251
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Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. Chem Commun (Camb) 2016; 52:179-82. [DOI: 10.1039/c5cc08242k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Liya Ji
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
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252
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Xu L, Wang J, Sun N, Liu M, Cao Y, Wang Z, Pei R. Neutral red as a specific light-up fluorescent probe for i-motif DNA. Chem Commun (Camb) 2016; 52:14330-14333. [DOI: 10.1039/c6cc07674b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neutral red as the first specific light-up fluorescent probe for i-motif DNA is presented.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Min Liu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Yi Cao
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Zhili Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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253
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Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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254
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Ren J, Wang T, Wang E, Wang J. I-motif-stapled and spacer-dependent multiple DNA nanostructures. RSC Adv 2016. [DOI: 10.1039/c6ra15201e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The DNA spacers between duplexes and i-motif structures are critical for the morphology of assembled pH-responsive DNA nanostructures, which is very instructive for fabrication of distinct-scale molecular devices in the future.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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255
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Marín-Luna M, Alkorta I, Elguero J. The effect of cytosine methylation on its halogen-bonding properties. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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256
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Rehm C, Wurmthaler LA, Li Y, Frickey T, Hartig JS. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PLoS One 2015; 10:e0144275. [PMID: 26695179 PMCID: PMC4692102 DOI: 10.1371/journal.pone.0144275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/16/2015] [Indexed: 12/04/2022] Open
Abstract
In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5
nucleotides (nt) are causative for phase and antigenic variation. Although an
increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs
of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity
to fold into G-quadruplex (G4) structures have received little attention. In silico
analysis of prokaryotic genomes show putative G4 forming sequences to be abundant.
This report focuses on a surprisingly enriched G-rich repeat of the type
GGGNATC in Xanthomonas and cyanobacteria
such as Nostoc. We studied in detail the genomes of
Xanthomonas campestris pv. campestris ATCC 33913
(Xcc), Xanthomonas axonopodis pv.
citri str. 306 (Xac), and Nostoc
sp. strain PCC7120 (Ana). In all three organisms repeats
are spread all over the genome with an over-representation in non-coding regions.
Extensive variation of the number of repetitive units was observed with repeat
numbers ranging from two up to 26 units. However a clear preference for four units
was detected. The strong bias for four units coincides with the requirement of four
consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus
repeat sequences was found in biophysical studies utilizing CD spectroscopy. The
G-rich repeats are preferably located between aligned open reading frames (ORFs) and
are under-represented in coding regions or between divergent ORFs. The G-rich repeats
are preferentially located within a distance of 50 bp upstream of an ORF on the
anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis
of whole transcriptome sequence data showed that the majority of repeat sequences are
transcribed. The genetic loci in the vicinity of repeat regions show increased
genomic stability. In conclusion, we introduce and characterize a special class of
highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.
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Affiliation(s)
- Charlotte Rehm
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Lena A Wurmthaler
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Yuanhao Li
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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257
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GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1. Sci Rep 2015; 5:18097. [PMID: 26674223 PMCID: PMC4682182 DOI: 10.1038/srep18097] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
HRAS is regulated by two neighbouring quadruplex-forming GC-elements (hras-1 and hras-2), located upstream of the major transcription start sites (doi: 10.1093/nar/gku 5784). In this study we demonstrate that the C-rich strands of hras-1 and hras-2 fold into i-motif conformations (iMs) characterized under crowding conditions (PEG-300, 40% w/v) by semi-transitions at pH 6.3 and 6.7, respectively. Nondenaturing PAGE shows that the HRAS C-rich sequences migrate at both pH 5 and 7 as folded intramolecular structures. Chromatin immunoprecipitation shows that hnRNP A1 is associated under in vivo conditions to the GC-elements, while EMSA proves that hnRNP A1 binds tightly to the iMs. FRET and CD show that hnRNP A1 unfolds the iM structures upon binding. Furthermore, when hnRNP A1 is knocked out in T24 bladder cancer cells by a specific shRNA, the HRAS transcript level drops to 44 ± 5% of the control, suggesting that hnRNP A1 is necessary for gene activation. The sequestration by decoy oligonucleotides of the proteins (hnRNP A1 and others) binding to the HRAS iMs causes a significant inhibition of HRAS transcription. All these outcomes suggest that HRAS is regulated by a G-quadruplex/i-motif switch interacting with proteins that recognize non B-DNA conformations.
