101
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Monchaud D, Yang P, Lacroix L, Teulade-Fichou MP, Mergny JL. A Metal-Mediated Conformational Switch Controls G-Quadruplex Binding Affinity. Angew Chem Int Ed Engl 2008; 47:4858-61. [DOI: 10.1002/anie.200800468] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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102
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Wilcox JM, Rempel DL, Gross ML. Method of measuring oligonucleotide-metal affinities: interactions of the thrombin binding aptamer with K+ and Sr2+. Anal Chem 2008; 80:2365-71. [PMID: 18318508 DOI: 10.1021/ac701903w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new, mass spectrometry-based method for measuring affinity constants for specific metal ion binding to DNA, particularly for quadruplex DNA. This method, which is applicable to other systems, utilizes the gas-phase signal fractions, as determined by mass spectrometry, from the bound and unbound species as input into a mathematical model that determines various parameters, one of which is the binding affinity constant. The system used to develop and test the model was the thrombin-binding aptamer, an appropriate quadruplex structure that binds both K+ and Sr2+ cations. Using this method, we measured the binding constants of potassium and strontium cations with the quadruplex structure to be 5000 and 240 nM, respectively. We then applied the method to measure the change in enthalpy of the binding of strontium cations to the thrombin binding aptamer. The DeltaH for this interaction is -71 kJ/mol (-17 kcal/mol). The binding constant measurements are consistent with earlier measurements on the same system, and the measured change in enthalpy is in excellent agreement with previous work.
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Affiliation(s)
- J Micah Wilcox
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, Missouri 63130, USA
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103
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Higher-order RNA structural requirements and small-molecule induction of tombusvirus subgenomic mRNA transcription. J Virol 2008; 82:3864-71. [PMID: 18256151 DOI: 10.1128/jvi.02416-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subgenomic (sg) mRNAs are small viral messages that are synthesized by polycistronic positive-strand RNA viruses to allow for the translation of certain viral proteins. Tombusviruses synthesize two such sg mRNAs via a premature termination mechanism. This transcriptional process involves the viral RNA-dependent RNA polymerase terminating minus-strand RNA synthesis prematurely at internal RNA signals during copying of the viral genome. The 3'-truncated minus-strand RNAs generated by the termination events then serve as templates for sg mRNA transcription. A higher-order RNA structure in the viral genome, located just upstream from the termination site, is a critical component of the RNA-based polymerase attenuation signal. Here, we have analyzed the role of this RNA structure in mediating efficient sg mRNA2 transcription. Our results include the following: (i) we define the minimum overall thermodynamic stability required for an operational higher-order RNA attenuation structure; (ii) we show that the distribution of stability within an attenuation structure affects its function; (iii) we establish that an RNA quadruplex structure can act as an effective attenuation structure; (iv) we prove that the higher-order RNA structure forms and functions in the plus strand; (v) we provide evidence that a specific attenuation structure-binding protein factor is not required for transcription; (vi) we demonstrate that sg mRNA transcription can be controlled artificially through small-molecule activation using RNA aptamer technology. These findings provide important new insights into the premature termination mechanism and present a novel approach to regulate the transcriptional process.
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104
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Abstract
Melting curves are commonly used to determine the stability of folded nucleic acid structures and their interaction with ligands. This paper describes how the technique can be applied to study the properties of four-stranded nucleic acid structures that are formed by G-rich oligonucleotides. Changes in the absorbance (at 295nm), circular dichroism (at 260 or 295nm) or fluorescence of appropriately labelled oligonucleotides, can be used to measure the stability and kinetics of folding. This paper focuses on a fluorescence melting technique, and explains how this can be used to determine the T(m) (T((1/2))) of intramolecular quadruplexes and the effects of quadruplex-binding ligands. Quantitative analysis of these melting curves can be used to determine the thermodynamic (DeltaH, DeltaG, and DeltaS) and kinetic (k(1), k(-1)) parameters. The method can also be adapted to investigate the equilibrium between quadruplex and duplex DNA and to explore the selectivity of ligands for one or other structure.
