1
|
Díaz-Casado L, Serrano-Chacón I, Montalvillo-Jiménez L, Corzana F, Bastida A, Santana AG, González C, Asensio JL. De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot. Chemistry 2021; 27:6204-6212. [PMID: 33368678 DOI: 10.1002/chem.202005026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex-duplex junctions, while presenting a poorer affinity for G-quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex-duplex junctions, including the one observed in the HIV-1 LTR-III sequence. The structure of the complex between a quadruplex-duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex-duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G-tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G-quadruplex-forming regions of the genome.
Collapse
Affiliation(s)
- Laura Díaz-Casado
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Israel Serrano-Chacón
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Laura Montalvillo-Jiménez
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Madre de Dios, 53., 26006, Logroño, Spain
| | - Agatha Bastida
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| |
Collapse
|
2
|
Abou Assi H, Lin YC, Serrano I, González C, Damha MJ. Probing Synergistic Effects of DNA Methylation and 2′-β-Fluorination on i-Motif Stability. Chemistry 2017; 24:471-477. [PMID: 29096420 DOI: 10.1002/chem.201704591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Hala Abou Assi
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Yu Chen Lin
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Israel Serrano
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Masad J. Damha
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| |
Collapse
|
3
|
Lietard J, Abou Assi H, Gómez-Pinto I, González C, Somoza MM, Damha MJ. Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res 2017; 45:1619-1632. [PMID: 28100695 PMCID: PMC5389548 DOI: 10.1093/nar/gkw1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/28/2016] [Indexed: 01/13/2023] Open
Abstract
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.
Collapse
Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.,Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | - Hala Abou Assi
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| |
Collapse
|
4
|
Dans PD, Ivani I, Hospital A, Portella G, González C, Orozco M. How accurate are accurate force-fields for B-DNA? Nucleic Acids Res 2017; 45:4217-4230. [PMID: 28088759 PMCID: PMC5397185 DOI: 10.1093/nar/gkw1355] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 12/27/2016] [Indexed: 11/28/2022] Open
Abstract
Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing ‘experimental models’, which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of 1H nuclear magnetic resonance (NMR). The study allowed us to check directly for experimental NMR observables on duplexes previously not solved, and also to assess the reliability of ‘experimental structures’. We observed that technical details in the annealing procedures can induce non-negligible local changes in the final structures. We also found that while not all theoretical simulations are equally reliable, those obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive power in the multi-microsecond timescale and can be safely used to reproduce global structure of DNA duplexes and fine sequence-dependent details.
Collapse
Affiliation(s)
- Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Ivan Ivani
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Guillem Portella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Carlos González
- Instituto Química Física Rocasolano. Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| |
Collapse
|
5
|
Kellner S, DeMott MS, Cheng CP, Russell BS, Cao B, You D, Dedon PC. Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol 2017; 13:888-894. [PMID: 28604692 PMCID: PMC5577368 DOI: 10.1038/nchembio.2407] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/30/2017] [Indexed: 12/12/2022]
Abstract
Genomic modification with sulfur as phosphorothioate (PT) is widespread among prokaryotes, including human pathogens. Apart from its physiological functions, the redox and nucleophilic properties of PT sulfur suggest effects on bacterial fitness in stressful environments. Here we show that PTs are dynamic and labile DNA modifications that cause genomic instability during oxidative stress. Using coupled isotopic labeling-mass spectrometry, we observed sulfur replacement in PTs at a rate of ~2%/h in unstressed Escherichia coli and Salmonella enterica. While PT levels were unaffected by exposure to hydrogen peroxide (H2O2) or hypochlorous acid (HOCl), PT turnover increased to 3.8–10%/h for HOCl and was unchanged for H2O2, consistent with repair of HOCl-induced sulfur damage. PT-dependent HOCl sensitivity extended to cytotoxicity and DNA strand-breaks, which occurred at orders-of-magnitude lower doses of HOCl than H2O2. The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during human infections.
