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Tymchenko EE, Soldatova AA, Chikhirzhina EV, Polyanichko AM. Analysis of Changes in the Structure of DNA when Interacting with Platinum Coordination Compounds by IR Spectroscopy. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922010195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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2
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Grueso E, Roldan E, Perez-Tejeda P, Kuliszewska E, Molero B, Brecker L, Giráldez-Pérez RM. Reversible DNA compaction induced by partial intercalation of 16-Ph-16 gemini surfactants: evidence of triple helix formation. Phys Chem Chem Phys 2018; 20:24902-24914. [PMID: 30234871 DOI: 10.1039/c8cp02791a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction between calf thymus DNA and the gemini surfactants N,N'-[α,ω-phenylenebis(methylene)bis [N,N'-dimethyl-N-(1-hexadecyl)]-ammonium dibromide], p-16-Ph-16 (α = 1, ω = 3) and m-16-Ph-16 (α = 1, ω = 2), has been investigated via circular dichroism, fluorescence and UV-vis spectroscopy, zeta potential, dynamic light scattering, and AFM microscopy. Measurements were carried out in aqueous media at different molar ratios, R = (C16-Ph-16)/CDNA and C16-Ph-16 always below the critical micellar concentration (CMC) of the surfactant. Under these conditions, DNA undergoes two reversible conformational changes, compaction and decompaction, due to interaction with the surfactant molecules at low and high molar ratios, respectively. The extent of such conformational changes is correlated with both the degree of surfactant partial intercalation, and the size and charge of the surfactant aggregates formed, in each case. Comparison of the results shows that the para-form of the surfactant intercalates into the DNA to a major extent; therefore, the compaction/decompaction processes are more effective. Among these, the structure of the resulting 16-Ph-16/DNA decompacted complex is worthy of note. For the first time it can be demonstrated that the partial intercalation of the 16-Ph-16 gemini surfactants induces the formation of triplex DNA-like structures at a high R ratio.
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Affiliation(s)
- Elia Grueso
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, C/ Profesor García González, s/n, 41012, Sevilla, Spain.
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3
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Ye MY, Zhu RT, Li X, Zhou XS, Yin ZZ, Li Q, Shao Y. Adaptively Recognizing Parallel-Stranded Duplex Structure for Fluorescent DNA Polarity Analysis. Anal Chem 2017; 89:8604-8608. [DOI: 10.1021/acs.analchem.7b02467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mei-Yun Ye
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Rui-Tao Zhu
- Department
of Chemistry, Taiyuan Normal University, Taiyuan 030031, China
| | - Xiang Li
- Langzhong People’s Hospital, Langzhong 637400, Sichuan, China
| | - Xiao-Shun Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Zheng-Zhi Yin
- College
of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang, China
| | - Qian Li
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yong Shao
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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4
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Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM. Robust IR-based detection of stable and fractionally populated G-C + and A-T Hoogsteen base pairs in duplex DNA. FEBS Lett 2017; 591:1770-1784. [PMID: 28524232 PMCID: PMC5584567 DOI: 10.1002/1873-3468.12681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 11/11/2022]
Abstract
Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
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Affiliation(s)
- Allison L Stelling
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Seung H Choi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Mary C Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
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5
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Kim YH, Oh JH, Lytton-Jean AKR, Lee JS. Pyridine: a Denaturant or Stabilizer of Spherical Nucleic Acids? Anal Chem 2017; 89:4581-4586. [DOI: 10.1021/acs.analchem.7b00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yoon Hyuck Kim
- Department
of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ju-Hwan Oh
- Department
of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Abigail K. R. Lytton-Jean
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jae-Seung Lee
- Department
of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
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6
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Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 2015; 43:3420-33. [PMID: 25813047 PMCID: PMC4402545 DOI: 10.1093/nar/gkv241] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/01/2015] [Indexed: 11/14/2022] Open
Abstract
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Bradley J Hintze
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | | | - Shan Yang
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University, Durham, NC 27710, USA Department of Chemistry, Duke University, Durham, NC 27708, USA
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7
