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García JF, Reguera D, Valls A, Aviñó A, Dominguez A, Eritja R, Gargallo R. Detection of pyrimidine-rich DNA sequences based on the formation of parallel and antiparallel triplex DNA and fluorescent silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122752. [PMID: 37084680 DOI: 10.1016/j.saa.2023.122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.
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Affiliation(s)
- Juan Fernando García
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - David Reguera
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Andrea Valls
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Arnau Dominguez
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain.
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2
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Bielecka P, Dembska A, Juskowiak B. Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC. Molecules 2019; 24:molecules24050952. [PMID: 30857134 PMCID: PMC6429216 DOI: 10.3390/molecules24050952] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023] Open
Abstract
The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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3
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Noothalapati H, Iwasaki K, Yamamoto T. Biological and Medical Applications of Multivariate Curve Resolution Assisted Raman Spectroscopy. ANAL SCI 2018; 33:15-22. [PMID: 28070069 DOI: 10.2116/analsci.33.15] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Biological specimens such as cells, tissues and biofluids (urine, blood) contain mixtures of many different biomolecules, all of which contribute to a Raman spectrum at any given point. The separation and identification of pure biochemical components remains one of the biggest challenges in Raman spectroscopy. Multivariate curve resolution, a matrix factorization method, is a powerful, yet flexible, method that can be used with constraints, such as non-negativity, to decompose a complex spectroscopic data matrix into a small number of physically meaningful pure spectral components along with their relative abundances. This paper reviews recent applications of multivariate curve resolution by alternating least squares analysis to Raman spectroscopic and imaging data obtained either in vivo or in vitro from biological and medical samples.
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4
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Pandey S, Agarwala P, Jayaraj GG, Gargallo R, Maiti S. The RNA Stem-Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell. Biochemistry 2015; 54:7067-78. [PMID: 26554903 DOI: 10.1021/acs.biochem.5b00574] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K(+) and Mg(2+) ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quadruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.
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Affiliation(s)
- Satyaprakash Pandey
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Prachi Agarwala
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Gopal G Jayaraj
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Raimundo Gargallo
- Solution Equilibria and Chemometrics Group, Department of Analytical Chemistry, University of Barcelona , Diagonal 645, E-08028 Barcelona, Spain
| | - Souvik Maiti
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.,Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
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5
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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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6
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Kolganova NA, Varizhuk AM, Novikov RA, Florentiev VL, Pozmogova GE, Borisova OF, Shchyolkina AK, Smirnov IP, Kaluzhny DN, Timofeev EN. Anomeric DNA quadruplexes. ARTIFICIAL DNA, PNA & XNA 2015; 5:e28422. [PMID: 25483931 DOI: 10.4161/adna.28422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Thrombin-binding aptamer (TBA) is a 15-nt DNA oligomer that efficiently inhibits thrombin. It has been shown that TBA folds into an anti-parallel unimolecular G-quadruplex. Its three-dimensional chair-like structure consists of two G-tetrads connected by TT and TGT loops. TBA undergoes fast degradation by nucleases in vivo. To improve the nuclease resistance of TBA, a number of modified analogs have been proposed. Here, we describe anomeric modifications of TBA. Non-natural α anomers were used to replace selected nucleotides in the loops and core. Significant stabilization of the quadruplex was observed for the anomeric modification of TT loops at T4 and T13. Replacement of the core guanines either prevents quadruplex assembly or induces rearrangement in G-tetrads. It was found that the anticoagulant properties of chimeric aptamers could be retained only with intact TT loops. On the contrary, modification of the TGT loop was shown to substantially increase nuclease resistance of the chimeric aptamer without a notable disturbance of its anticoagulant activity.