Collapse
Affiliation(s)
- Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ching Pin Cheng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Brandon S Russell
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bo Cao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Delin You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Singapore
| |
Collapse
|
6
|
Mir B, Solés X, González C, Escaja N. The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures. Sci Rep 2017; 7:2772. [PMID: 28584239 PMCID: PMC5459817 DOI: 10.1038/s41598-017-02723-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/05/2017] [Indexed: 01/07/2023] Open
Abstract
Incorporation of pseudoisocytidine (psC), a neutral analogue of protonated cytidine, in i-motifs has been studied by spectroscopic methods. Our results show that neutral psC:C base pairs can stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C+ stacks. When psC occupies central positions, the resulting i-motifs are only observed at low pH and psC:C+ or psC:psC+ hemiprotonated base pairs are formed instead of their neutral analogs. Overall, our results suggest that positively charged base pairs are necessary to stabilize this non-canonical DNA structure.
Collapse
Affiliation(s)
- B Mir
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - X Solés
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - C González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain. .,BIOESTRAN, associated unit UB-CSIC, Spain.
| | - N Escaja
- Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain. .,BIOESTRAN, associated unit UB-CSIC, Spain.
| |
Collapse
|
7
|
Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ. Stabilization of i-motif structures by 2'-β-fluorination of DNA. Nucleic Acids Res 2016; 44:4998-5009. [PMID: 27166371 PMCID: PMC4914123 DOI: 10.1093/nar/gkw402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.
Collapse
Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Robert W Harkness
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Christopher J Wilds
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | | | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| |
Collapse
|
8
|
Garavís M, Escaja N, Gabelica V, Villasante A, González C. Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs. Chemistry 2015; 21:9816-24. [PMID: 26013031 DOI: 10.1002/chem.201500448] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.
Collapse
Affiliation(s)
- Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).,Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit 33600 Pessac (France).,Inserm, ARNA Laboratory, 146 Rue Leo Saignat, 33000 Bordeaux (France)
| | - Alfredo Villasante
- Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).
| |
Collapse
|
9
|
Escaja N, Gómez-Pinto I, Viladoms J, Pedroso E, González C. The effect of loop residues in four-stranded dimeric structures stabilized by minor groove tetrads. Org Biomol Chem 2014; 11:4804-10. [PMID: 23764570 DOI: 10.1039/c3ob40741a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some DNA oligonucleotides can fold back and self-associate forming dimeric structures stabilized by intermolecular base pairs. The resulting antiparallel dimer is a tightly packed four-stranded structure formed by a core of minor groove tetrads connected by short loops of unpaired nucleotides. We have explored the sequential requirements for the loop residues and have found that this family of structures is only stable with one- and two-residue loops, with the stability of the former ones being only marginal. Two-residue loops with purines in the first position give rise to the most stable structures due to their enhanced stacking interaction with the adjacent minor groove tetrad. On the other hand, pyrimidines confer more stability than purines in the second position of the loop.
Collapse
Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica, Universitat de Barcelona, C/Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | |
Collapse
|
10
|
Escaja N, Viladoms J, Garavís M, Villasante A, Pedroso E, González C. A minimal i-motif stabilized by minor groove G:T:G:T tetrads. Nucleic Acids Res 2012; 40:11737-47. [PMID: 23042679 PMCID: PMC3526289 DOI: 10.1093/nar/gks911] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d<pTCGTTTCGTT>. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.
Collapse
Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
11
|
Vishnyakov A, Gor GY, Lee MT, Neimark AV. Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions. J Phys Chem A 2011; 115:5201-9. [DOI: 10.1021/jp200509u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aleksey Vishnyakov
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Gennady Yu. Gor
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Ming-Tsung Lee
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| | - Alexander V. Neimark
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854, United States
| |
Collapse
|
12
|
Lucas R, Gómez-Pinto I, Aviñó A, Reina JJ, Eritja R, González C, Morales JC. Highly polar carbohydrates stack onto DNA duplexes via CH/π interactions. J Am Chem Soc 2011; 133:1909-16. [PMID: 21244028 DOI: 10.1021/ja108962j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbohydrate-nucleic acid contacts are known to be a fundamental part of some drug-DNA recognition processes. Most of these interactions occur through the minor groove of DNA, such as in the calicheamicin or anthracycline families, or through both minor and major groove binders such as in the pluramycins. Here, we demonstrate that carbohydrate-DNA interactions are also possible through sugar capping of a DNA double helix. Highly polar mono- and disaccharides are capable of CH/π stacking onto the terminal DNA base pair of a duplex as shown by NMR spectroscopy. The energetics of the carbohydrate-DNA interactions vary depending on the stereochemistry, polarity, and contact surface of the sugar involved and also on the terminal base pair. These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials.