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258
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Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins. Sci Rep 2015; 5:17944. [PMID: 26632347 PMCID: PMC4668579 DOI: 10.1038/srep17944] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022] Open
Abstract
The G4C2 hexanucleotide repeat expansion mutation (HREM) in C9ORF72, represents the most common mutation associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Three main disease mechanisms have been proposed to date: C9ORF72 haploinsufficiency, RNA toxicity, and accumulation of dipeptide repeat proteins. Pure GC content of the HREM potentially enables the formation of various non-B DNA structures such as G-quadruplexes and i-motifs. These structures are proposed to act as promoters and regulatory elements affecting replication, transcription and translation of the surrounding region. G-quadruplexes have already been shown on the G-rich sense DNA and RNA strands (G4C2)n, the structure of the anti-sense (G2C4)n strand remains unresolved. Similar C-rich sequences may, under acidic conditions, form i-motifs consisting of two parallel duplexes in a head to tail orientation held together by hemi-protonated C+-C pairs. We show that d(G2C4)n repeats do form i-motif and protonated hairpins even under near-physiological conditions. Rather than forming a DNA duplex, i-motifs persist even in the presence of the sense strand. This preferential formation of G-quadruplex and i-motif/hairpin structures over duplex DNA, may explain HREM replicational and transcriptional instability. Furthermore, i-motifs/hairpins can represent a novel pharmacological target for C9ORF72 associated ALS and FTLD.
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259
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Fujiwara N, Mazzola M, Cai E, Wang M, Cave JW. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor. PLoS One 2015; 10:e0139167. [PMID: 26402367 PMCID: PMC4581631 DOI: 10.1371/journal.pone.0139167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/08/2015] [Indexed: 01/03/2023] Open
Abstract
The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine), is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th), which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study sought to establish whether treatment with TMPyP4 could modify mouse Th expression levels in vivo. Intraperitoneal administration of low TMPyP4 doses (10mg/kg), similar to those used for photosensitization, did not significantly reduce Th transcript levels in several catecholaminergic regions. Administration of a high dose (40 mg/kg), similar to those used for tumor xenograph reduction, unexpectedly induced flaccid paralysis in an age and sex-dependent manner. In vitro analyses revealed that TMPyP4, but not putative metabolites, inhibited Acetylcholinesterase activity and pre-treatment of TMPyP4 with Hemeoxygenase-2 (HO-2) rescued Acetylcholinesterase function. Age-dependent differences in HO-2 expression levels may account for some of the variable in vivo effects of high TMPyP4 doses. Together, these studies indicate that only low doses of TMPyP4, such as those typically used for photosensitization, are well tolerated in vivo. Thus, despite its widespread use in vitro, TMPyP4 is not ideal for modifying neuronal gene expression in vivo by manipulating nucleic acid secondary structure stability, which highlights the need to identify more clinically suitable compounds that can modulate nucleic acid secondary structure and gene expression.
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Affiliation(s)
- Nana Fujiwara
- Burke Medical Research Institute, White Plains, New York, United States of America
| | - Michael Mazzola
- Burke Medical Research Institute, White Plains, New York, United States of America
| | - Elizabeth Cai
- Burke Medical Research Institute, White Plains, New York, United States of America
| | - Meng Wang
- Burke Medical Research Institute, White Plains, New York, United States of America
| | - John W. Cave
- Burke Medical Research Institute, White Plains, New York, United States of America
- Weill Cornell Medical College, Brain and Mind Research Institute, New York, New York, United States of America
- * E-mail:
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260
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Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene. CHEMOSENSORS 2015. [DOI: 10.3390/chemosensors3030211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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261
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Garavís M, Méndez-Lago M, Gabelica V, Whitehead SL, González C, Villasante A. The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs. Sci Rep 2015; 5:13307. [PMID: 26289671 PMCID: PMC4542561 DOI: 10.1038/srep13307] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022] Open
Abstract
Centromeres are the chromosomal loci at which spindle microtubules attach to mediate chromosome segregation during mitosis and meiosis. In most eukaryotes, centromeres are made up of highly repetitive DNA sequences (satellite DNA) interspersed with middle repetitive DNA sequences (transposable elements). Despite the efforts to establish complete genomic sequences of eukaryotic organisms, the so-called 'finished' genomes are not actually complete because the centromeres have not been assembled due to the intrinsic difficulties in constructing both physical maps and complete sequence assemblies of long stretches of tandemly repetitive DNA. Here we show the first molecular structure of an endogenous Drosophila centromere and the ability of the C-rich dodeca satellite strand to form dimeric i-motifs. The finding of i-motif structures in simple and complex centromeric satellite DNAs leads us to suggest that these centromeric sequences may have been selected not by their primary sequence but by their ability to form noncanonical secondary structures.
