Here we demonstrate gquadruplex formation by oligodeoxynucleotides containing. To date, various gquadruplex structures have been reported in human telomeric sequences. I definitely recommend this book, which can be considered an outstanding source of information that addresses several problems in the investigation of gquadruplex structures. Unimolecular antiparallel gquadruplex folding topology of 2. Furthermore, we determined the topology of a g quadruplex formed by dg4c2 4. Although knowledge on existing topologies of the dna and rna gquadru plexes has been growing constantly, a recent analysis by. Human telomeric repeats can form many topological structures depending on conditions and on base modification. Among them, the most promising one could light up parallel g4s at two separate excitation wavelengths, exhibiting dualchannel emission, and light up nonparallel g4s at.
A sequenceindependent analysis of the loop length dependence of intramolecular rna gquadruplex stability and topology. First, we monitored the gquadruplex topology by circular dichroism cd spectroscopy. Gquadruplexes can form in protein coding and noncoding segments such as the untranslated regions and introns of the mrna transcript of several genes. Gquadruplexes, a noncannonical nucleic acid topology with little established biological role, is rarely considered for conserved regulatory element discovery. Telomeric dna sequences can form fourstranded quadruplex structures, which may be involved in the structure of telomere ends. A sequenceindependent analysis of the loop length dependence of intramolecular rna g quadruplex stability and topology. This work outlines a new roadmap for implementation of targeted design of. For example, the topology of the gquadruplex structure can be determined. G quadruplex is a dna secondary structure that has been shown to play an important role in biological systems. Thus far the discovery of novel dna quadruplex topologies was either serendipitous or through coincidental emergence. The g4forming sequences can generate three kinds of topologies, i. The folding principle of form 3 indicates that the overall g. Written in the highly successful methods in molecular biology series format, chapters include brief introductions to their respective topics, lists of the. Recent studies on tba and variants suggest that they can be used for biosensing.
A fluorescencebased gquadruplex dna cleavage assay. Characterization of pyridostatin and its interactions with c. Molecular models for intrastrand dna gquadruplexes bmc. The crystal structure of tba revealed that the dna g quadruplex is in antiparallel topology with twoquartet planes 10, and data suggested that the presence of thrombin induces the tba to fold into a g quadruplex conformation for binding 11. Since g quadruplex structures can adopt various topologies, attaining specific stabilization of a g quadruplex topology to halt a particular biological process is daunting. Sequence, stability, structure of gquadruplexes and their drug.
The crystal structure of tba revealed that the dna gquadruplex is in antiparallel topology with twoquartet planes 10, and data suggested that the presence of thrombin induces the tba to fold into a gquadruplex conformation for binding 11. Effect of gtract length on the topology and stability of. Gquadruplex is a dna secondary structure that has been shown to play an important role in biological systems. G4 structures with only two stacks of guanines are possible but have low stability. Probing gquadruplex topologies and recognition concurrently in. Like its first version, grsdb, it contains information on composition and distribution of putative quadruplex forming g rich sequences qgrs mapped in the. However, the detailed mechanism of g quadruplexes topologies formed by telomeric sequences requires further investigation. However, the absence of a suitable model and multitude of predicted physical.
G quadruplex is a quadruple helical form of nucleic acids that can appear in guaninerich parts of the genome. Major groove gcgcquartets are characterized by alternating narrow and wide grooves. Gquadruplex recognition and isolation with small molecules. Gquadruplexes is largely dictated by the loop length, and it is kn. Telomeric g quadruplex topology has the ability to regulate telomerase activity, which counteracts the shortening of telomere with successive cell divisions, thereby causing genomic longevity. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding. We identify and detail structural elements describing all 14 feasible canonical quadruplex scaffolds and demonstrate their use in control of design. Highly specific and tightbinding nucleic acid aptamers have been selected against a variety of molecular targets for over 20 years. The main challenge in dna quadruplex design is to encode a threedimensional structure into the primary sequence, despite its multiple, repetitive guanine segments. A comprehensive evaluation of a typical plant telomeric g. In a previous study, we identified 1998 gquadruplexforming sequences using a mouse cpg islands dna microarray with a fluorescentlabeled gquadruplex ligand. Gquadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. G quadruplexes, a noncannonical nucleic acid topology with little established biological role, is rarely considered for conserved regulatory element discovery.