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Brovarets’ OO, Yurenko YP, Hovorun DM. Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study. J Biomol Struct Dyn 2013; 32:993-1022. [PMID: 23730732 DOI: 10.1080/07391102.2013.799439] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Jain AK, Gupta SK, Tawar U, Dogra SK, Tandon V. Benzimidazoles: a minor groove-binding ligand-induced stabilization of triple helix. Oligonucleotides 2010; 19:53-62. [PMID: 19232004 DOI: 10.1089/oli.2008.0169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Nonintercalating minor groove-binding ligands netropsin, Hoechst 33258, and DAPI are reported to destabilize the triplex. Ligands with different substitutions on the phenyl ring of bis- and terbenzimidazoles were evaluated for their effect on the stability of C+.GC triplex and Hoogsteen duplex. We found that newly synthesized benzimidazoles stabilize the triplex as shown by fluorescence and melting studies. Modeling studies showed that these molecules bind in the Watson-Crick minor groove of triplex, which can exert a profound impact on the properties of the host triplex. Circular dichroism-binding studies indicate 5.77 base triplets/ligand as an apparent binding site for bis- and 8.66 for terbenzimidazoles. The stabilization of triplex can be attributed to the protonation of nitrogens and amines of benzimidazoles at pH 5.2 that compensate the negative charge of phosphate backbone to reduce the repulsion between the strands resulting in the stabilization.
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Affiliation(s)
- Akash K Jain
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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Jain AK, Bhattacharya S. Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA. Bioconjug Chem 2010; 21:1389-403. [DOI: 10.1021/bc900247s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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10
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Lestienne PP. Are there three polynucleotide strands in the catalytic centre of DNA polymerases? Biochimie 2009; 91:1523-30. [PMID: 19628017 DOI: 10.1016/j.biochi.2009.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
Abstract
Mitochondrial DNA may undergo large-scale rearrangements, thus leading to diseases. The mechanisms of these rearrangements are still the matter of debates. Several lines of evidence indicate that breakpoints are characterized by direct repeats (DR), one of them being eliminated from the normal genome. Analysis of DR showed their skewed nucleotide content compatible with the formation of known triple helices. Here, I propose a novel mechanism involving the formation of triplex structures that result from the dissociation of the [synthesized repeat-DNA polymerase] complex. Upon binding to the homologous sequence, replication is initiated from the primer bound in a triple helix manner. This feature implies the initiation of replication on the double-stranded DNA from the triple helix primer. Hereby, I review evidences supporting this model. Indeed, all short d(G)-rich primers 10 nucleotides long can be elongated on double-stranded DNA by phage, bacterial, reverse transcriptases and eukaryotic DNA polymerases. Mismatches may be tolerated between the primer and its double-stranded binding site. In contrast to previous studies, evidences for the parallel binding of the triple helix to its homologous strand are provided. This suggest the displacement of the non-template strand by the triple helix primer upon binding within the DNA polymerase catalytic centre. Computer modelling indicates that the triple helix primer lies within the major groove of the double helix, with its 3' hydroxyl end nearby the catalytic amino acids. Taken together, I bring new concepts on DNA rearrangements, and novel features of triple helices and DNA polymerases that can bind three polynucleotide strands similar to RNA polymerases.
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Affiliation(s)
- Patrick P Lestienne
- U 889 INSERM, Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France
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11
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Filichev VV, Pedersen EB. Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions. J Am Chem Soc 2006; 127:14849-58. [PMID: 16231939 DOI: 10.1021/ja053645d] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (5) into the middle of homopyrimidine oligodeoxynucleotides (twisted intercalating nucleic acids, TINA) obtained via postsynthetic Sonogashira coupling reaction led to extraordinary high thermal stability of Hoogsteen-type triplexes and duplexes, whereas Watson-Crick-type duplexes of the same nucleotide content were destabilized. Modified oligonucleotides were synthesized using the phosphoramidite of (S)-1-(4,4'-dimethoxytriphenylmethyloxy)-3-(4-iodo-benzyloxy)-propan-2-ol followed by treatment of the oligonucleotide on a CPG-support with the Sonogashira-coupling reaction mixture containing different ethynylaryls. Bulged insertion of the pyrene derivative 5 into oligonucleotides was found to be the best among the tested modifications for binding to the Hoogsteen-type triplexes and duplexes. Thus, at pH 7.2 an oligonucleotide with cytidine content of 36% possessing two bulged insertions of 5 separated by three bases formed a stable triplex (T(m) = 43.0 degrees C), whereas the native oligonucleotide was unable to bind to the target duplex. The corresponding Watson-Crick-type duplex with the same oligonucleotide had T(m) of 38.0 degrees C at pH 7.2, while the T(m) of unmodified dsDNA was 47.0 degrees C. Experiments with mismatched oligonucleotides, luminescent properties, and potential applications of TINA technology is discussed.