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Affiliation(s)
- Miguel Garavís
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain.,Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Méndez-Lago
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France.,Inserm ARNA Laboratory, 146 rue Leo Saignat, F-33000 Bordeaux, France
| | - Siobhan L Whitehead
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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262
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Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res 2015; 43:e142. [PMID: 26184874 PMCID: PMC4666379 DOI: 10.1093/nar/gkv716] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/02/2015] [Indexed: 12/16/2022] Open
Abstract
Insight into the three-dimensional architecture of RNA is essential for understanding its cellular functions. However, even the classic transfer RNA structure contains features that are overlooked by existing bioinformatics tools. Here we present DSSR (Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures. The software identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any tautomeric or protonation state. DSSR detects higher-order coplanar base associations, termed multiplets. It finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR identifies coaxial stacking of multiple stems within a single helix and lists isolated canonical pairs that lie outside of a stem. The program characterizes 'closed' loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of arbitrary complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops. This new, inclusive definition provides a novel perspective on the spatial organization of RNA. Tests on all nucleic acid structures in the Protein Data Bank confirm the efficiency and robustness of the software, and applications to representative RNA molecules illustrate its unique features. DSSR and related materials are freely available at http://x3dna.org/.
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Affiliation(s)
- Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA
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263
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Greco ML, Folini M, Sissi C. Double stranded promoter region of BRAF undergoes to structural rearrangement in nearly physiological conditions. FEBS Lett 2015; 589:2117-23. [DOI: 10.1016/j.febslet.2015.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/10/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
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264
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Kikuta K, Piao H, Brazier J, Taniguchi Y, Onizuka K, Nagatsugi F, Sasaki S. Stabilization of the i-motif structure by the intra-strand cross-link formation. Bioorg Med Chem Lett 2015; 25:3307-10. [PMID: 26105193 DOI: 10.1016/j.bmcl.2015.05.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 02/06/2023]
Abstract
The i-motif structures are formed by oligonucleotides containing cytosine tracts under acidic conditions. The folding of the i-motif under physiological conditions is of great interest because of its biological role. In this study, we investigated the effect of the intra-strand cross-link on the stability of the i-motif structure. The 4-vinyl-substituted analog of thymidine (T-vinyl) was incorporated into the 5'-end of the human telomere complementary strand, which formed the intra-strand cross-link with the internal adenine. The intra-strand cross-linked i-motif displayed CD spectra similar to that of the natural i-motif at acidic pH, which was transformed into a random coil with the increasing pH. The pH midpoint for the transition from the i-motif to random coil increased from pH 6.1 for the natural one to pH 6.8 for the cross-linked one. The thermodynamic parameters were obtained by measuring the thermal melting behaviors by CD and UV, and it was determined that the intra-strand cross-linked i-motif is stabilized due to a favorable entropy effect. Thus, this study has clearly indicated the validity of the intra-strand cross-linking for stabilization of the i-motif structure.
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Affiliation(s)
- Kenji Kikuta
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Haishun Piao
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - John Brazier
- School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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265
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Garavís M, Escaja N, Gabelica V, Villasante A, González C. Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs. Chemistry 2015; 21:9816-24. [PMID: 26013031 DOI: 10.1002/chem.201500448] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.
