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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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2
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Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis. Molecules 2021; 26:molecules26195871. [PMID: 34641414 PMCID: PMC8510488 DOI: 10.3390/molecules26195871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.
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3
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Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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4
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Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function. Comput Struct Biotechnol J 2019; 17:797-804. [PMID: 31312417 PMCID: PMC6607312 DOI: 10.1016/j.csbj.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i) selective recognition of DNA by proteins; ii) regulation of RNA cleavage by site-specific mutations; iii) intermolecular interaction of proteins with their target DNA or RNA; iv) formation of PNA:DNA hybrid duplexes. This review systematically summarizes hydrogen exchange theory for base-paired imino protons of nucleic acids. Base-pair opening kinetics explain how the DNA can be selectively recognized by its target proteins. Base-pair opening kinetics explain the mechanisms by which site-specific mutations regulate RNA cleavage. Hydrogen exchange studies can elucidate the intermolecular interaction of proteins with their target DNA or RNA.
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5
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Lindahl V, Villa A, Hess B. Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput Biol 2017; 13:e1005463. [PMID: 28369121 PMCID: PMC5393899 DOI: 10.1371/journal.pcbi.1005463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
- * E-mail:
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6
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Bianchi C, Zangi R. Dual base-flipping of cytosines in a CpG dinucleotide sequence. Biophys Chem 2013; 187-188:14-22. [PMID: 24469333 DOI: 10.1016/j.bpc.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022]
Abstract
Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.
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Affiliation(s)
- Caterina Bianchi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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Stellwagen E, Peters JP, Maher LJ, Stellwagen NC. DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. Biochemistry 2013; 52:4138-48. [PMID: 23675817 PMCID: PMC3727640 DOI: 10.1021/bi400118m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The intrinsic curvature of seven 98 bp DNA molecules containing up to four centrally located A6-tracts has been measured by gel and capillary electrophoresis as a function of the number and arrangement of the A-tracts. At low cation concentrations, the electrophoretic mobility observed in polyacrylamide gels and in free solution decreases progressively with the increasing number of phased A-tracts, as expected for DNA molecules with increasingly curved backbone structures. Anomalously slow electrophoretic mobilities are also observed for DNA molecules containing two pairs of phased A-tracts that are out of phase with each other, suggesting that out-of-phase distortions of the helix backbone do not cancel each other out. The mobility decreases observed for the A-tract samples are due to curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities are observed for a molecule with four out-of-phase A-tracts and one with no A-tracts. Surprisingly, the curvature of DNA A-tracts is gradually lost when the monovalent cation concentration is increased to ∼200 mM, regardless of whether the cation is a hydrophilic ion like Na+, NH4+, or Tris+ or a hydrophobic ion like tetrabutylammonium. The decrease in A-tract curvature with increasing ionic strength, along with the known decrease in A-tract curvature with increasing temperature, suggests that DNA A-tracts are not significantly curved under physiological conditions.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 United States
| | - Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905 United States
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905 United States
| | - Nancy C. Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 United States
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8
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Bianchi C, Zangi R. Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites. J Phys Chem B 2013; 117:2348-58. [DOI: 10.1021/jp312145b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caterina Bianchi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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9
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Bruylants G, Boccongelli M, Snoussi K, Bartik K. Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex. Biochemistry 2009; 48:8473-82. [PMID: 19670874 DOI: 10.1021/bi900615z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.
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Affiliation(s)
- Gilles Bruylants
- Molecular and Biomolecular Engineering, Service Matières et Matériaux, CP165/64, Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, 1050 Bruxelles, Belgium
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10
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Abstract
AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.
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11
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González-Bulnes L, Gallego J. Indirect Effects Modulating the Interaction between DNA and a Cytotoxic Bisnaphthalimide Reveal a Two-Step Binding Process. J Am Chem Soc 2009; 131:7781-91. [DOI: 10.1021/ja901505p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luis González-Bulnes
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain
| | - José Gallego
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain
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12
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Dupont JA, Snoussi K. Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G*C) base-pair kinetics. J Biol Phys 2009; 35:231-43. [PMID: 19669575 DOI: 10.1007/s10867-009-9151-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 03/23/2009] [Indexed: 10/20/2022] Open
Abstract
NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino proton have been used to probe enhanced thermostability and conformational rearrangements induced by Mg(2+) in two key activity fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) of the encephalomyocarditis virus (EMCV) picornavirus internal ribosome entry site (IRES). We have measured some of their r(G*C) base-pair lifetimes and dissociation constants under different MgCl(2) conditions, and we compare them with those of other short RNA duplexes. The RNA fragment r(CACCUGGCGACAGGUG) adopts two topologies, a palindromic duplex with two conformations and a hairpin, whose equilibrium can be monitored: the duplex form is destabilized by Mg(2+) and temperature, a delicate balance wherein the entropic contribution of the free energy helps populate the hairpin state. For both fragments, the opening rates of the r(G*C) pairs are lower in the presence of Mg(2+) and their dissociation constants are smaller or comparable. Analysis of the results suggests that Mg(2+) has a preferential and specific effect on the r(CACCUGGCGACAGGUG) hairpin in the region close to the r(G*C) closing pair of the GCGA tetraloop, and the ion moves diffusively around r(GGCCAAAAGCC), thereby differentiating the GNRA and RAAA hairpin motifs that are both involved in the biological regulation functions of the EMCV IRES.