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Affiliation(s)
- Vyacheslav V Filichev
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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12
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Triple helix-tetraplex equilibrium for G-rich oligonucleotide N3′→P5′ phosphoramidates: role of molecular concentration and counterions. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2005.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Abstract
T(m) is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. Beyond a simple numerical value (the T(m)), a thermal denaturation experiment, in which the folded fraction of a structure is plotted vs. temperature, yields important thermodynamic information. We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves.
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Affiliation(s)
- Jean-Louis Mergny
- Laboratoire de Biophysique, INSERM UR565, CNRS UMR 5153, Muséum National d'Histoire Naturelle, 75231 Paris, France.
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14
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Ray A, Kumar GS, Maiti M. Molecular aspects on the interaction of aristololactam-beta-D-glucoside with H(L)-form deoxyribonucleic acid structures. J Biomol Struct Dyn 2003; 21:141-51. [PMID: 12854966 DOI: 10.1080/07391102.2003.10506912] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Synthetic alternating GC-rich DNA polymers can adopt Hoogsteen base-paired structures (H(L)-form) under the influence of low pH and temperature. The interaction of aristololactam-beta-D-glucoside (ADG), a natural glucoside derivative of aristolochia group of alkaloids, with protonation-induced structures (H(L)-form) of poly(dG-dC).poly(dG-dC) and poly(dG-m(5)dC).poly(dG-m(5)dC) has been studied using different biophysical techniques. The binding of ADG to protonated DNA is characterized by typical hypochromism and bathochromism of the absorption spectrum of the alkaloid, quenching of steady state fluorescence intensity, decrease in quantum yield, increase in fluorescence polarization anisotropy values, increase in thermal transition temperature of polynucleotides following alkaloid binding and perturbation of circular dichroic spectrum of polynucleotides as a result of its interaction with the alkaloid. Scatchard analysis of the data indicates that ADG binds to protonated structures in a nonlinear noncooperative manner. The binding parameters determined from spectrophotometric titration data employing excluded site model indicate that protonated poly(dG-m(5)dC).poly(dG-m(5)dC) is more favorable for ADG binding than the corresponding nonmethylated analog. The binding of ADG to protonated structures renders a higher degree of stabilization against thermal denaturation compared to respective B-form-ADG interactions and induces a conformational switch to a bound altered form which is different from its interaction with B- and Z-form DNA structures. Thermodynamic parameters (Delta G degrees, Delta H degrees and Delta S degrees ) obtained by van't Hoff analysis of the data indicate that the binding of alkaloid to protonated structures is an exothermic process and the binding free energy arises primarily from a negative enthalpy change. Moreover, the binding leads to an increase in the contour length of protonated DNAs. These results suggest that ADG possibly binds to protonated DNAs by the mechanism of intercalation.
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Affiliation(s)
- Arghya Ray
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Calcutta 700 032, India.
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15
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Abstract
This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800-800 cm(-1) relevant for DNA/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base-sugar, sugar-phosphate and sugar moiety. The approach allows comparisons of information obtained from one spectral region with another. The IR band library should facilitate detailed and unambiguous assignment of structural changes, ligand binding, etc. in nucleic acids from IR spectra. is aimed at highlighting specific features that are useful for following major changes in nucleic acid structures. also concerns some recent results, where IR spectroscopy has been used to obtain semi-quantitative information on coexisting modes of sugar pucker in oligonucleotides.