Collapse
Affiliation(s)
- Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain
| | | | | | | | | | | | | |
Collapse
|
13
|
León E, Navarro-Avilés G, Santiveri CM, Flores-Flores C, Rico M, González C, Murillo FJ, Elías-Arnanz M, Jiménez MA, Padmanabhan S. A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix. Nucleic Acids Res 2010; 38:5226-41. [PMID: 20410074 PMCID: PMC2926617 DOI: 10.1093/nar/gkq277] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Direct targeting of critical DNA-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. Structural descriptions for this, though often proposed for bacterial and phage repressor–antirepressor systems, are unavailable. Here, we describe the structural and functional basis of how the Myxococcus xanthus CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarA and CarH repress the carB operon in the dark. CarS, produced in the light, physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB. The NMR structure of CarS1, a functional CarS variant, reveals a five-stranded, antiparallel β-sheet fold resembling SH3 domains, protein–protein interaction modules prevalent in eukaryotes but rare in prokaryotes. NMR studies and analysis of site-directed mutants in vivo and in vitro unveil a solvent-exposed hydrophobic pocket lined by acidic residues in CarS, where the CarA DNA recognition helix docks with high affinity in an atypical ligand-recognition mode for SH3 domains. Our findings uncover an unprecedented use of the SH3 domain-like fold for protein–protein recognition whereby an antirepressor mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription.
Collapse
Affiliation(s)
- Esther León
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Watts JK, Martín-Pintado N, Gómez-Pinto I, Schwartzentruber J, Portella G, Orozco M, González C, Damha MJ. Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res 2010; 38:2498-511. [PMID: 20071751 PMCID: PMC2853132 DOI: 10.1093/nar/gkp1225] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybrids of RNA with arabinonucleic acids 2′F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2′F-ANA•RNA and ANA•RNA hybrids indicates that the increased binding affinity of 2′F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2′F–purine H8) which contrasts with unfavorable 2′-OH–nucleobase steric interactions in the case of ANA. While both 2′F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2′F-ANA strand’s structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA•RNA duplex showed lower uptake of counterions than its 2′F-ANA•RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2′F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2′F-ANA•RNA and ANA•RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important.
Collapse
Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Popova AM, Kálai T, Hideg K, Qin PZ. Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes. Biochemistry 2009; 48:8540-50. [PMID: 19650666 DOI: 10.1021/bi900860w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to "scan" a given DNA molecule in order to interrogate its local structural and dynamic features.
Collapse
Affiliation(s)
- Anna M Popova
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | | | | | | |
Collapse
|
16
|
Viladoms J, Escaja N, Frieden M, Gómez-Pinto I, Pedroso E, González C. Self-association of short DNA loops through minor groove C:G:G:C tetrads. Nucleic Acids Res 2009; 37:3264-75. [PMID: 19321501 PMCID: PMC2691830 DOI: 10.1093/nar/gkp191] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d<pCGCTCCGT>, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes.