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Affiliation(s)
- Natalia A Kolganova
- a Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
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7
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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8
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Dembska A, Rzepecka P, Juskowiak B. Spectroscopic characterization of i-motif forming c-myc derived sequences double-labeled with pyrene. J Fluoresc 2013; 23:807-12. [PMID: 23519528 PMCID: PMC3696180 DOI: 10.1007/s10895-013-1184-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/24/2013] [Indexed: 11/25/2022]
Abstract
In current studies we use the oligonucleotides based on c-myc sequence: CCC CAC CCT CCC CAC CCT CCC C (cmyc22) and CCC CAC CCT CCC CAC CCT CCC CA (cmyc22A) functionalized by pyrene moieties at both termini. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of pyrene-modified i-motifs as well as their unlabeled precursors are presented and discussed here. The pyrene labels have a remarkable influence on i-motif stability which was deduced from CD spectra and confirmed by UV melting experiments. Both probes emit fluorescence band of pyrene monomer with intensity decreasing upon pH lowering.
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Affiliation(s)
- Anna Dembska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznań, Poland.
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9
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Choi J, Majima T. Reversible conformational switching of i-motif DNA studied by fluorescence spectroscopy. Photochem Photobiol 2013; 89:513-22. [PMID: 23311444 DOI: 10.1111/php.12042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/04/2013] [Indexed: 12/19/2022]
Abstract
Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology.
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Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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10
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Influence of pH, temperature and the cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5′-(C3TA2)4-3′ sequence of the human telomere. Int J Biol Macromol 2011; 49:729-36. [DOI: 10.1016/j.ijbiomac.2011.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/04/2011] [Accepted: 07/05/2011] [Indexed: 12/11/2022]
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11
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Dettler JM, Buscaglia R, Le VH, Lewis EA. DSC deconvolution of the structural complexity of c-MYC P1 promoter G-quadruplexes. Biophys J 2011; 100:1517-25. [PMID: 21402034 DOI: 10.1016/j.bpj.2011.01.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/21/2011] [Accepted: 01/25/2011] [Indexed: 01/01/2023] Open
Abstract
We completed a biophysical characterization of the c-MYC proto-oncogene P1 promoter quadruplex and its interaction with a cationic porphyrin, 5,10,15,20-tetra(N-methyl-4-pyridyl)porphyrin (TMPyP4), using differential scanning calorimetry, isothermal titration calorimetry, and circular dichroism spectroscopy. We examined three different 24-mer oligonucleotides, including the wild-type (WT) sequence found in the c-MYC P(1) promoter and two mutant G→T sequences that are known to fold into single 1:2:1 and 1:6:1 loop isomer quadruplexes. Biophysical experiments were performed on all three oligonucleotide sequences at two different ionic strengths (30 mM [K(+)] and 130 mM [K(+)]). Differential scanning calorimetry experiments demonstrated that the WT quadruplex consists of a mixture of at least two different folded conformers at both ionic strengths, whereas both mutant sequences exhibit a single two-state melting transition at both ionic strengths. Isothermal titration calorimetry experiments demonstrated that both mutant sequences bind 4 mols of TMPyP4 to 1 mol of DNA, in similarity to the WT sequence. The circular dichroism spectroscopy signatures for all three oligonucleotides at both ionic strengths are consistent with an intramolecular parallel stranded G-quadruplex structure, and no change in quadruplex structure is observed upon addition of saturating amounts of TMPyP4 (i.e., 4:1 TMPyP4/DNA).
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Affiliation(s)
- Jamie M Dettler
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
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12
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Zikich D, Liu K, Sagiv L, Porath D, Kotlyar A. I-motif nanospheres: unusual self-assembly of long cytosine strands. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1029-34. [PMID: 21381197 DOI: 10.1002/smll.201002213] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 01/14/2011] [Indexed: 05/25/2023]
Abstract
The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i-motifs or i-tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C-strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i-motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)-poly(dC) molecules in similar conditions.