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Affiliation(s)
- Martina Banyay
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, S-106 91, Stockholm, Sweden
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16
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Dias N, Sénamaud-Beaufort C, Forestier El EL, Auvin C, Hélène C, Ester Saison-Behmoaras T. RNA hairpin invasion and ribosome elongation arrest by mixed base PNA oligomer. J Mol Biol 2002; 320:489-501. [PMID: 12096905 DOI: 10.1016/s0022-2836(02)00474-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recently, we have shown that peptide nucleic acid (PNA) tridecamers targeted to the codon 74, 128 and 149 regions of Ha-ras mRNA arrested translation elongation in vitro. Our data demonstrated for the first time that PNAs with mixed base sequence targeted to the coding region of a messenger RNA could arrest the translation machinery and polypeptide chain elongation. The peculiarity of the complexes formed with PNA tridecamers and Ha-ras mRNA rests upon the stability of PNA-mRNA hybrids, which are not dissociated by cellular proteins or multiple denaturing conditions. In the present study, we show that shorter PNAs such as a dodecamer or an undecamer targeted to the codon 74 region arrest translation elongation in vitro. The 13, 12, and 11-mer PNAs contain eight and the 10-mer PNA seven contiguous pyrimidine residues. Upon binding with parallel Hoogsteen base-pairing to the PNA-RNA duplex, six of the cytosine bases and one thymine base of a second PNA can form C.G*C(+) and T.A*T triplets. Melting experiments show two well-resolved transitions corresponding to the dissociation of the third strand from the core duplex and to melting of duplex at higher temperature. The enzymatic structure mapping of a target 27-mer RNA revealed a hairpin structure that is disrupted upon binding of tri-, dodeca-, undeca- and decamer PNAs. We show that the non-bonded nucleobase overhangs on the RNA stabilize the PNA-RNA hybrids and probably assist the PNA in overcoming the stable secondary structure of the RNA target. The great stability of PNA-RNA duplex and triplex structures allowed us to identify both 1:1 and 2:1 PNA-RNA complexes using matrix-assisted laser desorption/ionization time-of -flight mass spectrometry. Therefore, it is possible to successfully target mixed sequences in structured regions of messenger RNA with short PNA oligonucleotides that form duplex and triplex structures that can arrest elongating ribosomes.
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Affiliation(s)
- Nathalie Dias
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U201 CNRS UMR, 8646, 43 rue Cuvier 75231, Paris Cédex 05, France
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Abstract
Mainly driven by the needs of antisense research, a large number of oligonucleotide analogues have been prepared and evaluated over the last 15 years. Besides minor structural modifications of the building blocks of DNA and RNA itself, a considerable effort has been devoted to the de novo design of nucleoside analogues with improved binding properties. A particularly successful concept turned out to be that of conformational restriction. This review focuses on recent advances in this area and tries to summarize scope and limitations of this design principle.
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Affiliation(s)
- Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland.
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Cubero E, Aviñó A, de la Torre BG, Frieden M, Eritja R, Luque FJ, González C, Orozco M. Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives. J Am Chem Soc 2002; 124:3133-42. [PMID: 11902902 DOI: 10.1021/ja011928+] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of parallel-stranded duplexes of DNA-containing a mixture of guanines (G) and adenines (A) is studied by means of molecular dynamics (MD) simulation, as well as NMR and circular dichroism (CD) spectroscopy. Results demonstrate that the structure is based on the Hoogsteen motif rather than on the reverse Watson-Crick one. Molecular dynamics coupled to thermodynamic integration (MD/TI) calculations and melting experiments allowed us to determine the effect of 8-amino derivatives of A and G and of 8-amino-2'-deoxyinosine on the stability of parallel-stranded duplexes. The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes.