Collapse
Affiliation(s)
- Júlia Viladoms
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, C/. Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
17
|
An S, Barany G, Musier-Forsyth K. Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase. Nucleic Acids Res 2008; 36:2514-21. [PMID: 18310681 PMCID: PMC2377447 DOI: 10.1093/nar/gkn063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) are an essential family of enzymes that catalyze the attachment of amino acids to specific tRNAs during translation. Previously, we showed that base-specific recognition of the tRNA(Pro) acceptor stem is critical for recognition by Escherichia coli prolyl-tRNA synthetase (ProRS), but not for human ProRS. To further delineate species-specific differences in acceptor stem recognition, atomic group mutagenesis was used to probe the role of sugar-phosphate backbone interactions in recognition of human tRNA(Pro). Incorporation of site-specific 2'-deoxynucleotides, as well as phosphorothioate and methylphosphonate modifications within the tRNA acceptor stem revealed an extensive network of interactions with specific functional groups proximal to the first base pair and the discriminator base. Backbone functional groups located at the base of the acceptor stem, especially the 2'-hydroxyl of A66, are also critical for aminoacylation catalytic efficiency by human ProRS. Therefore, in contrast to the bacterial system, backbone-specific interactions contribute significantly more to tRNA recognition by the human enzyme than base-specific interactions. Taken together with previous studies, these data show that ProRS-tRNA acceptor stem interactions have co-adapted through evolution from a mechanism involving 'direct readout' of nucleotide bases to one relying primarily on backbone-specific 'indirect readout'.
Collapse
Affiliation(s)
- Songon An
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | |
Collapse
|
18
|
López de la Osa J, Bateman DA, Ho S, González C, Chakrabartty A, Laurents DV. Getting specificity from simplicity in putative proteins from the prebiotic earth. Proc Natl Acad Sci U S A 2007; 104:14941-6. [PMID: 17855563 PMCID: PMC1986592 DOI: 10.1073/pnas.0706876104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Indexed: 11/18/2022] Open
Abstract
Can unique protein structures arise from a limited set of amino acids present on the prebiotic earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited "alphabet" of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic earth.
Collapse
Affiliation(s)
- Jaime López de la Osa
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - David A. Bateman
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Sylvia Ho
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Carlos González
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - Avijit Chakrabartty
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Douglas V. Laurents
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| |
Collapse
|
19
|
Escaja N, Gómez-Pinto I, Viladoms J, Rico M, Pedroso E, González C. Induced-fit recognition of DNA by small circular oligonucleotides. Chemistry 2007; 12:4035-42. [PMID: 16607659 DOI: 10.1002/chem.200600050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have investigated the molecular interaction between cyclic and linear oligonucleotides. We have found that short cyclic oligonucleotides can induce hairpinlike structures in linear DNA fragments. By using NMR and CD spectroscopy we have studied the interaction of the cyclic oligonucleotide d<pCCTTCGGT> with d<pCAGTCCCT>, as well as with its two linear analogs d(GTCCCTCA) and d(CTCAGTCC). Here we report the NMR structural study of these complexes. Recognition between these oligonucleotides occurs through formation of four intermolecular Watson-Crick base pairs. The three-dimensional structure is stabilized by two tetrads, formed by facing the minor-groove side of the Watson-Crick base pairs. Overall, the structure is similar to those observed previously in other quadruplexes formed by minor-groove alignment of Watson-Crick base pairs. However, in this case the complexes are heterodimeric and are formed by two different tetrads (G:C:A:T and G:C:G:C). These complexes represent a new model of DNA recognition by small cyclic oligonucleotides, increasing the number of potential applications of these interesting molecules.