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Affiliation(s)
- J A Dupont
- Free University of Brussels, 1050 Brussels, Belgium
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13
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Dong Q, Stellwagen E, Stellwagen NC. Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry 2009; 48:1047-55. [PMID: 19154116 DOI: 10.1021/bi8020718] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding of five different monovalent cations to DNA oligomers containing A-tracts, runs of four or more contiguous adenine residues, has been assessed by capillary electrophoresis, using the Replacement Ion method. In this method, a nonbinding cation in the background electrolyte is gradually replaced by a binding cation, keeping the ionic strength of the solution constant. Monovalent cation binding reduces the effective charge of an A-tract-containing oligomer, decreasing its free solution mobility. The cations bind in the A-tract minor groove, because the binding site can be blocked by the minor groove binding drug netropsin. Li(+), NH(4)(+), and Tris(+) ions bind to A-tracts with similar affinities; the binding of Na(+) ions is weaker, and K(+) ion binding is highly variable. Each A-tract appears to bind one monovalent cation upon saturation of the binding site(s). For a given cation, the apparent dissociation constants depend on A-tract sequence and orientation, but not on the phasing of the A-tracts with respect to the helix repeat. Differences in the cooperativity of binding of the various cations to A-tracts with different sequences suggest that monovalent cation binding may be coupled with a conformational transition leading to the formation of the characteristic narrow minor groove A-tract structure.
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Affiliation(s)
- Qian Dong
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA
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14
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Ding H, Majumdar A, Tolman JR, Greenberg MM. Multinuclear NMR and kinetic analysis of DNA interstrand cross-link formation. J Am Chem Soc 2008; 130:17981-7. [PMID: 19053196 PMCID: PMC2653107 DOI: 10.1021/ja807845n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Recently, a phenylselenyl-modified thymidine (2) was shown to produce DNA interstrand cross-links (ICLs) via two mechanisms. Photolysis of 2 generates 5-(2'-deoxyuridinyl)methyl radical (1), the reactive intermediate that results from formal hydrogen atom abstraction from the thymine methyl group. This reactive intermediate reacts with the opposing dA and is the first example of a DNA radical that produces ICLs. Kinetic competition studies support the proposal that the rate-limiting step in ICL formation from 1 involves rotation about the glycosidic bond and that the rate constant for this process is influenced by the flanking sequence. Cross-links also form with the opposing dA when 2 is treated with mild oxidants that result in the formation of an intermediate methide-like species (4). Kinetic experiments reveal that 4 reacts with azide, a model nucleophile, via an S(N)2' pathway. Previous experiments suggested that the same product is produced via 1 or 4 but that the initially formed cross-link rearranges during the enzyme digestion and isolation procedures. In situ product analysis by NMR using synthetic, doubly labeled duplex DNA containing (13)C-2 and (15)N(1)-dA provides definitive evidence that the kinetic ICL products formed via the radical and oxidative pathways are the same and correspond to that arising from formal alkylation of N(1)-dA. Furthermore, analysis of the thermodynamic product formed upon rearrangement indicates that the primary product isomerizes via an associative mechanism in DNA.
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Affiliation(s)
- Hui Ding
- Department of Chemistry and Biomolecular NMR Center, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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15
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Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36:4941-55. [PMID: 18653524 PMCID: PMC2528173 DOI: 10.1093/nar/gkn473] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein···DNA recognition in the ‘κB’ family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate κB site recognized by the proto-oncogenic ‘c-Rel’ subfamily of NF-κB transcription factors. Simulations of the κB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation—including a peculiar state arising at ≈0.7 μs and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at ≈1 μs) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-κB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
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Affiliation(s)
- Cameron Mura
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093-0365, USA.
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16
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Hydrogen Exchange Rates of the DNA Oligomer Duplex, d[CGCGCGCCATAAC]/d[GTTATGGCGCGCG] Determined by NMR Spectroscopy. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.12.2543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT. Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 2007; 449:433-7. [PMID: 17704764 PMCID: PMC2754044 DOI: 10.1038/nature06131] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 07/27/2007] [Indexed: 01/07/2023]
Abstract
The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U*A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U*A or U*G base pairs in a background of approximately 10(9) T*A or C*G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T*A and U*A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.