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Affiliation(s)
- Elena Cubero
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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Cubero E, Luque FJ, Orozco M. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes. J Am Chem Soc 2001; 123:12018-25. [PMID: 11724610 DOI: 10.1021/ja011200t] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Poly d(A:T) parallel-stranded DNA duplexes based on the Hoogsteen and reverse Watson-Crick hydrogen bond pairing are studied by means of extensive molecular dynamics (MD) simulations and molecular mechanics coupled to Poisson-Boltzmann (MM-PB/SA) calculations. The structural, flexibility, and reactivity characteristics of Hoogsteen and reverse Watson-Crick parallel duplexes are described from the analysis of the trajectories. Theoretical calculations show that the two parallel duplexes are less stable than the antiparallel Watson-Crick duplex. The difference in stability between antiparallel and parallel duplexes increases steadily as the length of the duplex increases. The reverse Watson-Crick arrangement is slightly more stable than the Hoogsteen duplex, the difference being also increased linearly with the length of the duplex. A subtle balance of intramolecular and solvation terms is responsible for the preference of a given helical structure.
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Affiliation(s)
- E Cubero
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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20
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Arya DP, Coffee RL, Willis B, Abramovitch AI. Aminoglycoside-nucleic acid interactions: remarkable stabilization of DNA and RNA triple helices by neomycin. J Am Chem Soc 2001; 123:5385-95. [PMID: 11389616 DOI: 10.1021/ja003052x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stabilization of poly(dA).2poly(dT) triplex, a 22-base DNA triplex, and poly(rA).2poly(rU) triple helix by neomycin is reported. The melting temperatures, the association and dissociation kinetic parameters, and activation energies (E(on) and E(off)) for the poly(dA).2poly(dT) triplex in the presence of aminoglycosides and other triplex binding ligands were determined by UV thermal analysis. Our results indicate that: (i) neomycin stabilizes DNA triple helices, and the double helical structures composed of poly(dA).poly(dT) are virtually unaffected. (ii) Neomycin is the most active and triplex-selective stabilization agent among all aminoglycosides, previously studied minor groove binders, and polycations. Its selectivity (DeltaT(m3-->2) vs DeltaT(m2)(-->)(1)) exceeds most intercalating drugs that bind to triple helices. (iii) Neomycin selectively stabilizes DeltaT(m3)(-->)(2) for a mixed 22-base DNA triplex containing C and T bases in the pyrimidine strand. (iv) The rate constants of formation of triplex (k(on)) are significantly enhanced upon increasing molar ratios of neomycin, making triplex association rates closer to duplex association rates. (v) E(on) values become more negative upon increasing concentration of aminoglycosides (paromomycin and neomycin). E(off) values do not show any change for most aminoglycosides except neomycin. (vi) Aminoglycosides can effectively stabilize RNA [poly(rA).2poly(rU)] triplex, with neomycin[being one of the most active ligands discovered to date (second only to ellipticine). (vii) The stabilization effect of aminoglycosides on triple helices is parallel to their toxic behavior, suggesting a possible role of intramolecular triple helix (H-DNA) stabilization by the aminoglycosides.
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Affiliation(s)
- D P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
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21
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Geinguenaud F, Liquier J, Brevnov MG, Petrauskene OV, Alexeev YI, Gromova ES, Taillandier E. Parallel self-associated structures formed by T,C-rich sequences at acidic pH. Biochemistry 2000; 39:12650-8. [PMID: 11027145 DOI: 10.1021/bi000746+] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligonucleotides of nonregular heteropyrimidine sequences incorporating or not incorporating purine residues 5'-d(ACTCCCTTCTCCTCTCTA), 5'-d(ACTCCCTGGTCCTCTCTA), 5'-d(TCTCTCCTGGTCCCTCC), and 5'-d(TCTCTCCTCTTCCCTCC) can form self-associated parallel-stranded (ps) structures at pH 4-5.5. The ps structures were identified by studying at neutral and acidic pH UV melting transitions, FTIR spectra, and fluorescence of pyrene-labeled oligonucleotides as well as by chemical joining of 5'-phosphorylated oligonucleotides. A gel electrophoresis run for oligonucleotides 5'-d(TCTCTCCTCTTCCCTCC) and 5'-d(ACTCCCTTCTCCTCTCTA) has shown the formation of homoduplexes at low DNA strand concentrations. Ps structures are held by C-C(+) base pairs and have N- and S-types of sugar puckering as detected by FTIR spectroscopy in the millimolar concentration range. Guanine inserts as well as thymine and purine inserts into an oligomeric cytosine sequence make the formation of the tetraplex i-motif unfavorable. MvaI restriction endonuclease, which recognizes the CCT/AGG sequence in DNA, does not cleave parallel pseudosubstrates.