Collapse
Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica, Universitat de Barcelona, Martí I Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
20
|
Escaja N, Gómez-Pinto I, Pedroso E, Gonzalez C. Four-Stranded DNA Structures Can Be Stabilized by Two Different Types of Minor Groove G:C:G:C Tetrads. J Am Chem Soc 2007; 129:2004-14. [PMID: 17260988 DOI: 10.1021/ja066172z] [Citation(s) in RCA: 26] [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
Four-stranded nucleic acid structures are central to many processes in biology and in supramolecular chemistry. It has been shown recently that four-stranded DNA structures are not only limited to the classical guanine quadruplex but also can be formed by tetrads resulting from the association of Watson-Crick base pairs. Such an association may occur through the minor or the major groove side of the base pairs. Structures stabilized by minor groove tetrads present distinctive features, clearly different from the canonical guanine quadruplex, making these quadruplexes a unique structural motif. Within our efforts to study the sequence requirements for the formation of this unusual DNA motif, we have determined the solution structure of the cyclic oligonucleotide dpCCGTCCGT by two-dimensional NMR spectroscopy and restrained molecular dynamics. This molecule self-associates, forming a symmetric dimer stabilized by two G:C:G:C tetrads with intermolecular G-C base pairs. Interestingly, although the overall three-dimensional structure is similar to that found in other cyclic and linear oligonucleotides of related sequences, the tetrads that stabilize the structure of dpCCGTCCGT are different to other minor groove G:C:G:C tetrads found earlier. Whereas in previous cases the G-C base pairs aligned directly, in this new tetrad the relative position of the two base pairs is slipped along the axis defined by the base pairs. This is the first time that a quadruplex structure entirely stabilized by slipped minor groove G:C:G:C tetrads is observed in solution or in the solid state. However, an analogous arrangement of G-C base pairs occurs between the terminal residues of contiguous duplexes in some DNA crystals. This structural polymorphism between minor groove GC tetrads may be important in stabilization of higher order DNA structures.
Collapse
Affiliation(s)
- Núria Escaja
- Instituto de Química Física "Rocasolano", CSIC, C/, Serrano 119, 28006 Madrid, Spain
| | | | | | | |
Collapse
|
21
|
Affiliation(s)
- Mark Lukin
- Department of Pharmacological Sciences, State University of New York at Stony Brook, School of Medicine, 11794-8651, USA
| | | |
Collapse
|
22
|
Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2006. [DOI: 10.1016/s1574-1400(06)02013-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
23
|
Gómez-Pinto I, Marchán V, Gago F, Grandas A, González C. Solution structure and stability of a disulfide cross-linked nucleopeptide duplex. Chem Commun (Camb) 2004:2558-9. [PMID: 14594279 DOI: 10.1039/b307300a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NMR methods are used to study the structure and stability of the duplex formed by the nucleopeptide [Ac-Cys-Gly-Ala-Hse(p3'dGCATGC)-Ala-OH]2[S-S], in which the oligonucleotide is self-complementary and the cysteine residues of the two peptide chains form a disulfide bridge; thermal transitions and NMR-derived structural calculations are consistent with a 3-D structure in which the oligonucleotide forms a standard B-DNA helix without significant distortions; the peptide chains are relatively disordered in solution and lie in the minor groove of the DNA helix; this nucleopeptide duplex exhibits a high melting temperature, indicating that peptide-oligonucleotide conjugates containing cysteines are suitable molecules to establish cross-links between DNA strands and stabilize the duplex.
Collapse
Affiliation(s)
- Irene Gómez-Pinto
- Instituto de Química Física Rocasolano, C/Serrano 119, 28006 Madrid, Spain
| | | | | | | | | |
Collapse
|
24
|
Gómez-Pinto I, Cubero E, Kalko SG, Monaco V, van der Marel G, van Boom JH, Orozco M, González C. Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct. J Biol Chem 2004; 279:24552-60. [PMID: 15047709 DOI: 10.1074/jbc.m311751200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional solution structure of two DNA decamers of sequence d(CCACXGGAAC)-(GTTCCGGTGG) with a modified nucleotide containing a cholesterol derivative (X) in its C1 '(chol)alpha or C1 '(chol)beta diastereoisomer form has been determined by using NMR and restrained molecular dynamics. This DNA derivative is recognized with high efficiency by the UvrB protein, which is part of the bacterial nucleotide excision repair, and the alpha anomer is repaired more efficiently than the beta one. The structures of the two decamers have been determined from accurate distance constraints obtained from a complete relaxation matrix analysis of the NOE intensities and torsion angle constraints derived from J-coupling constants. The structures have been refined with molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long range electrostatic interactions. These calculations converge to well defined structures whose conformation is intermediate between the A- and B-DNA families as judged by the root mean square deviation but with sugar puckerings and groove shapes corresponding to a distorted B-conformation. Both duplex adducts exhibit intercalation of the cholesterol group from the major groove of the helix and displacement of the guanine base opposite the modified nucleotide. Based on these structures and molecular dynamics calculations, we propose a tentative model for the recognition of damaged DNA substrates by the UvrB protein.
