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. Stabilization of g quadruplex dna structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. Gquadruplex recognition and isolation with small molecules. Deoxyguanosine can switch dna gquadruplex topologies. Based on our previous results, ckit2 g quadruplex dna representing a parallel structure. Since gquadruplex structures can adopt various topologies, attaining specific stabilization of a gquadruplex topology to halt a particular biological process is daunting. Methods and protocols, experts in the field present a collection of detailed techniques for studying gquartet formation, dynamics, and molecular recognition. 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.
Using 2d roesy nmr spectra a new sequential walk was established for. Probing gquadruplex topologies and recognition concurrently in. Here we present the use of g quadruplex prediction algorithm to identify putative g quadruplex forming and conserved elements in li genome. 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. The folding principle of form 3 indicates that the overall g.
Gquadruplexes are higherorder dna and rna structures formed from grich sequences that are built around tetrads of hydrogenbonded. Nov 25, 2015 application of in situ click chemistry to identify fluorescent probe for specific g quadruplex topology. Unimolecular antiparallel gquadruplex folding topology of 2. Gquadruplexes is largely dictated by the loop length, and it is kn. Gquadruplex templates with an antiparallel topology were found to produce ag ncs with stronger fluorescence compared with parallel and hybrid configurations.
Highly specific and tightbinding nucleic acid aptamers have been selected against a variety of molecular targets for over 20 years. Like its first version, grsdb, it contains information on composition and distribution of putative quadruplex forming g rich sequences qgrs mapped in the. Gquadruplex prediction in li genome reveals a conserved. Stabilization of gquadruplex dna structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. Gquadruplex is a dna secondary structure that has been shown to play an important role in biological systems. In recent years, the mammalian telomeric grich repeats have been shown to form gquadruplex g4 structures, which are crucial for modulating telomere functions. G quadruplexes, a noncannonical nucleic acid topology with little established biological role, is rarely considered for conserved regulatory element discovery. Effect of gtract length on the topology and stability of.
Recent studies on tba and variants suggest that they can be used for biosensing. Gquadruplex dna structures are highly polymorphic and can be subgrouped into various families. Pdf gquadruplexes are higherorder dna and rna structures formed from g rich sequences that are built around tetrads of hydrogenbonded guanine. Pdf dna and rna gquadruplexes are nonb, fourstranded nucleic acid structures, which can selfassemble from guaninerich sequences in vitro. Grsdb2 is a second generation database of g quadruplexes. A folding topology of the baskettype intramolecular gquadruplex formed by. Effects of gquadruplex topology on electronic transfer integrals. Characterization of pyridostatin and its interactions with c. I definitely recommend this book, which can be considered an outstanding source of information that addresses several problems in the investigation of gquadruplex structures. Therefore, the development of smallmolecule gquadruplex probes has attracted signi. On characterizing the interactions between proteins and. Structure and function of multimeric gquadruplexes mdpi. Encoding canonical dna quadruplex structure science advances.
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. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding. Major groove gcgcquartets are characterized by alternating narrow and wide grooves. Among these putative gquadruplexforming sequences, gquadruplex formation was verified for 10 randomly. Topology of a g quadruplex dna formed by c9orf72 hexanucleotide repeats associated with als and ftd. The effect of loop length on gquadruplex topology andor stability has been studied by many authors 34, 35, 3739, 5861 under different conditions. Pdf a topological classification of gquadruplex structures. Gquadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. A comprehensive evaluation of a typical plant telomeric g. However, the absence of a suitable model and multitude of predicted physical. Tanner department of biochemistry, university of hong kong, pokfulam, hong kong, china abstract. In the stem, a guanine from each of the four guanine tracts gtracts engages in. For example, the topology of the gquadruplex structure can be determined.
New fluorescent lightup quinoxalines differentiate. 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. Based on the scaffold of this family, an affinity probe was developed, which can mediate the isolation. The book gquadruplex dna provides an excellent collection of important methods for the study of the dna gquadruplex structures. Among these putative g quadruplex forming sequences, g quadruplex formation was verified for 10 randomly selected sequences.
Nov, 2015 they exhibited diverse g quadruplex folds in potassium ions. Since g quadruplex structures can adopt various topologies, attaining specific stabilization of a g quadruplex topology to halt a particular biological process is daunting. 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. Topology of a gquadruplex dna formed by c9orf72 hexanucleotide repeats associated with als and ftd. G quadruplex is a dna secondary structure that has been shown to play an important role in biological systems. Gc ends control topology of dna gquadruplexes and their. They exhibited diverse gquadruplex folds in potassium ions. A fluorescencebased gquadruplex dna cleavage assay. 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 may be assumed that different groove dimensions of 3. Hydroxyl groups in cosolutes regulate the gquadruplex.
Gquadruplex structures can be computationally predicted from dna or rna sequence motifs, but their actual structures can be quite varied within and between the motifs, which can number over 100,000 per genome. Dna gquadruplexes are dna secondary structures formed in specific grich. In a previous study, we identified 1998 gquadruplexforming sequences using a mouse cpg islands dna microarray with a fluorescentlabeled gquadruplex ligand. Folding and misfolding pathways of gquadruplex dna pdf. Mar 19, 2018 g quadruplex templates with an antiparallel topology were found to produce ag ncs with stronger fluorescence compared with parallel and hybrid configurations. 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. Many of these structures are highly thermally stable, especially in the presence of monovalent cations, such as those found under physiological conditions. 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. 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. G quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Pdf design of a gquadruplex topology through glycosidic. Click the analyze button after entering a valid nucleotide sequence for qgrs mapper to search for qgrs subsequences. A parallel gquadruplex, all four strands have the same direction.
