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You searched for: Journal Methods Remove constraint Journal: Methods Publication Year 2012 Remove constraint Publication Year: 2012 Source 2012 v.57 no.1 Remove constraint Source: 2012 v.57 no.1
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1. A FRET-based screening assay for nucleic acid ligands

Author:
Renčiuk, Daniel; Zhou, Jun; Beaurepaire, Lionel; Guédin, Aurore; Bourdoncle, Anne; Mergny, Jean-Louis
Source:
Methods 2012 v.57 no.1 pp. 122-128
ISSN:
1046-2023
Subject:
DNA; RNA; fluorescence; genes; ligands; melting; melting point; oligonucleotides; patients; protein synthesis; screening; telomeres; temperature
Abstract:
... Some of the most serious diseases are characterized by the presence of a specific secondary structure within DNA or RNA, often in the promoter or the coding region of the responsible gene, that enhances or disrupts expression of the protein. Structural elements that impact cellular function may also be formed in other genomic regions such as telomeres. Compounds that interact with such structural ...
DOI:
10.1016/j.ymeth.2012.03.020

2. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes

Author:
Largy, Eric; Hamon, Florian; Teulade-Fichou, Marie-Paule
Source:
Methods 2012 v.57 no.1 pp. 129-137
ISSN:
1046-2023
Subject:
DNA; RNA; binding properties; fluorescence; gel electrophoresis; humans; microscopy; oligonucleotides; streptavidin; telomeres
Abstract:
... Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nuc ...
DOI:
10.1016/j.ymeth.2012.02.008

3. Circular dichroism and guanine quadruplexes

Author:
Vorlíčková, Michaela; Kejnovská, Iva; Sagi, Janos; Renčiuk, Daniel; Bednářová, Klára; Motlová, Jitka; Kypr, Jaroslav
Source:
Methods 2012 v.57 no.1 pp. 64-75
ISSN:
1046-2023
Subject:
DNA; RNA; X-ray diffraction; circular dichroism spectroscopy; guanine; nuclear magnetic resonance spectroscopy; thermodynamics
Abstract:
... Circular dichroism (CD) is remarkably sensitive to the conformational states of nucleic acids; therefore, CD spectroscopy has been used to study most features of DNA and RNA structures. Quadruplexes are among the significant noncanonical nucleic acids architectures that have received special attentions recently. This article presents examples on the contribution of CD spectroscopy to our knowledge ...
DOI:
10.1016/j.ymeth.2012.03.011

4. Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex forming potential

Author:
Cao, Kajia; Ryvkin, Paul; Brad Johnson, F.
Source:
Methods 2012 v.57 no.1 pp. 3-10
ISSN:
1046-2023
Subject:
DNA; DNA helicases; bioinformatics; loci; nucleotide sequences; yeasts
Abstract:
... Bioinformatic approaches to the identification of genomic sequences having G-quadruplex forming potential (QFP) has enabled important tests of the structure of these sequences in vitro and of their behavior under conditions where the formation or function of G-quadruplexes is modulated in vivo. Several similar approaches to identifying intramolecular QFP (i.e. forming among G-runs on one strand of ...
DOI:
10.1016/j.ymeth.2012.05.002
PubMed:
22652626
PubMed Central:
PMC3701776

5. Experimental approaches to identify cellular G-quadruplex structures and functions

Author:
Di Antonio, Marco; Rodriguez, Raphaël; Balasubramanian, Shankar
Source:
Methods 2012 v.57 no.1 pp. 84-92
ISSN:
1046-2023
Subject:
DNA; fluorescence; genomics; image analysis; metabolism; proteins; telomeres; translation (genetics)
Abstract:
... Guanine-rich nucleic acids can fold into non-canonical DNA secondary structures called G-quadruplexes. The formation of these structures can interfere with the biology that is crucial to sustain cellular homeostases and metabolism via mechanisms that include transcription, translation, splicing, telomere maintenance and DNA recombination. Thus, due to their implication in several biological proces ...
DOI:
10.1016/j.ymeth.2012.01.008
PubMed:
22343041
PubMed Central:
PMC3563962