Collapse
Affiliation(s)
- Irene Gómez-Pinto
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, C/. Serrano 119, 28006 Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Vishnyakov A, Neimark AV. Molecular Model of Dimethylmethylphosphonate and Its Interactions with Water. J Phys Chem A 2004. [DOI: 10.1021/jp035708p] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aleksey Vishnyakov
- Center for Modeling and Characterization of Nanoporous Materials, TRI/Princeton, 601 Prospect Avenue, Princeton, New Jersey 08542
| | - Alexander V. Neimark
- Center for Modeling and Characterization of Nanoporous Materials, TRI/Princeton, 601 Prospect Avenue, Princeton, New Jersey 08542
| |
Collapse
|
26
|
Escaja N, Gómez-Pinto I, Rico M, Pedroso E, González C. Structures and stabilities of small DNA dumbbells with Watson-Crick and Hoogsteen base pairs. Chembiochem 2003; 4:623-32. [PMID: 12851932 DOI: 10.1002/cbic.200300578] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The structures and stabilities of cyclic DNA octamers of different sequences have been studied by NMR and CD spectroscopy and by restrained molecular dynamics. At low oligonucleotide concentrations, some of these molecules form stable monomeric structures consisting of a short stem of two base pairs connected by two mini-loops of two residues. To our knowledge, these dumbbell-like structures are the smallest observed to date. The relative stabilities of these cyclic dumbbells have been established by studying their melting transitions. Dumbbells made up purely of GC stems are more stable than those consisting purely of AT base pairs. The order of the base pairs closing the loops also has an important effect on the stabilities of these structures. The NMR data indicate that there are significant differences between the solution structures of dumbbells with G-C base pairs in the stem compared to those with A-T base pairs. In the case of dumbbells with G-C base pairs, the residues in the stem form a short segment of a BDNA helix stabilized by two Watson-Crick base pairs. In contrast, in the case of d<pCATTCATT>, the stem is formed by two A-T base pairs with the glycosidic angles of the adenine bases in a syn conformation, most probably forming Hoogsteen base pairs. Although the conformations of the loop residues are not very well defined, the thymine residues at the first position of the loop are observed to fold back into the minor groove of the stem.
Collapse
Affiliation(s)
- Nuria Escaja
- Departament de Química Orgànica, Universitat de Barcelona, C/. Martì I Franquès 1-11, 08028-Barcelona, Spain
| | | | | | | | | |
Collapse
|
27
|
Escaja N, Gelpí JL, Orozco M, Rico M, Pedroso E, González C. Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad. J Am Chem Soc 2003; 125:5654-62. [PMID: 12733903 DOI: 10.1021/ja0344157] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution structure of a cyclic oligonucleotide d<pCGCTCATT> has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson-Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson-Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na(+) cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson-Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA-DNA recognition.
Collapse
Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica, Universitat de Barcelona, C/, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
28
|
Abstract
The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model).
Collapse
Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta 30332, USA.