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Affiliation(s)
- F Geinguenaud
- Laboratoire de Spectroscopie Biomoléculaire, UPRES-A CNRS 7031, UFR de Médecine, Université Paris Nord, F-93017 Bobigny Cedex, France
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22
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Lacroix L, Mergny JL. Chemical modification of pyrimidine TFOs: effect on i-motif and triple helix formation. Arch Biochem Biophys 2000; 381:153-63. [PMID: 11019831 DOI: 10.1006/abbi.2000.1934] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to form more stable triple helical structures or to prevent their degradation in cells, oligonucleotide analogs are routinely used, either in the backbone or among the bases. The target sequence chosen for this study is a 16-base-long oligopurine-oligopyrimidine region present in the human neurotrophin 4/5 gene. Seven different chemical modifications were tested for their effect on (i) triple helix formation and (ii) i-DNA stability. i-DNA is a tetrameric structure involving hemiprotonated C x C+ base pairs, which may act as a competing structure for triplex formation, especially in the case of a cytosine-rich third strand. At acid pH, oligophosphoramidates formed the most stable triple helix, whereas oligonucleotides including 5-propynyl-dU formed a stable i-motif which precluded triplex formation. Only two candidates stabilized triple helices at neutral pH: oligonucleotides with phosphoramidate linkage and phosphodiester oligonucleotides containing 5-methyl-dC and 5-propynyl-dU.
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Affiliation(s)
- L Lacroix
- Laboratoire de Biophysique, Muséum National d'Historie Naturelle, INSERM U201, CNRS UMR 8646, Paris, France
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Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 1999; 13:3217-30. [PMID: 10617571 PMCID: PMC317201 DOI: 10.1101/gad.13.24.3217] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.
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Affiliation(s)
- G A Patikoglou
- Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021 USA
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Praseuth D, Guieysse AL, Hélène C. Triple helix formation and the antigene strategy for sequence-specific control of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:181-206. [PMID: 10807007 DOI: 10.1016/s0167-4781(99)00149-9] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Specific gene expression involves the binding of natural ligands to the DNA base pairs. Among the compounds rationally designed for artificial regulation of gene expression, oligonucleotides can bind with a high specificity of recognition to the major groove of double helical DNA by forming Hoogsteen type bonds with purine bases of the Watson-Crick base pairs, resulting in triple helix formation. Although the potential target sequences were originally restricted to polypurine-polypyrimidine sequences, considerable efforts were devoted to the extension of the repertoire by rational conception of appropriate derivatives. Efficient tools based on triple helices were developed for various biochemical applications such as the development of highly specific artificial nucleases. The antigene strategy remains one of the most fascinating fields of triplex application to selectively control gene expression. Targeting of genomic sequences is now proved to be a valuable concept on a still limited number of studies; local mutagenesis is in this respect an interesting application of triplex-forming oligonucleotides on cell cultures. Oligonucleotide penetration and compartmentalization in cells, stability to intracellular nucleases, accessibility of the target sequences in the chromatin context, the residence time on the specific target are all limiting steps that require further optimization. The existence and the role of three-stranded DNA in vivo, its interaction with intracellular proteins is worth investigating, especially relative to the regulation of gene transcription, recombination and repair processes.