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Affiliation(s)
- Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).,Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit 33600 Pessac (France).,Inserm, ARNA Laboratory, 146 Rue Leo Saignat, 33000 Bordeaux (France)
| | - Alfredo Villasante
- Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).
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266
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Böttcher A, Kowerko D, Sigel RKO. Explicit analytic equations for multimolecular thermal melting curves. Biophys Chem 2015; 202:32-9. [PMID: 25910861 DOI: 10.1016/j.bpc.2015.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
The analysis of thermal melting curves requires the knowledge of equations for the temperature dependence of the relative fraction of folded and unfolded components. To implement these equations as standard tools for curve fitting, they should be as explicit as possible. From the van't Hoff formalism it is known that the equilibrium constant and hence the folded fraction is a function of the absolute temperature, the van't Hoff transition enthalpy, and the melting temperature. The work presented here is devoted to the mathematically self-contained derivation and the listing of explicit equations for the folded fraction as a function of the thermodynamic parameters in the case of arbitrary molecularities. Part of the results are known, others are new. It is in particular shown for the first time that the folded fraction is the composition of a universal function which depends solely on the molecularity and a dimensionless function which is governed by the concrete thermodynamic regime but is independent of the molecularity. The results will prove useful for extracting the thermodynamic parameters from experimental data on the basis of regression analysis. As supporting information, open-source Matlab scripts for the computer implementation of the equations are provided.
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Affiliation(s)
- Albrecht Böttcher
- Chemnitz University of Technology, Department of Mathematics, 09107 Chemnitz, Germany.
| | - Danny Kowerko
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Roland K O Sigel
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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267
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Tripathi S, Zhang D, Paukstelis PJ. An intercalation-locked parallel-stranded DNA tetraplex. Nucleic Acids Res 2015; 43:1937-44. [PMID: 25628357 PMCID: PMC4330391 DOI: 10.1093/nar/gkv033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5′-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
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Affiliation(s)
- Shailesh Tripathi
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | - Paul J Paukstelis
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
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268
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Pérez-Rentero S, Gargallo R, González C, Eritja R. Modulation of the stability of i-motif structures using an acyclic threoninol cytidine derivative. RSC Adv 2015. [DOI: 10.1039/c5ra10096h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The effect of aTNA (acyclic threoninol nucleic acids) units on the stability of intramolecular i-motifs was investigated by spectroscopic techniques.
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Affiliation(s)
- Sonia Pérez-Rentero
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN
- E-08034 Barcelona
- Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona
- Spain
| | - Carlos González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid
- Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN
- E-08034 Barcelona
- Spain
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269
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Lu L, Wang M, Liu LJ, Wong CY, Leung CH, Ma DL. A luminescence switch-on probe for terminal deoxynucleotidyl transferase (TdT) activity detection by using an iridium(iii)-based i-motif probe. Chem Commun (Camb) 2015; 51:9953-6. [DOI: 10.1039/c5cc02790j] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An iridium(iii) complex exhibiting higher responce towards i-motif DNA over dsDNA and ssDNA was employed for the construction of a TdT activity detection platform. The limit of detection for TdT was 0.25 U ML−1.
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Affiliation(s)
- Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Modi Wang
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Chun-Yuen Wong
- Department of Biology and Chemistry
- City University of Hong Kong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
- Partner State Key Laboratory of Environmental and Biological Analysis
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270
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Huang H, Hong X, Liu F, Li N. A simple approach to study the conformational switching of i-motif DNA by fluorescence anisotropy. Analyst 2015; 140:5987-91. [DOI: 10.1039/c5an01011j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorescence anisotropy is a simple, reliable and sensitive approach to study the conformational switching of the i-motif structure.
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Affiliation(s)
- Hongduan Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Xinying Hong
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
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271
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Minero GAS, Wagler PF, Oughli AA, McCaskill JS. Electronic pH switching of DNA triplex reactions. RSC Adv 2015. [DOI: 10.1039/c5ra02628h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remote electronic control of fast DNA processing reactions such as S–S-ligation is achievedviapH switching of triplex structures.
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Affiliation(s)
- Gabriel Antonio S. Minero
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Patrick F. Wagler
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Alaa A. Oughli
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - John S. McCaskill
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
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272
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DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
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