| | | |
Collapse
|
29
|
Gómez-Pinto I, Marchán V, Gago F, Grandas A, González C. Solution structure and stability of tryptophan-containing nucleopeptide duplexes. Chembiochem 2003; 4:40-9. [PMID: 12512075 DOI: 10.1002/cbic.200390012] [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: 11/09/2022]
Abstract
Covalently linked peptide-oligonucleotide hybrids were used as models for studying tryptophan-DNA interactions. The structure and stability of several hybrids in which peptides and oligonucleotides are linked through a phosphodiester bond between the hydroxy group of a homoserine (Hse) side chain and the 3'-end of the oligonucleotide, have been studied by both NMR and CD spectroscopy and by restrained molecular dynamics methods. The three-dimensional solution structure of the complex between Ac-Lys-Trp-Lys-Hse(p3'dGCATCG)-Ala-OH (p=phosphate, Ac=acetyl) and its complementary strand 5'dCGTAGC has been determined from a set of 276 experimental NOE distances and 33 dihedral angle constraints. The oligonucleotide structure is a well-defined duplex that belongs to the B-form family of DNA structures. The covalently linked peptide adopts a folded structure in which the tryptophan side chain stacks against the 3'-terminal guanine moiety, which forms a cap at the end of the duplex. This stacking interaction, which resembles other tryptophan-nucleobase interactions observed in some protein-DNA complexes, is not observed in the single-stranded form of Ac-Lys-Trp-Lys-Hse(p3'dGCATCG)-Ala-OH, where the peptide chain is completely disordered. A comparison with the pure DNA duplex, d(5'GCTACG3')-(5'CGTAGC3'), indicates that the interaction between the peptide and the DNA contributes to the stability of the nucleopeptide duplex. The different contributions that stabilize this complex have been evaluated by studying other nucleopeptide compounds with related sequences.
Collapse
Affiliation(s)
- Irene Gómez-Pinto
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | | | | | | | | |
Collapse
|
30
|
Kosikov KM, Gorin AA, Lu XJ, Olson WK, Manning GS. Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J Am Chem Soc 2002; 124:4838-47. [PMID: 11971734 DOI: 10.1021/ja0125218] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have been subjected to energy minimization to determine the conformational effect of the asymmetric elimination of phosphate charge. We report bending angles, directions of bending, and detailed structural characteristics such as groove widths and local base-pair parameters. Our principal results are that charge neutralization on one face of the DNA induces significant bending toward the neutralized face, in agreement with theoretical predictions on a simplified model and experimental data on a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methylphosphonate substitutions is nearly the same as the conformation produced by charge neutralization of the phosphates. Individual isomers, however, cover a wide range of structures, with the magnitude and direction of overall bending sensitive to the precise stereochemical pattern of neutralization. Our simulation does not explicitly contain counterions, and the results therefore suggest that counterions can influence DNA structure by neutralizing the phosphate charge. These data provide new hints into the molecular mechanisms which underlie the deformations of DNA structure induced by the binding of positively charged proteins and other tightly associated cationic species.
Collapse
Affiliation(s)
- Konstantin M Kosikov
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Wright-Rieman Laboratories, Piscataway, New Jersey 08854-8087, USA
| | | | | | | | | |
Collapse
|
31
|
Barvík I, Stĕpánek J, Bok J. Explicit solvent molecular dynamics simulation of duplex formed by the modified oligonucleotide with alternating phosphate/phosphonate internucleoside linkages and its natural counterpart. J Biomol Struct Dyn 2002; 19:863-75. [PMID: 11922841 DOI: 10.1080/07391102.2002.10506790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Impact of the internucleoside linkage modification by inserting a methylene group on the ability of the modified oligonucleotide to hybridize with a natural DNA strand was studied by fully solvated molecular dynamics (MD) simulations. Three undecamer complexes were analyzed: natural dT(11).dA(11) duplex as a reference and two its analogs with alternating modified and natural linkages in the deoxyadenosine chain. The isopolar, non-isosteric modified linkages were of 5'-O-PO(2)-CH(2)-O-3' (5'PC3') or 5'-O-CH(2)-PO(2)-O-3' (5'CP3') type. Simulations were performed by using the AMBER 5.0 software package with the force field completed by a set of parameters needed to model the modified segments. Both modifications were found to lead to double helical complexes, in which the thymidine strand as well as deoxyriboses and unmodified linkages in the adenosine strand adopted conformations typical for the B-type structure. For each of the two conformational richer modified linkages two stable conformations were found at 300 K: the -ggt and ggt for the 5'PC3' and ggg, tgg for the 5'CP3', respectively. Both modified chains adopted helical conformations with heightened values of the inclination parameter but without affecting the Watson-Crick hydrogen bonds.
Collapse
Affiliation(s)
- Ivan Barvík
- Institute of Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic.
| | | | | |
Collapse
|