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105
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Eddy J, Maizels N. Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res 2008; 36:1321-33. [PMID: 18187510 PMCID: PMC2275096 DOI: 10.1093/nar/gkm1138] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are G-rich, but the downstream region displays a clear bias toward G-richness on the nontemplate strand. Upstream of the TSS, much of the G-richness and potential for G-quadruplex formation derives from the presence of well-defined canonical regulatory motifs in duplex DNA, including CpG dinucleotides which are sites of regulatory methylation, and motifs recognized by the transcription factor SP1. This challenges the notion that quadruplex formation upstream of the TSS contributes to regulation of gene expression. Downstream of the TSS, G-richness is concentrated in the first intron, and on the nontemplate strand, where polymorphic sequence elements with potential to form G-quadruplex structures and which cannot be accounted for by known regulatory motifs are found in almost 3000 (16%) of the human RefSeq genes, and are conserved through frogs. These elements could in principle be recognized either as DNA or as RNA, providing structural targets for regulation at the level of transcription or RNA processing.
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Affiliation(s)
- Johanna Eddy
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195-7650, USA
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106
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Bugaut A, Balasubramanian S. A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry 2007; 47:689-97. [PMID: 18092816 DOI: 10.1021/bi701873c] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
G-Rich sequences found within biologically important regions of the genome have been shown to form intramolecular G-quadruplexes with varied loop lengths and sequences. Many of these quadruplexes will be distinguishable from each other on the basis of their thermodynamic stabilities and folded conformations. It has been proposed that loop lengths can strongly influence the topology and stability of intramolecular G-quadruplexes. Previous studies have been limited to the analysis of quadruplex sequences with particular loop sequences, making it difficult to make generalizations. Here, we describe an original study that aimed to elucidate the effect of loop length on the biophysical properties of G-quadruplexes in a sequence-independent context. We employed UV melting and circular dichroism spectroscopy to examine and compare the properties of 21 DNA quadruplex libraries, each comprising partially randomized loop sequences with lengths ranging from one to three nucleotides. Our work supports a number of general predictions that can be made solely on the basis of loop lengths. In particular, the results emphasize the strong influence of single-nucleotide loops on quadruplex properties. This study provides a predictive framework that may help identify or classify biologically relevant G-quadruplex-forming sequences.
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Affiliation(s)
- Anthony Bugaut
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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107
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108
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Patel DJ, Phan AT, Kuryavyi V. Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res 2007; 35:7429-55. [PMID: 17913750 PMCID: PMC2190718 DOI: 10.1093/nar/gkm711] [Citation(s) in RCA: 729] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Guanine-rich DNA sequences can form G-quadruplexes stabilized by stacked G–G–G–G tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent solution NMR-based G-quadruplex structures formed by the four-repeat human telomere in K+ solution and the guanine-rich strands of c-myc, c-kit and variant bcl-2 oncogenic promoters, as well as a bimolecular G-quadruplex that targets HIV-1 integrase. Such structure determinations have helped to identify unanticipated scaffolds such as interlocked G-quadruplexes, as well as novel topologies represented by double-chain-reversal and V-shaped loops, triads, mixed tetrads, adenine-mediated pentads and hexads and snap-back G-tetrad alignments. The review also highlights the recent identification of guanine-rich sequences positioned adjacent to translation start sites in 5′-untranslated regions (5′-UTRs) of RNA oncogenic sequences. The activity of the enzyme telomerase, which maintains telomere length, can be negatively regulated through G-quadruplex formation at telomeric ends. The review evaluates progress related to ongoing efforts to identify small molecule drugs that bind and stabilize distinct G-quadruplex scaffolds associated with telomeric and oncogenic sequences, and outlines progress towards identifying recognition principles based on several X-ray-based structures of ligand–G-quadruplex complexes.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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109
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Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR. Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 2007; 35:4214-22. [PMID: 17576685 PMCID: PMC1919480 DOI: 10.1093/nar/gkm316] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.
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Affiliation(s)
- Phillip A. Rachwal
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - I. Stuart Findlow
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Joern M. Werner
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- *To whom correspondence should be addressed. +44 23 8059 4374+44 23 8059 4459
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