However, the detailed mechanism of g quadruplexes topologies formed by telomeric sequences requires further investigation. Written in the highly successful methods in molecular biology series format, chapters include brief introductions to their respective topics, lists of the. A toolbox for predicting gquadruplex formation and stability. Search and analyze transcribed regions of genes for putative qgrs quadruplex forming grich sequences near rna. The main challenge in dna quadruplex design is to encode a threedimensional structure into the primary sequence, despite its multiple, repetitive guanine segments. Although knowledge on existing topologies of the dna and rna gquadru plexes has been growing constantly, a recent analysis by. Short sequences, consisting of only a single contiguous run of three or more guanine bases, require four individual strands to form a quadruplex. Effects of gquadruplex topology on electronic transfer. Based on circular dichroism spectra we observed that all. Not all studies however address the formation of intramolecular gquadruplexes. This work outlines a new roadmap for implementation of targeted design of. 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.
Gquadruplex g4 is one of the higherorder structures occurring in guaninerich sequences of nucleic acids, and plays critical roles in biological processes. Sequence, stability, structure of gquadruplexes and their drug. G4 structures with only two stacks of guanines are possible but have low stability. In several cases, native dna structures that usually adopt an antiparallel topology were converted to more thermally stable gquadruplexes of parallel topology. The g quadruplex resource site serves as a portal to our suite of software programs and databases for analysis of g quadruplexes. Furthermore, we determined the topology of a g quadruplex formed by dg4c2 4. This implies that amino acid forms of the gquadruplex may have important consequences for protein homeostasis and the diseases caused by their alterations thereof.
Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. Available structural data show a great conformational diversity of unimolecular g quadruplexes, including the number of gtetrads, folding topologies and loop. 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. G quadruplex g4 is one of the higherorder structures occurring in guaninerich sequences of nucleic acids, and plays critical roles in biological processes. Characterization of pyridostatin and its interactions with. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural.
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. In a previous study, we identified 1998 g quadruplex forming sequences using a mouse cpg islands dna microarray with a fluorescentlabeled g quadruplex ligand. There are many structures that can be adopted by nucleic acids other than the watson. 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. Specific stabilization of cmyc and ckit gquadruplex dna. A sequenceindependent analysis of the loop length dependence of intramolecular rna gquadruplex stability and topology. Thus far the discovery of novel dna quadruplex topologies was either serendipitous or through coincidental emergence. To date, various gquadruplex structures have been reported in human telomeric sequences.
Stable dna secondary structures that can form from motifs containing tracts of tandem guanines. Gquadruplex is a quadruple helical form of nucleic acids that can appear in guaninerich parts of the genome. The length of the nucleic acid sequences involved in tetrad formation determines how the quadruplex folds. Their activities in basic genetic processes are an active area of research in telomere, gene regulation, and functional genomics research. How gquadruplex topology and loop sequences affect.
Singlemolecule investigation of gquadruplex folds of the. Design of a g quadruplex topology through glycosidic bond angles. Design of a gquadruplex topology through glycosidic bond angles. The basic unit is the g tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. We identify and detail structural elements describing all 14 feasible canonical quadruplex scaffolds and demonstrate their use in control of design.
Furthermore, we determined the topology of a gquadruplex formed by dg4c2 4. To achieve this, we have designed and synthesized simple structural scaffolds. 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. Here we present the use of gquadruplex prediction algorithm to identify putative gquadruplexforming and conserved elements in li genome. A fluorescencebased g quadruplex dna cleavage assay. The g4forming sequences can generate three kinds of topologies, i. Gquadruplexes, a noncannonical nucleic acid topology with little established biological role, is rarely considered for conserved regulatory element discovery. Here we demonstrate gquadruplex formation by oligodeoxynucleotides containing.
Understanding of their physiological roles is expanding rapidly, and they have been implicated in. Surprisingly, even though plant telomeres are essential for plant growth, development, and environmental adaptions, only few reports exist on plant telomeric g4 dna ptg4. Molecular models for intrastrand dna gquadruplexes bmc. The basic unit is the gtetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Pdf gquadruplexes are higherorder dna and rna structures formed from grich sequences that are built around tetrads of hydrogenbonded guanine. A sequenceindependent analysis of the loop length dependence of intramolecular rna g quadruplex stability and topology. 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. Telomeric dna sequences can form fourstranded quadruplex structures, which may be involved in the structure of telomere ends. How gquadruplex topology and loop sequences affect optical. Human telomeric repeats can form many topological structures depending on conditions and on base modification. Specifically, the topologies for all feasible canonical quadruplexes are described, and. Pdf designing gquadruplex topologies by focusing on sequence. G quadruplex is a quadruple helical form of nucleic acids that can appear in guaninerich parts of the genome.
783 1217 784 682 1385 1600 455 862 1333 1265 1575 1023 677 438 160 660 1204 218 920 1435 1087 1413 650 789 713 207 621 1169 1116 93 393 479 1245 626 1386 1303