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Affiliation(s)
- Dragoslav Zikich
- Department of Biochemistry George S. Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv 69978, Israel
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13
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Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site. Anal Chim Acta 2010; 683:69-77. [DOI: 10.1016/j.aca.2010.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 10/04/2010] [Accepted: 10/06/2010] [Indexed: 12/30/2022]
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14
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Chemical equilibria studies using multivariate analysis methods. Anal Bioanal Chem 2010; 399:1983-97. [DOI: 10.1007/s00216-010-4310-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 10/02/2010] [Accepted: 10/06/2010] [Indexed: 12/30/2022]
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15
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Dettler JM, Buscaglia R, Cui J, Cashman D, Blynn M, Lewis EA. Biophysical characterization of an ensemble of intramolecular i-motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence. Biophys J 2010; 99:561-7. [PMID: 20643075 DOI: 10.1016/j.bpj.2010.04.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022] Open
Abstract
i-Motif-forming sequences are present in or near the regulatory regions of >40% of all genes, including known oncogenes. We report here the results of a biophysical characterization and computational study of an ensemble of intramolecular i-motifs that model the polypyrimidine sequence in the human c-MYC P1 promoter. Circular dichroism results demonstrate that the mutant sequence (5'-CTT TCC TAC CCTCCC TAC CCT AA-3') can adopt multiple "i-motif-like," classical i-motif, and single-stranded structures as a function of pH. The classical i-motif structures are predominant in the pH range 4.2-5.2. The "i-motif-like" and single-stranded structures are the most significant species in solution at pH higher and lower, respectively, than that range. Differential scanning calorimetry results demonstrate an equilibrium mixture of at least three i-motif folded conformations with Tm values of 38.1, 46.6, and 49.5 degrees C at pH 5.0. The proposed ensemble of three folded conformations includes the three lowest-energy conformations obtained by computational modeling and two folded conformers that were proposed in a previous NMR study. The NMR study did not report the most stable conformer found in this study.
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Affiliation(s)
- Jamie M Dettler
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
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16
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Brooks TA, Hurley LH. The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics. Nat Rev Cancer 2009; 9:849-61. [PMID: 19907434 DOI: 10.1038/nrc2733] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MYC is deregulated in most tumour types, but an effective means to selectively target its aberrant expression is not yet available. Supercoiling that is induced by transcription has been demonstrated to have dynamic effects on DNA in the MYC promoter element: it converts duplex DNA to non-duplex DNA structures, even at considerable distances from the transcriptional start site. These non-duplex DNA structures, which control both turning on and off of transcription and the rate of transcription firing, are amenable to small-molecule targeting. This dynamic system provides a unique opportunity for the treatment of tumours in which MYC is an important oncogene.
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Affiliation(s)
- Tracy A Brooks
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
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17
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Huang J, Wang M, Zhou Y, Weng X, Shuai L, Zhou X, Zhang D. Visual observation of G-quadruplex DNA with the label-free fluorescent probe silole with aggregation-induced emission. Bioorg Med Chem 2009; 17:7743-8. [DOI: 10.1016/j.bmc.2009.09.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/18/2009] [Accepted: 09/19/2009] [Indexed: 11/26/2022]
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18
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Wang G, Zhao J, Vasquez KM. Methods to determine DNA structural alterations and genetic instability. Methods 2009; 48:54-62. [PMID: 19245837 PMCID: PMC2693251 DOI: 10.1016/j.ymeth.2009.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/15/2009] [Indexed: 11/16/2022] Open
Abstract
Chromosomal DNA is a dynamic structure that can adopt a variety of non-canonical (i.e., non-B) conformations. In this regard, at least 10 different forms of non-B DNA conformations have been identified; many of them have been found to be mutagenic, and associated with human disease development. Despite the importance of non-B DNA structures in genetic instability and DNA metabolic processes, mechanisms by which instability occurs remain largely undefined. The purpose of this review is to summarize current methodologies that are used to address questions in the field of non-B DNA structure-induced genetic instability. Advantages and disadvantages of each method will be discussed. A focused effort to further elucidate the mechanisms of non-B DNA-induced genetic instability will lead to a better understanding of how these structure-forming sequences contribute to the development of human disease.
