ua, 5-Si, 8-Si, triazine, the M+7 product, and 4-hydroxy-2,5-dioxo-imidazolidine-4-carboxylic acid (HICA) in G-C transversions requires further experiments. In addition, we describe base pairs that target the RNA-dependent RNA polymerase (RdRp) of RNA viruses and describe implications for the 2019 novel coronavirus (SARS-CoV-2): When products of oxidative guanine damage are adapted for the ribonucleoside analogs, mimics of oxidative guanine damages, which can form base pairs, may become antiviral agents for SARS-CoV-2.
Topics: Animals; Base Pairing; Betacoronavirus; DNA Damage; Guanine; Humans; Oxidation-Reduction; Point Mutation; SARS-CoV-2
PubMed: 33076559
DOI: 10.3390/ijms21207645 -
International Journal of Molecular... Sep 2020Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine-guanine base pair, two different types of...
Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine-guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).
Topics: Base Pairing; DNA; Electrons; Guanine; Halogenation; Halogens; Hydrogen; Hydrogen Bonding; Macromolecular Substances
PubMed: 32911856
DOI: 10.3390/ijms21186571 -
Photochemical & Photobiological... Apr 2020The main insights into the photoactivated dynamics of guanine quadruplexes (G4s) recently provided by quantum mechanical computations are concisely reviewed here. The... (Review)
Review
The main insights into the photoactivated dynamics of guanine quadruplexes (G4s) recently provided by quantum mechanical computations are concisely reviewed here. The experimental steady state absorption and circular dichroism spectra of different topologies can be reproduced and assigned. After light absorption from excited states delocalized over multiple bases, the most important decay pathways involve localization of the excitation over a single base or on two stacked guanines, excimers with different degrees of charge transfer character. Two main photochemical reactions are discussed. One involves the photodimerization of two stacked guanine bases on the 'neutral' excimer path. The other, ionization of guanine, which triggers deprotonation of the resulting cation to form (G-H2)˙ and (G-H1)˙ radicals. Both the static and dynamical properties of G4 excited states are ruled by their topology and modulated by the inner coordinated metal ions.
Topics: DNA; Electrons; G-Quadruplexes; Guanine; Light; Quantum Theory
PubMed: 32255446
DOI: 10.1039/d0pp00065e -
Proceedings of the National Academy of... Feb 1977DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments...
DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave DNA preferentially at guanines, at adenines, at cytosines and thymines equally, and at cytosines alone. When the products of these four reactions are resolved by size, by electrophoresis on a polyacrylamide gel, the DNA sequence can be read from the pattern of radioactive bands. The technique will permit sequencing of at least 100 bases from the point of labeling.
Topics: Adenine; Base Sequence; Biochemical Phenomena; Biochemistry; Cytosine; DNA; DNA Restriction Enzymes; Guanine; Hydrazines; Methods; Nucleic Acid Hybridization; Thymine
PubMed: 265521
DOI: 10.1073/pnas.74.2.560 -
Biophysical Chemistry Aug 2000We review the extra-helical guanine interactions present in many oligonucleotide crystals. Very often terminal guanines interact with other guanines in the minor groove... (Review)
Review
We review the extra-helical guanine interactions present in many oligonucleotide crystals. Very often terminal guanines interact with other guanines in the minor groove of neighboring oligonucleotides through N2 x N3 hydrogen bonds. In other cases the interaction occurs with the help of Ni2+ ions. Guanine/netropsin stacking in the minor groove has also been found. From these studies we conclude that guanine may have multiple extra-helical interactions. In particular it may be considered a very effective minor groove binder, which could be used in the design of sequence selective binding drugs. Interactions through the major groove are seldom encountered, but might be present when DNA is stretched. Such interactions are also analyzed, since they might be important for homologous chromosome pairing during meiosis.
Topics: Base Sequence; Crystallization; DNA; Guanine; Hydrogen Bonding; Meiosis; Models, Molecular; Netropsin; Nickel; Nucleic Acid Conformation; Recombination, Genetic
PubMed: 11026683
DOI: 10.1016/s0301-4622(00)00168-x -
The Journal of Physical Chemistry. B Jan 2023The paper deals with the fluorescence of guanine quadruplexes (G4) formed by association of two DNA strands d(GGGGTTTTGGGG) in the presence of K cations, noted as OXY/K...
The paper deals with the fluorescence of guanine quadruplexes (G4) formed by association of two DNA strands d(GGGGTTTTGGGG) in the presence of K cations, noted as OXY/K in reference to the protozoon , whose telomere contains TTTTGGGG repeats. They were studied by steady-state and time-resolved techniques, time-correlated single photon counting, and fluorescence upconversion. The maximum of the OXY/K fluorescence spectrum is located at 334 nm, and the quantum yield is 5.8 × 10. About 75% of the photons are emitted before 100 ps and stem from ππ* states, possibly with a small contribution of charge transfer. Time-resolved fluorescence anisotropy measurements indicate that ultrafast (<330 fs) excitation transfer, due to internal conversion among exciton states, is more efficient in OXY/K compared to previously studied G4 structures. This is attributed to the arrangement of the peripheral thymines in two diagonal loops with restricted mobility, facilitating the interaction among them and with guanines. Thymines should also be responsible for a weak intensity excimer/exciplex emission band, peaking at 445 nm. Finally, the longest living fluorescence component (∼2.1 ns) is observed at the blue side of the spectrum. So far, high-energy long-lived emitting states had been reported only for double-stranded structures but not for G4.
Topics: G-Quadruplexes; DNA; Spectrometry, Fluorescence; Telomere; Guanine
PubMed: 36577031
DOI: 10.1021/acs.jpcb.2c07647 -
Chemical Research in Toxicology Apr 2006
Review
Topics: Guanine; Mutagenicity Tests; Mutation; Oxidation-Reduction
PubMed: 16608160
DOI: 10.1021/tx0600043 -
International Journal of Molecular... Aug 2020Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating...
Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.
Topics: Amino Acid Substitution; Circular Dichroism; DNA; G-Quadruplexes; Guanine; Hydrogen Bonding; Models, Molecular; Nucleic Acid Conformation; Thermodynamics
PubMed: 32854410
DOI: 10.3390/ijms21176123 -
Methods in Enzymology 2022DNA can, in addition to the B-DNA conformation, fold into a variety of additional conformations. Among them are G-quadruplex structures that have gained a lot of...
DNA can, in addition to the B-DNA conformation, fold into a variety of additional conformations. Among them are G-quadruplex structures that have gained a lot of attention in recent years. G-quadruplex structures (G4s) are highly stable nucleic acid structures that can fold within DNA and RNA molecules. They form in guanine-rich regions that harbor a specific G4 motif. The three-dimensional structure forms via Hoogsteen hydrogen bonding, where the guanines form hydrogen bonds to each other in order to generate G quartets, which stack in order to become G4 structures. The existence and relevance of G4s was controversial as discussed in the past. However, accumulating data was published that supported the model that G4s form in living cells and importantly support biological processes. G4 formation and unfolding is tightly regulated in vivo. If G4s persist in the cell, they can lead to cellular defects such as genome instability. To avoid G4 accumulation in cells, and by this prevent cellular defect, cells has evolved a variety of proteins, mostly helicases, that efficiently unfold G4 DNA and RNA structures. Here, we describe a detailed protocol to monitor G4 structure unfolding by helicases.
Topics: DNA; DNA Helicases; G-Quadruplexes; Guanine; Nucleic Acid Conformation; RNA
PubMed: 35934478
DOI: 10.1016/bs.mie.2022.03.034