RNA quadruplex

R658 M. Katahira, Structure of Telomere-Sequence DNA/RNA-Binding Protein, hnRNP DO, and Transformation of DNA/RNA Quadruplex to a Single Strand by hnRNP DO , Seibutsu Butsuri, 2000,40, 326... 

Figure 3 Tetramolecular quadruplex dissociation, (a) Example of an irreversible melting curve (TG4T) in 0.11 M Na recorded at 245 nm with a temperature gradient of 0.2°C min Directions of temperature changes are indicated by arrows. The small difference observed at high temperature between the heating and cooling profiles results from a partial evaporation of the sample, (b) Arrhenius representation of the dissociation rate (In (k ff) shown on the left Y-scale) and lifetime (right Y-scale) of the TG4T (DNA) and IIG4U (RNA) quadruplexes in 0.11 M Na" (ref 27)...

We have summarized various time constants collected during this study (Figure 8) and the impact of a number of parameters on the kinetics of association and dissociation of these complexes (Table 2). This might be helpful for a variety of applications. Finally, one should emphasize the extraordinary stability of RNA quadruplexes, coupled with their relatively fast kinetics of association. 

B. Pan, K. Shi and M. Sundaralingam, Base-tetrad swapping results in dimerization of RNA quadruplexes Implications for formation of the i-motif RNA octaplex, Proc. Natl. Acad. Sci. USA, 2006, 103, 3130-3134. 

One possible explanation is the simple observation that the G-rich codons do not code for the same amino acids as C-rich codons, but modelling based on codon frequencies shows that the predicted discrimination from this alone is not sufficient to account for the observation. An alternative explanation is based on the observation that the G-patterns would lead to potential quadruplexes in the mRNA strand in addition to the DNA duplex, whereas C-patterns could only lead to quadruplexes in the (complementary strand of) DNA. This evidence is consistent with an evolutionary pressure to reduce the number of quadruplexes allowed to form in mRNA. This may be particularly strong as it seems that RNA quadruplexes are more stable, both thermodynamically and kinetically, than their DNA counterparts. To date, there has been relatively little work focused on RNA quadruplexes, although it has evoked some interest. However these results suggest that RNA quadruplexes could play a significant physiological role, and should be investigated further. 

Abstract Protoberberine alkaloids and related compounds represent an important class of molecules and have attracted recent attention for their various pharmacological activities. This chapter deals with the physicochemical properties of several isoquinoline alkaloids (berberine, palmatine and coralyne) and many of their derivatives under various environmental conditions. The interaction of these compounds with polymorphic DNA structures (B-form, Z-form, H -form, protonated form, triple helical form and quadruplex form) and polymorphic RNA structures (A-form, protonated form, triple helical form and quadruplex form) reported by several research groups, employing various analytical techniques such as spectrophotometry, spectrofluorimetry, circular dichro-ism, NMR spectroscopy, viscometry as well as molecular modelling and thermodynamic analysis to elucidate their mode and mechanism of action for structure-activity relationships, are also presented. 

It is worth to mention that this definition is not always consistent with the nature of the macromolecular assembly when applying to nucleic acids. For example, from all different types of quadruplex nucleic acids only quadruplex monomers are covered by lUPAC definition of tertiary structure being a single chain of DNA or RNA. However, also the quadruplexes with higher molecularity of the formed structures (dimers, tetramers) belong to this important tertiary structure family. 

Patel DJ, Phan AT, Ruryavyi V (2007) Hiunan telomere, oncogenic promoter and 5 -UTR G-quadruplexes diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 35 7429-7455. Epub 2 Oct 2007. 

Kumari S, Bugaut A, Huppert JL et al (2007) An RNA G-quadruplex in the 5 UTR of the NRAS proto-oncogene modulates translation. Nat Chem Biol 4 218-221. Epub 25 Feb 2007. 

Keywords DNA G-quadruplex Nucleic acid recognition Resin-bound DCC RNA Transition metal complex... 

Considered together, these four studies ably demonstrate the ability of DCC to rapidly yield lead structures for interesting targets. Despite the relatively small size of the libraries examined in each case, the diversity of structures accessible by the methodology is remarkable. G-quadruplex RNA has also been described [17], and therefore it is likely that future discovery efforts will also expand to targeting these sequences. Finally, as we will discuss later, G-quartets have served as scaffolds for the generation of novel materials via dynamic methods. 

Morris MJ, Negishi Y, Pazsint C, Schonhoft JD, Basu S (2010) An RNA G-quadruplex is essential for cap-independent translation initiation in human VEGF IRES. J Am Chem Soc 132 17831-17839... 

Marin VL, Armitage BA. RNA guanine quadruplex invasion by complementary and homologous PNA probes. J. Am. Chem. Soc. 2005 127 8032-8033. 

A number of oligonucleotide hairpin, quadruplexes and other higher ordered tertiary structures have also been reported the solution structure of the transcriptional antiterminator LicT from Bacillus subtilis bound to a 29 bp ribonucleic antiterminator RNA hairpin " a crystal structure of a kissing complex of the HIV-1 RNA dimerisation initiation site " the crystal structure of the Za high affinity-binding domain of the RNA editing enzyme ADARl bound to left-handed Z-DNA " the crystal structure of parallel quadruplexes from human telomeric DNA. " ... 

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