Understanding of their physiological roles is expanding rapidly, and they have been implicated in. A toolbox for predicting gquadruplex formation and stability. Surprisingly, even though plant telomeres are essential for plant growth, development, and environmental adaptions, only few reports exist on plant telomeric g4 dna ptg4. Deoxyguanosine can switch dna gquadruplex topologies. In several cases, native dna structures that usually adopt an antiparallel topology were converted to more thermally stable gquadruplexes of parallel topology. Gquadruplex dna structures are highly polymorphic and can be subgrouped into various families. Pdf gquadruplexes are higherorder dna and rna structures formed from grich sequences that are built around tetrads of hydrogenbonded guanine. Based on the scaffold of this family, an affinity probe was developed, which can mediate the isolation of its nucleic acid targets from human cells.
Structure and function of multimeric gquadruplexes mdpi. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. This implies that amino acid forms of the gquadruplex may have important consequences for protein homeostasis and the diseases caused by their alterations thereof. Stabilization of gquadruplex dna structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. Therefore, the development of smallmolecule gquadruplex probes has attracted signi. Stabilization of g quadruplex dna structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. How gquadruplex topology and loop sequences affect. Not all studies however address the formation of intramolecular gquadruplexes. The g quadruplex resource site serves as a portal to our suite of software programs and databases for analysis of g quadruplexes. Formation of these structures in either genomic dna or cellular rna has the potential to affect cell biology in many facets including telomere maintenance. It favors a monomeric fold and forms a chairtype g quadruplex with a fourlayer antiparallel g tetra core and three edgewise loops, which is distinct from known structures of chairtype g quadruplexes. In recent years, the mammalian telomeric grich repeats have been shown to form gquadruplex g4 structures, which are crucial for modulating telomere functions. Methods and protocols, experts in the field present a collection of detailed techniques for studying gquartet formation, dynamics, and molecular recognition.
Singlemolecule investigation of gquadruplex folds of the. There are many structures that can be adopted by nucleic acids other than the watson. Gquadruplex prediction in li genome reveals a conserved. Pdf dna and rna gquadruplexes are nonb, fourstranded nucleic acid structures, which can selfassemble from guaninerich sequences in vitro. Encoding canonical dna quadruplex structure science advances. The cd spectra of tet in the absence of cosolute showed a positive peak at 295 nm and a small shoulder at 265 nm, indicating the formation of hybrid type gquadruplexes. How gquadruplex topology and loop sequences affect optical. It favors a monomeric fold and forms a chairtype gquadruplex with a fourlayer antiparallel gtetra core and three edgewise loops, which is distinct from known structures of chairtype gquadruplexes. Characterization of pyridostatin and its interactions with. Now a deductive system, based on the glycosidic bond angle of guanosines, can be used to derive a set of inference rules for the prediction of both known and theoretical quadruplex topologies. Pdf gquadruplexes are higherorder dna and rna structures formed from g rich sequences that are built around tetrads of hydrogenbonded guanine. Since gquadruplex structures can adopt various topologies, attaining specific stabilization of a gquadruplex topology to halt a particular biological process is daunting. Short sequences, consisting of only a single contiguous run of three or more guanine bases, require four individual strands to form a quadruplex.
Stable dna secondary structures that can form from motifs containing tracts of tandem guanines. The length of the nucleic acid sequences involved in tetrad formation determines how the quadruplex folds. Guanine quadruplexes g4s are fourstranded secondary structures of nucleic acids which are stabilized by noncanonical hydrogen bonding systems between the nitrogenous bases as well as extensive base stacking, or pipi, interactions. The book gquadruplex dna provides an excellent collection of important methods for the study of the dna gquadruplex structures. Topology of a gquadruplex dna formed by c9orf72 hexanucleotide repeats associated with als and ftd. Nov 25, 2015 application of in situ click chemistry to identify fluorescent probe for specific g quadruplex topology. Loop bases adjacent to gtetrads have a more significant impact on the fluorescence of ag ncs compared with those in the middle of the loop, with adenine largely exhibiting an.