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Affiliation(s)
- Guliang Wang
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957
| | - Junhua Zhao
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957
| | - Karen M. Vasquez
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957
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Yu H, Wang X, Fu M, Ren J, Qu X. Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA. Nucleic Acids Res 2008; 36:5695-703. [PMID: 18776218 PMCID: PMC2553577 DOI: 10.1093/nar/gkn569] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.
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Affiliation(s)
- Haijia Yu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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20
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Yafe A, Shklover J, Weisman-Shomer P, Bengal E, Fry M. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin. Nucleic Acids Res 2008; 36:3916-25. [PMID: 18511462 PMCID: PMC2475631 DOI: 10.1093/nar/gkn340] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Four myogenic regulatory factors (MRFs); MyoD, Myf-5, MRF4 and Myogenin direct muscle tissue differentiation. Heterodimers of MRFs with E-proteins activate muscle-specific gene expression by binding to E-box motifs d(CANNTG) in their promoters or enhancers. We showed previously that in contrast to the favored binding of E-box by MyoD-E47 heterodimers, homodimeric MyoD associated preferentially with quadruplex structures of regulatory sequences of muscle-specific genes. To inquire whether other MRFs shared the DNA binding preferences of MyoD, the DNA affinities of hetero- and homo-dimeric MyoD, MRF4 and Myogenin were compared. Similarly to MyoD, heterodimers with E47 of MRF4 or Myogenin bound E-box more tightly than quadruplex DNA. However, unlike homodimeric MyoD or MRF4, Myogenin homodimers associated weakly and nonpreferentially with quadruplex DNA. By reciprocally switching basic regions between MyoD and Myogenin we demonstrated dominance of MyoD in determining the quadruplex DNA-binding affinity. Thus, Myogenin with an implanted MyoD basic region bound quadruplex DNA nearly as tightly as MyoD. However, a grafted Myogenin basic region did not diminish the high affinity of homodimeric MyoD for quadruplex DNA. We speculate that the dissimilar interaction of MyoD and Myogenin with tetrahelical domains in muscle gene promoters may differently regulate their myogenic activities.
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Affiliation(s)
- Anat Yafe
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649 Bat Galim, Haifa 31096, Israel
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Multivariate curve resolution-alternating least squares (MCR-ALS) applied to spectroscopic data from monitoring chemical reactions processes. Anal Bioanal Chem 2008; 390:2059-66. [PMID: 18320174 DOI: 10.1007/s00216-008-1955-6] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/30/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
Abstract
This paper overviews the application of multivariate curve resolution (optimized by alternating least squares) to spectroscopic data acquired by monitoring chemical reactions and other processes. The goals of the resolution methods and the principles for understanding their applications are described. Some of the problems arising from these evolving systems and the limitations of the multivariate curve resolution methods are also discussed. This article reviews most of the applications of multivariate curve resolution applied to reacting systems published between January 2000 and June 2007. Some basic papers dated before 2000 have also been included.
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Khan N, Aviñó A, Tauler R, González C, Eritja R, Gargallo R. Solution equilibria of the i-motif-forming region upstream of the B-cell lymphoma-2 P1 promoter. Biochimie 2007; 89:1562-72. [PMID: 17850948 DOI: 10.1016/j.biochi.2007.07.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 07/30/2007] [Indexed: 11/19/2022]
Abstract
The 5'-end of the P1 promoter of the B-cell lymphoma-2 (bcl-2) gene contains a highly guaninecytosine-rich region, which has a role in the regulation of bcl-2 transcription. Whereas the guanine-rich region has been the focus of recent studies, little attention has been paid to the cytosine-rich strand. Here we examine the structural transitions of the cytosine-rich sequence by means of acid-base, mole-ratio and melting experiments monitored by molecular absorption, circular dichroism, and NMR spectroscopies. Two intramolecular i-motif structures have been detected in the pH range 2-7, with maximal formation at pH 4 and 6, respectively. At pH 7.6 the majority species has been associated with a hairpin involving Watson-Crick base pairs. Upon addition of the quadruplex-interacting ligand TmPyP4, bcl-2c structures at pH 6.1 and 7.6 yield identical interaction species with stoichiometries 1:2 (DNA:ligand) and logarithms of formation constant 12.4+/-0.2 and 11.7+/-0.1, respectively. The initial i-motif structure at pH 6.1 is lost upon interaction with TmPyP4.
