Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Curtis, Edward A.; Liu, David Ruchien

doi:10.1016/j.chembiol.2013.02.015

Cited by 36 publications

(67 citation statements)

References 52 publications

(66 reference statements)

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“…A second requirement was that this construct could bind GTP and promote peroxidase reactions efficiently. A previously characterized sequence with sets of guanosines of the correct size appeared to be a promising candidate (Figure 2B) (17). This sequence binds GTP 700-fold better than a random sequence control oligonucleotide of the same length (17).…”

Section: Resultsmentioning

confidence: 94%

“…In the work described here we have identified some of these mutations for G-quadruplexes that bind guanosine 5′-triphosphate (GTP) and promote peroxidase reactions. To do this, the central tetrad in a reference G-quadruplex was mutated and each of the 256 possible sequence variants was tested for the ability to bind GTP (17) and to promote a model peroxidase reaction in the presence of hemin and hydrogen peroxide (19). The ability of the most active of these variants to form G-quadruplex structures was also investigated using circular dichroism spectroscopy (41–42).…”

Section: Introductionmentioning

confidence: 99%

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Altered biochemical specificity of G-quadruplexes with mutated tetrads

et al. 2016

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A fundamental motif in canonical nucleic acid structure is the base pair. Mutations that disrupt base pairs are typically destabilizing, but stability can often be restored by a second mutation that replaces the original base pair with an isosteric variant. Such concerted changes are a way to identify helical regions in secondary structures and to identify new functional motifs in sequenced genomes. In principle, such analysis can be extended to non-canonical nucleic acid structures, but this approach has not been utilized because the sequence requirements of such structures are not well understood. Here we investigate the sequence requirements of a G-quadruplex that can both bind GTP and promote peroxidase reactions. Characterization of all 256 variants of the central tetrad in this structure indicates that certain mutations can compensate for canonical G-G-G-G tetrads in the context of both GTP-binding and peroxidase activity. Furthermore, the sequence requirements of these two motifs are significantly different, indicating that tetrad sequence plays a role in determining the biochemical specificity of G-quadruplex activity. Our results provide insight into the sequence requirements of G-quadruplexes, and should facilitate the analysis of such motifs in sequenced genomes.

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Section: Resultsmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Altered biochemical specificity of G-quadruplexes with mutated tetrads

et al. 2016

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“…The fundamental role played by GTP in cells, as well as the emerging realization that the functions of biological proteins and RNAs may not be as distinct as once thought, led us to hypothesize that RNA molecules that bind GTP might also be widespread in nature. To test this hypothesis, we used in vitro selection to search a pool of phylogenetically diverse genome-derived RNA fragments for new examples of naturally occurring GTP aptamers 4 . This study revealed that such aptamers are abundant, especially in the genomes of eukaryotes.…”

Section: Introductionmentioning

confidence: 99%

A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats

Curtis

Liu

2014

RNA Biology

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Recently, we used in vitro selection to identify a new class of naturally occurring GTP aptamer called the G motif. Here we report the discovery and characterization of a second class of naturally occurring GTP aptamer, the “CA motif.” The primary sequence of this aptamer is unusual in that it consists entirely of tandem repeats of CA-rich motifs as short as three nucleotides. Several active variants of the CA motif aptamer lack the ability to form consecutive Watson-Crick base pairs in any register, while others consist of repeats containing only cytidine and adenosine residues, indicating that noncanonical interactions play important roles in its structure. The circular dichroism spectrum of the CA motif aptamer is distinct from that of A-form RNA and other major classes of nucleic acid structures. Bioinformatic searches indicate that the CA motif is absent from most archaeal and bacterial genomes, but occurs in at least 70 percent of approximately 400 eukaryotic genomes examined. These searches also uncovered several phylogenetically conserved examples of the CA motif in rodent (mouse and rat) genomes. Together, these results reveal the existence of a second class of naturally occurring GTP aptamer whose sequence requirements, like that of the G motif, are not consistent with those of a canonical secondary structure. They also indicate a new and unexpected potential biochemical activity of certain naturally occurring tandem repeats.

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“…More recently, modifications to the in vitro selection procedure have aimed to identify naturally occurring aptamers and other functional nucleic acids by using genome-derived DNA pools as templates for selections. In the case of adenosine, but not GTP, both synthetic and genomic DNA selections revealed a number of structurally conserved aptamer sequences (Burke & Gold, 1997;Curtis & Liu, 2013;Davis & Szostak, 2002;Sassanfar & Szostak, 1993;Vu et al, 2012). These adenosine-binding motifs are sequence-independent and represent a rare example of convergent molecular evolution spanning both genomic and synthetic sequence space.…”

Section: Methods In Enzymology Volume 549mentioning

confidence: 99%