6. In silico screening of quadruplex-binding ligands

Author:
Ma, Dik-Lung; Ma, Victor Pui-Yan; Chan, Daniel Shiu-Hin; Leung, Ka-Ho; Zhong, Hai-Jing; Leung, Chung-Hang
Source:
Methods 2012 v.57 no.1 pp. 106-114
ISSN:
1046-2023
Subject:
DNA; RNA; algorithms; databases; ligands; molecular models; screening
Abstract:
... Recent advances in computational processing power and molecular docking algorithms have facilitated the development of computer-aided methods for the rapid and efficient discovery of G-quadruplex-interacting molecules. In this article, we provide an introductory framework for the methodology of in silico screening for the identification of novel DNA G-quadruplex ligands from chemical libraries. We ...
DOI:
10.1016/j.ymeth.2012.02.001

7. Isothermal folding of G-quadruplexes

Author:
Gray, Robert D.; Chaires, Jonathan B.
Source:
Methods 2012 v.57 no.1 pp. 47-55
ISSN:
1046-2023
Subject:
X-ray diffraction; absorbance; denaturation; fluorescence; monitoring; nuclear magnetic resonance spectroscopy; temperature; thermodynamics; titration
Abstract:
... Thermodynamic studies of G-quadruplex stability are an essential complement to structures obtained by NMR or X-ray crystallography. An understanding of the energetics of quadruplex folding provides a necessary foundation for the physical interpretation of quadruplex formation and reactivity. While thermal denaturation methods are most commonly used to evaluate quadruplex stability, it is also poss ...
DOI:
10.1016/j.ymeth.2012.04.006
PubMed:
22525787
PubMed Central:
PMC3407330

8. Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT)

Author:
Ferreira, Rubén; Marchand, Adrien; Gabelica, Valérie
Source:
Methods 2012 v.57 no.1 pp. 56-63
ISSN:
1046-2023
Subject:
DNA; acetonitrile; ammonium acetate; electrospray ionization mass spectrometry; ethanol; gases; ionization; isomers; isopropyl alcohol; methanol; nucleotide sequences; solvents; stoichiometry; telomeres
Abstract:
... We survey here state of the art mass spectrometry methodologies for investigating G-quadruplexes, and will illustrate them with a new study on a simple model system: the dimeric G-quadruplex of the 12-mer telomeric DNA sequence d(TAGGGTTAGGGT), which can adopt either a parallel or an antiparallel structure. We will discuss the solution conditions compatible with electrospray ionisation, the quanti ...
DOI:
10.1016/j.ymeth.2012.03.021

9. Methods of studying telomere damage induced by quadruplex-ligand complexes

Author:
Rizzo, Angela; Salvati, Erica; Biroccio, Annamaria
Source:
Methods 2012 v.57 no.1 pp. 93-99
ISSN:
1046-2023
Subject:
DNA damage; telomeres; drugs; ligands; binding properties; telomerase
Abstract:
... The burgeoning knowledge about the structure of telomeres and the roles of various factors involved in telomere maintenance provides several possible targets for pharmacological intervention. To date the area that has received major attention regarding drug discovery is the targeting the telomeric G-quadruplex (G4) structure. G4 ligands were initially designed to counteract telomerase action at te ...
DOI:
10.1016/j.ymeth.2012.02.010

10. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

Author:
Šponer, Jiří; Cang, Xiaohui; Cheatham, Thomas E., III
Source:
Methods 2012 v.57 no.1 pp. 25-39
ISSN:
1046-2023
Subject:
guanine; molecular dynamics; nucleic acids; solvents
Abstract:
... The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several ...
DOI:
10.1016/j.ymeth.2012.04.005
PubMed:
22525788
PubMed Central:
PMC3775459