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Affiliation(s)
- Nasiruddin Khan
- Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona, Spain
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Peng Y, Li X, Ren J, Qu X. Single-walled carbon nanotubes binding to human telomeric i-motif DNA: significant acceleration of S1 nuclease cleavage rate. Chem Commun (Camb) 2007:5176-8. [PMID: 18060133 DOI: 10.1039/b710950d] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-walled carbon nanotubes (SWNTs) binding to human telomeric i-motif DNA can significantly accelerate S1 nuclease cleavage rate by increasing the enzyme turnover number.
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Affiliation(s)
- Yinghua Peng
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
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Li X, Peng Y, Ren J, Qu X. Carboxyl-modified single-walled carbon nanotubes selectively induce human telomeric i-motif formation. Proc Natl Acad Sci U S A 2006; 103:19658-63. [PMID: 17167055 PMCID: PMC1750900 DOI: 10.1073/pnas.0607245103] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Indexed: 11/18/2022] Open
Abstract
As the leading nanodevice candidate, single-walled carbon nanotubes (SWNTs) have potential therapeutic applications in gene therapy and novel drug delivery. We found that SWNTs can inhibit DNA duplex association and selectively induce human telomeric i-motif DNA formation by binding to the 5'-end major groove under physiological conditions or even at pH 8.0. SWNT binding to telomeric DNA was studied by UV melting, NMR, S1 nuclease cleavage, CD, and competitive FRET methods. These results suggest that SWNTs might have the intriguing potential to modulate human telomeric DNA structures in vivo, like biologically relevant B-A and B-Z DNA transitions, which is of great interest for drug design and cancer therapy.
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Affiliation(s)
- Xi Li
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Yinghua Peng
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jinsong Ren
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaogang Qu
- Division of Biological Inorganic Chemistry, Key Laboratory of Rare Earth Chemistry and Physics, Graduate School of the Chinese Academy of Sciences, and Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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Vives M, Tauler R, Eritja R, Gargallo R. Spectroscopic study of the interaction of actinomycin D with oligonucleotides carrying the central base sequences -XGCY- and -XGGCCY- using multivariate methods. Anal Bioanal Chem 2006; 387:311-20. [PMID: 17123067 DOI: 10.1007/s00216-006-0946-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 10/12/2006] [Indexed: 10/23/2022]
Abstract
The interactions of actinomycin D (ACTD) with the oligonucleotides 5'-CAAAGCTTTG-3', 5'-CATGGCCATG-3' and 5'-TATGGCCATA-3' were investigated by means of acid-base titrations and mole-ratio and melting experiments monitored by molecular absorption and circular dichroism (CD) spectroscopies. For each experiment, CD and molecular absorption spectra were recorded at each point in the experiment, and later analyzed via appropriate multivariate data analysis methods. The study of the interactions between these oligonucleotides and ACTD at 25 degrees C showed the formation of an interaction complex with a stoichiometry of 1:1 (ACTD:duplex) and values for the log(formation constant) of 5.1+/-0.3, 6.4+/-0.2, and 5.6+/-0.2, respectively. An additional interaction complex at higher temperatures was also detected, which might be related to the single-stranded forms of the oligonucleotides.
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Affiliation(s)
- M Vives
- Department of Environmental Chemistry, IIQAB-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
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