Gquadruplexes provide a fascinating case in which the cation and physical context play critical roles in defining the overall structural topology as well as the stability. Loop bases adjacent to g tetrads have a more significant impact on the fluorescence of ag ncs compared with those in the middle of the loop, with adenine largely exhibiting an. Many of these structures are highly thermally stable, especially in the presence of monovalent cations, such as those found under physiological conditions. The further development of another family of g quadruplex interacting small molecules is also presented in this thesis and some of their effects in cellulo were assessed.
Furthermore, we determined the topology of a gquadruplex formed by dg4c2 4. A parallel gquadruplex, all four strands have the same direction. They exhibited diverse gquadruplex folds in potassium ions. Folding and misfolding pathways of gquadruplex dna pdf. Using 2d roesy nmr spectra a new sequential walk was established for.
Specifically, the topologies for all feasible canonical quadruplexes are described, and. Design of a gquadruplex topology through glycosidic bond angles. Pdf a topological classification of gquadruplex structures. Among these putative gquadruplexforming sequences, gquadruplex formation was verified for 10 randomly. Gquadruplexes are higherorder dna and rna structures formed from grich sequences that are built around tetrads of hydrogenbonded. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural. Gquadruplexes are four stranded nucleic acid structures formed around a core of guanines, arranged in squares with mutual hydrogen bonding. New fluorescent lightup quinoxalines differentiate. Specific stabilization of cmyc and ckit gquadruplex dna. Based on our previous results, ckit2 g quadruplex dna representing a parallel structure. Based on the scaffold of this family, an affinity probe was developed, which can mediate the isolation. Effects of gquadruplex topology on electronic transfer. In a previous study, we identified 1998 g quadruplex forming sequences using a mouse cpg islands dna microarray with a fluorescentlabeled g quadruplex ligand.
Gquadruplex g4 is one of the higherorder structures occurring in guaninerich sequences of nucleic acids, and plays critical roles in biological processes. However gquadruplexes, a noncanonical nucleic acid topology with little established biological role, is rarely considered for conserved regulatory element discovery. Here we present the use of g quadruplex prediction algorithm to identify putative g quadruplex forming and conserved elements in li genome. Search and analyze transcribed regions of genes for putative qgrs quadruplex forming grich sequences near rna. On characterizing the interactions between proteins and. To achieve this, we have designed and synthesized simple structural scaffolds. Pdf designing gquadruplex topologies by focusing on sequence. Tanner department of biochemistry, university of hong kong, pokfulam, hong kong, china abstract. A fluorescencebased g quadruplex dna cleavage assay. Topology of a g quadruplex dna formed by c9orf72 hexanucleotide repeats associated with als and ftd. Based on circular dichroism spectra we observed that all. A folding topology of the baskettype intramolecular gquadruplex formed by. Design of a g quadruplex topology through glycosidic bond angles.
G quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Gquadruplex templates with an antiparallel topology were found to produce ag ncs with stronger fluorescence compared with parallel and hybrid configurations. Effects of gquadruplex topology on electronic transfer integrals. G quadruplex g4 is one of the higherorder structures occurring in guaninerich sequences of nucleic acids, and plays critical roles in biological processes. It may be assumed that different groove dimensions of 3. The further development of another family of gquadruplex interacting small molecules is also presented in this thesis and some of their effects in cellulo were assessed. Application of in situ click chemistry to identify fluorescent probe for specific gquadruplex topology. Nov, 2015 they exhibited diverse g quadruplex folds in potassium ions. Pdf design of a gquadruplex topology through glycosidic. Among these putative g quadruplex forming sequences, g quadruplex formation was verified for 10 randomly selected sequences.
Hydroxyl groups in cosolutes regulate the gquadruplex. G quadruplexes are four stranded nucleic acid structures formed around a core of guanines, arranged in squares with mutual hydrogen bonding. Gquadruplex is a quadruple helical form of nucleic acids that can appear in guaninerich parts of the genome. Their activities in basic genetic processes are an active area of research in telomere, gene regulation, and functional genomics research. Click the analyze button after entering a valid nucleotide sequence for qgrs mapper to search for qgrs subsequences. Gc ends control topology of dna gquadruplexes and their. In the stem, a guanine from each of the four guanine tracts gtracts engages in. The basic unit is the g tetrad, a planar assembly of four guanines connected by eight hydrogen bonds.
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