11. NMR spectroscopy of G-quadruplexes

Author:
Adrian, Michael; Heddi, Brahim; Phan, Anh Tuân
Source:
Methods 2012 v.57 no.1 pp. 11-24
ISSN:
1046-2023
Subject:
DNA; RNA; nuclear magnetic resonance spectroscopy; nucleotide sequences
Abstract:
... G-rich DNA and RNA sequences can form four-stranded structures called G-quadruplexes. Such structures have gained significant interest in the past decade with increasing evidence of their biological role. G-quadruplex structures can be polymorphic and dynamic. NMR spectroscopy has played an important role in G-quadruplex research. Here we review on the application of NMR techniques to study struct ...
DOI:
10.1016/j.ymeth.2012.05.003

12. Reporter assays for studying quadruplex nucleic acids

Author:
Halder, Kangkan; Benzler, Martin; Hartig, Jörg S.
Source:
Methods 2012 v.57 no.1 pp. 115-121
ISSN:
1046-2023
Subject:
DNA; gene expression; messenger RNA; translation (genetics)
Abstract:
... DNA and RNA G-quadruplexes have gained increasing attention due to their potential role in a wide range of biological functions. The majority of functional studies characterize the influence of quadruplexes in gene expression including transcription and translation. Many of these studies have used reporter assays to elucidate the effect of quadruplexes at certain positions in promoters and untrans ...
DOI:
10.1016/j.ymeth.2012.02.005

13. Single-molecule investigation of G-quadruplex using a nanopore sensor

Author:
Shim, Jiwook; Gu, Li-Qun
Source:
Methods 2012 v.57 no.1 pp. 40-46
ISSN:
1046-2023
Subject:
biosensors; lipid bilayers; nanopores; nucleic acids; quantitative analysis
Abstract:
... This review article introduces the nanopore single-molecule method for the study of G-quadruplex nucleic acid structures. Single G-quadruplexes can be trapped into a 2nm protein pore embedded in the lipid bilayer membrane. The trapped G-quadruplex specifically blocks the current through the nanopore, creating a signature event for quantitative analysis of G-quadruplex properties, from cation-deter ...
DOI:
10.1016/j.ymeth.2012.03.026
PubMed:
22487183
PubMed Central:
PMC3572831

14. Structure, function and targeting of human telomere RNA

Author:
Xu, Yan; Komiyama, Makoto
Source:
Methods 2012 v.57 no.1 pp. 100-105
ISSN:
1046-2023
Subject:
DNA; RNA; X-ray diffraction; antineoplastic agents; genome; humans; ligands; nuclear magnetic resonance spectroscopy; telomeres; transcription (genetics)
Abstract:
... Human telomeres play an important role in critical processes underlying genome stability, cancer, and aging. For a long time, telomeres have been considered transcriptionally silent. A recent finding demonstrated that telomere DNA is transcribed into telomeric repeat-containing RNA (referred to as TERRA) in mammalian cells. The existence of TERRA RNA may reveal a new level of regulation and protec ...
DOI:
10.1016/j.ymeth.2012.02.015

15. Studying the effect of crowding and dehydration on DNA G-quadruplexes

Author:
Petraccone, Luigi; Pagano, Bruno; Giancola, Concetta
Source:
Methods 2012 v.57 no.1 pp. 76-83
ISSN:
1046-2023
Subject:
DNA; fluorescence; isomerization; ligands; proteins; solutes; spectroscopy; water activity
Abstract:
... Intracellular environment is crowded with biomolecules that occupy a significant fraction (up to 40%) of the cellular volume, with a total concentration in the range 300–400mg/ml. Recently, the effect of crowding/dehydrating agents on the DNA G-quadruplexes has become a subject of an increasing interest. Crowding and/or dehydrating agents have been used to simulate how G-quadruplexes behave under ...
DOI:
10.1016/j.ymeth.2012.02.011