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Affiliation(s)
- D Praseuth
- Laboratoire de Biophysique, INSERM U201, CNRS UMR 8646, Muséum National d'Histoire Naturelle, Paris, France
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25
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Mills M, Arimondo PB, Lacroix L, Garestier T, Hélène C, Klump H, Mergny JL. Energetics of strand-displacement reactions in triple helices: a spectroscopic study. J Mol Biol 1999; 291:1035-54. [PMID: 10518941 DOI: 10.1006/jmbi.1999.3014] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA triple helices offer exciting new perspectives toward oligonucleotide-directed inhibition of gene expression. Purine and GT triplexes appear to be the most promising motifs for stable binding under physiological conditions compared to the pyrimidine motif, which forms at relatively low pH. There are, however, very little data available for comparison of the relative stabilities of the different classes of triplexes under identical conditions. We, therefore, designed a model system which allowed us to set up a competition between the oligonucleotides of the purine and pyrimidine motifs targeting the same Watson-Crick duplex. Several conclusions may be drawn: (i) a weak hypochromism at 260 nm is associated with purine triplex formation; (ii) delta H degree of GA, GT and TC triplex formation (at pH 7.0) was calculated as -0.1, -2.5 and -6.1 kcal/mol per base triplet, respectively. This unexpectedly low delta H degree for the purine triple helix formation implies that its delta G degree is nearly temperature-independent and it explains why these triplexes may still be observed at high temperatures. In contrast, the pyrimidine triplex is strongly favoured at lower temperatures; (iii) as a consequence, in a system where two third-strands compete for triplex formation, displacement of the GA or GT strand by a pyrimidine strand may be observed at neutral pH upon lowering the temperature. This original purine-to-pyrimidine triplex conversion shows a significant hypochromism at 260 nm and a hyperchromism at 295 nm which is similar to the duplex-to-triplex conversion in the pyrimidine motif. Further evidence for this triplex-to-triplex conversion is provided by mung bean-nuclease foot-printing assay.
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Affiliation(s)
- M Mills
- Department of Biochemistry, University of Cape Town, Republic of South Africa
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27
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Escudé C, Nguyen CH, Kukreti S, Janin Y, Sun JS, Bisagni E, Garestier T, Hélène C. Rational design of a triple helix-specific intercalating ligand. Proc Natl Acad Sci U S A 1998; 95:3591-6. [PMID: 9520410 PMCID: PMC19880 DOI: 10.1073/pnas.95.7.3591] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.
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Affiliation(s)
- C Escudé
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Institut National de la Santé et de la Recherche Médicale U 201, Centre National de la Recherche Scientifique, Unité de Recherche Associ-ee 481, Paris, France
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28
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Nguyen CH, Marchand C, Delage S, Sun JS, Garestier T, Hélène C, Bisagni E. Synthesis of 13H-Benzo[6,7]- and 13H-Benzo[4,5]indolo[3,2-c]- quinolines: A New Series of Potent Specific Ligands for Triplex DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja971707x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chi Hung Nguyen
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Christophe Marchand
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Stéphane Delage
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Jian-Sheng Sun
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Thérèse Garestier
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Claude Hélène
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
| | - Emile Bisagni
- Contribution from the UMR 176 CNRS−Institut Curie, Section Recherche 15 rue Georges Clémenceau, 91405 Orsay, France, and Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U 201 et CNRS URA 481 43 rue Cuvier, 75231 Paris Cedex 05, France
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Baudoin O, Teulade-Fichou MP, Vigneron JP, Lehn JM. Cyclobisintercaland Macrocycles: Synthesis and Physicochemical Properties of Macrocyclic Polyamines Containing Two Crescent-Shaped Dibenzophenanthroline Subunits. J Org Chem 1997. [DOI: 10.1021/jo970496b] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Olivier Baudoin
- Laboratoire de Chimie des Interactions Moléculaires (CNRS, UPR 285), Collège de France, 11 place M. Berthelot, 75005 Paris, France
| | - Marie-Paule Teulade-Fichou
- Laboratoire de Chimie des Interactions Moléculaires (CNRS, UPR 285), Collège de France, 11 place M. Berthelot, 75005 Paris, France
| | - Jean-Pierre Vigneron
- Laboratoire de Chimie des Interactions Moléculaires (CNRS, UPR 285), Collège de France, 11 place M. Berthelot, 75005 Paris, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie des Interactions Moléculaires (CNRS, UPR 285), Collège de France, 11 place M. Berthelot, 75005 Paris, France
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Zhou-Sun B, Sun J, Gryaznov SM, Liquier J, Garestier T, Hélène C, Taillandier E. A physico-chemical study of triple helix formation by an oligodeoxythymidylate with N3'--> P5' phosphoramidate linkages. Nucleic Acids Res 1997; 25:1782-7. [PMID: 9108161 PMCID: PMC146641 DOI: 10.1093/nar/25.9.1782] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Non-denaturing gel retardation assay, DNA melting experiments and FTIR spectroscopy were used to characterize the triple helix formed by a 15mer 2'-deoxythymidylate with N3'-->P5'phosphoramidate linkages with its target sequence. The results indicate that: (i) the pentadecadeoxythymidylate with phosphoramidate linkages [dT15(np)] is highly potent to form a triple helix with a dT15*dA15target duplex through Hoogsteenbase-pairing; (ii) it forms a dT15(np)*dA15xdT15(np) triplex with the single-stranded oligo-2'-deoxyadenylate (dA15) without detectable double-helical intermediate; (iii) it does not only form a triple helix on the dT15*dA15target duplex, but also partially displaces the dT15 strand from the dT15*dA15duplex to form a dT15(np)*dA15xdT15(np) complex.