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Affiliation(s)
- Jared B Parker
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
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18
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Lee JH, Pardi A. Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme. Nucleic Acids Res 2007; 35:2965-74. [PMID: 17439958 PMCID: PMC1891724 DOI: 10.1093/nar/gkm184] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The thermodynamics and kinetics for base-pair opening of the P1 duplex of the Tetrahymena group I ribozyme were studied by NMR hydrogen exchange experiments. The apparent equilibrium constants for base pair opening were measured for most of the imino protons in the P1 duplex using the base catalysts NH3, HPO42− or TRIS. These equilibrium constants were also measured for several modified P1 duplexes, and the C-2·G23 base pair was the most stable base pair in all the duplexes. The conserved U-1·G22 base pair is required for activity of the ribozyme and the data here show that this wobble base pair destabilizes neighboring base pairs on only one side of the wobble. A 2′-OMe modification on the U-3 residue stabilized its own base pair but had little effect on the neighboring base pairs. Three base pairs, U-1·G22, C-2·G23 and A2·U21 showed unusual equilibrium constants for opening and possible implications of the opening thermodynamics of these base pairs on the undocking rates of the P1 helix with catalytic core are discussed.
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Affiliation(s)
- Joon-Hwa Lee
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA and Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Arthur Pardi
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA and Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
- *To whom correspondence should be addressed. +1-303-492-6263+1-303-492-5894
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19
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Priyakumar UD, MacKerell AD. Computational approaches for investigating base flipping in oligonucleotides. Chem Rev 2006; 106:489-505. [PMID: 16464016 DOI: 10.1021/cr040475z] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- U Deva Priyakumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 21201, USA
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20
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Grajcar L, El Amri C, Ghomi M, Fermandjian S, Huteau V, Mandel R, Lecomte S, Baron MH. Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy. Biopolymers 2006; 82:6-28. [PMID: 16425174 DOI: 10.1002/bip.20455] [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: 12/15/2022]
Abstract
We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl- and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA>pdA and (pA)n>>(pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity.
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Affiliation(s)
- Lydie Grajcar
- Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France
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21
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Várnai P, Canalia M, Leroy JL. Opening Mechanism of G·T/U Pairs in DNA and RNA Duplexes: A Combined Study of Imino Proton Exchange and Molecular Dynamics Simulation. J Am Chem Soc 2004; 126:14659-67. [PMID: 15521786 DOI: 10.1021/ja0470721] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The opening pathway of wobble pairs dG.T and rG.U has been investigated in four DNA and two RNA duplexes. Using NMR spectroscopy, we measured the imino proton exchange of both G(H1) and T/U(H3), catalyzed by ammonia, tris, and OH(-), and we calculated the free energy surface related to G.T/U opening by molecular dynamics simulations. Taken together the experimental and theoretical results, we suggest that wobble pairs open through a coupled rotation of the bases toward the major groove where exchange of both imino protons takes place with the surrounding water.
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Affiliation(s)
- Péter Várnai
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS UPR 9080, 13 Rue Pierre et Marie Curie, Paris 75005, France
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22
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Wärmländer S, Sandström K, Leijon M, Gräslund A. Base-pair dynamics in an antiparallel DNA triplex measured by catalyzed imino proton exchange monitored via 1H NMR spectroscopy. Biochemistry 2003; 42:12589-95. [PMID: 14580205 DOI: 10.1021/bi034479u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using (1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rate between the two forms (i.e., the on/off-rate of the third strand) was measured to be 5 s(-1) at 1 degrees C, and the base-pair dynamics of both forms were investigated separately. Both Watson-Crick and reverse Hoogsteen base pairs were found to have base-pair lifetimes in the order of milliseconds. The stability of the Watson-Crick base pairs was, however, substantially increased in the presence of the third strand. In the DNA triplex, the opening dynamics of the reverse Hoogsteen base pairs was significantly faster than the dynamics of the Watson-Crick pairs. We were able to conclude that, for both Watson-Crick and reverse Hoogsteen base pairs, spontaneous and individual opening from within the closed base triplet is the dominating opening pathway.
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Affiliation(s)
- Sebastian Wärmländer
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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23
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Bohon J, de los Santos CR. Structural effect of the anticancer agent 6-thioguanine on duplex DNA. Nucleic Acids Res 2003; 31:1331-8. [PMID: 12582253 PMCID: PMC150222 DOI: 10.1093/nar/gkg203] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The incorporation of 6-thioguanine (S6G) into DNA is an essential step in the cytotoxic activity of thiopurines. However, the structural effects of this substitution on duplex DNA have not been fully characterized. Here, we present the solution structures of DNA duplexes containing S6G opposite thymine (S6G.T) and opposite cytosine (S6G.C), solved by high-resolution NMR spectroscopy and restrained molecular dynamics. The data indicate that both duplexes adopt right-handed helical conformations with all Watson-Crick hydrogen bonding in place. The S6G.T structures exhibit a wobble-type base pairing at the lesion site, with thymine shifted toward the major groove and S6G displaced toward the minor groove. Aside from the lesion site, the helices, including the flanking base pairs, are not highly perturbed by the presence of the lesion. Surprisingly, thermal dependence experiments suggest greater stability in the S6G-T mismatch than the S6G-C base pair.
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Affiliation(s)
- Jen Bohon
- Department of Biophysics, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA
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