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Affiliation(s)
- B Zhou-Sun
- Laboratoire de Spectroscopie Biomoléculaire, CNRS URA 1430, UFR Santé Médecine Biologie Humaine, Université Paris-Nord, 74, rue Marcel Cachin, 93017 Bobigny, France
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Kandimalla ER, Agrawal S. Hoogsteen DNA duplexes of 3'-3'- and 5'-5'-linked oligonucleotides and trip formation with RNA and DNA pyrimidine single strands: experimental and molecular modeling studies. Biochemistry 1996; 35:15332-9. [PMID: 8952484 DOI: 10.1021/bi961505y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA oligonucleotide sequences containing two parallel complementary strands attached through 3'-3' and 5'-5' linkages were synthesized. These oligonucleotides from Hoogsteen base-paired parallel-stranded (PS) hairpin duplexes under appropriate conditions [Kandimalla, E. R., Agrawal, S., Venkataraman, G., & Sasisekharan, V. (1995a) J. Am. Chem. Soc. 117, 6416-6417]. UV melting experiments show that these Hoogsteen hairpin duplexes have a lower thermal stability than that of the Watson-Crick (WC) hairpin duplex (antiparallel) of the same sequence. The circular dichroism (CD) spectrum of the Hoogsteen duplex is different from the canonical B-DNA WC duplex spectrum. The formation of the Hoogsteen duplex is pH-dependent since protonation of cytosine requires lower pH conditions. Studies with oligonucleotides of different loop sizes revel that three- and two-base loops are optimum for the formation of stable Hoogsteen duplexes with 3'-3' and 5'-5' linkages, respectively. The guanine residues in the loop stabilize the duplex as a result of G-G interactions as confirmed by molecular modeling studies. The new PS Hoogsteen duplexes form stable triplexes with complementary (antiparallel to the purine domain) single-stranded RNA and DNA pyrimidine sequences in Py.Pu:Py (pyrimidine third strand-purine WC strand:pyrimidine WC strand) motif. The thermal stability of the resulting triplexes is much higher than that of the conventional triplex (binding of a Hoogsteen pyrimidine third strand to a WC duplex) of the same sequence. The CD spectra of the new triplexes are similar to those of conventional triplexes, suggesting that no conformational change occurs as a result of 3'-3' or 5'-5' linkage. A molecular modeling study was carried out to examine the stereochemical feasibility of the Hoogsteen duplexes and formation of triplexes with single-stranded pyrimidine complementary strands.
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Abstract
Oligonucleotide directed triple helix formation allows the sequence-specific recognition of the major groove of double-helical DNA. Recently synthesized base analogs and backbones, such as N3'-->P5' phosphoramidates, allow stable triplexes to be formed under physiological conditions. However, it remains a challenge to design new oligomers that would extend the range of recognition sequences (which are still limited to oligopurine-rich tracts). Oligonucleotide directed triple helix formation could be used to control biological processes such as transcription and replication. Three-stranded structures formed during recombination processes have been further characterized.
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Affiliation(s)
- J S Sun
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U201, Centre National de la Recherche Scientifique, URA481, Paris, France.
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