1
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Mondal S, Mukherjee S, Bagchi B. Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water. J Phys Chem B 2024; 128:2076-2086. [PMID: 38389118 DOI: 10.1021/acs.jpcb.3c06519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Saumyak Mukherjee
- Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum D-44780, Germany
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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2
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Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC. Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Nucleic Acids Res 2020; 48:10713-10725. [PMID: 33045724 DOI: 10.1093/nar/gkaa836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (>2 pN) and high salt concentration (>0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.
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Affiliation(s)
- Parth Rakesh Desai
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA.,Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Cao J, Ma W, Lyu K, Zhuang L, Cong H, Deng H. Twist and sliding dynamics between interpenetrated frames in Ti-MOF revealing high proton conductivity. Chem Sci 2020; 11:3978-3985. [PMID: 34122868 PMCID: PMC8152619 DOI: 10.1039/c9sc06500h] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/19/2020] [Indexed: 11/25/2022] Open
Abstract
We report the design and synthesis of a titanium catecholate framework, MOF-217, comprised of 2,4,6-tri(3,4-dihydroxyphenyl)-1,3,5-triazine (TDHT) and isolated TiO6 clusters, with 2-fold interpenetrated srs topology. The dynamics of the organic linker, breaking the C 3h symmetry, allowed for reversible twist and sliding between interpenetrated frames upon temperature change and the inclusion of small molecules. Introduction of 28 wt% imidazole into the pores of MOF-217, 28% Im-in-MOF-217, resulted in four orders of magnitude increase in proton conductivity, due to the appropriate accommodation of imidazole molecules and their proton transfer facilitated by the H-bond to the MOF structure across the pores. This MOF-based proton conductor can be operated at 100 °C with a proton conductivity of 1.1 × 10-3 S cm-1, standing among the best performing anhydrous MOF proton conductors at elevated temperature. The interframe dynamics represents a unique feature of MOFs that can be accessed in the future design of proton conductors.
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Affiliation(s)
- Jing Cao
- UC Berkeley-Wuhan University Joint Innovative Center, The Institute for Advanced Studies, Wuhan University Luojiashan Wuhan 430072 China
| | - Wenjie Ma
- College of Chemistry and Molecular Sciences, Wuhan University Luojiashan Wuhan 430072 China
| | - Kangjie Lyu
- College of Chemistry and Molecular Sciences, Wuhan University Luojiashan Wuhan 430072 China
| | - Lin Zhuang
- UC Berkeley-Wuhan University Joint Innovative Center, The Institute for Advanced Studies, Wuhan University Luojiashan Wuhan 430072 China
- College of Chemistry and Molecular Sciences, Wuhan University Luojiashan Wuhan 430072 China
| | - Hengjiang Cong
- College of Chemistry and Molecular Sciences, Wuhan University Luojiashan Wuhan 430072 China
| | - Hexiang Deng
- UC Berkeley-Wuhan University Joint Innovative Center, The Institute for Advanced Studies, Wuhan University Luojiashan Wuhan 430072 China
- College of Chemistry and Molecular Sciences, Wuhan University Luojiashan Wuhan 430072 China
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4
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Mandal S, Zhang X, Pandey S, Mao H. Single-Molecule Topochemical Analyses for Large-Scale Multiplexing Tasks. Anal Chem 2019; 91:13485-13493. [PMID: 31553880 PMCID: PMC7011503 DOI: 10.1021/acs.analchem.9b02483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multitasking is the pivotal feature in next-generation chemo- or bioanalyses. However, simultaneous analyses rarely exceed over three different tasks, which is ascribed to the limited space to accommodate analyzing units and the compromised signal-to-noise (S/N) level as the number of tasks increases. Here, by leveraging superior S/N of single-molecule techniques, we analyzed five microRNA biomarkers by spatially encoding miRNA recognition units with nanometers resolution in a DNA template, while decoding the analyte binding temporally in seconds. The hairpin stem is interspersed by internal loops to encode recognition units for miRNA. By mechanical unfolding of the hairpin, individual internal loops are sequentially interrogated for the binding of each miRNA. Using this so-called topochemical spatiotemporal analysis, we were able to achieve subpicomolar detection limits of miRNAs. We anticipate that this new single-molecule topochemical analysis can massively analyze single-molecule targets.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Xiaoqing Zhang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China), School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Shankar Pandey
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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5
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Jeong J, Kim HD. Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking. PHYSICAL REVIEW LETTERS 2019; 122:218101. [PMID: 31283336 PMCID: PMC7819736 DOI: 10.1103/physrevlett.122.218101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 05/13/2023]
Abstract
Base-pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule fluorescence resonance energy transfer, we measured the lifetimes of tightly bent DNA loops with and without base-pair mismatch. Surprisingly, for loops captured by stackable sticky ends which leave single-stranded DNA breaks (or nicks) upon annealing, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings suggest that base-pair mismatch increases bending stress at the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability.
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6
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Naked eye detection of an amplified gene using metal particle-based DNA transport within functionalized porous interfaces. Talanta 2019; 195:97-102. [DOI: 10.1016/j.talanta.2018.11.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 11/17/2022]
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7
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Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:23-32. [PMID: 28510218 DOI: 10.1007/s12551-016-0243-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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8
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Jha JK, Ramachandran R, Chattoraj DK. Opening the Strands of Replication Origins-Still an Open Question. Front Mol Biosci 2016; 3:62. [PMID: 27747216 PMCID: PMC5043065 DOI: 10.3389/fmolb.2016.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Dhruba K Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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9
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Levens D, Baranello L, Kouzine F. Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:259-268. [PMID: 28510225 DOI: 10.1007/s12551-016-0216-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Laura Baranello
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fedor Kouzine
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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10
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Saoji M, Zhang D, Paukstelis PJ. Probing the role of sequence in the assembly of three-dimensional DNA crystals. Biopolymers 2016; 103:618-26. [PMID: 26015367 DOI: 10.1002/bip.22688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/21/2015] [Accepted: 05/21/2015] [Indexed: 11/10/2022]
Abstract
DNA is a widely used biopolymer for the construction of nanometer-scale objects due to its programmability and structural predictability. One long-standing goal of the DNA nanotechnology field has been the construction of three-dimensional DNA crystals. We previously determined the X-ray crystal structure of a DNA 13-mer that forms a continuously hydrogen bonded three-dimensional lattice through Watson-Crick and non-canonical base pairs. Our current study sets out to understand how the sequence of the Watson-Crick duplex region influences crystallization of this 13-mer. We screened all possible self-complementary sequences in the hexameric duplex region and found 21 oligonucleotides that crystallized. Sequence analysis showed that one specific Watson-Crick pair influenced the crystallization propensity and the speed of crystal self-assembly. We determined X-ray crystal structures for 13 of these oligonucleotides and found sequence-specific structural changes that suggests that this base pair may serve as a structural anchor during crystal assembly. Finally, we explored the crystal self-assembly and nucleation process. Solution studies indicated that these oligonucleotides do not form base pairs in the absence of cations, but that the addition of divalent cations leads to rapid self-assembly to higher molecular weight complexes. We further demonstrate that crystals grown from mixtures of two different oligonucleotide sequences contain both oligonucleotides. These results suggest that crystal self-assembly is nucleated by the formation of the Watson-Crick duplexes initiated by a simple chemical trigger. This study provides new insight into the role of sequence for the assembly of periodic DNA structures.
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Affiliation(s)
- Maithili Saoji
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Daoning Zhang
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742.,Biomolecular NMR Facility, College Park, MD, 20742
| | - Paul J Paukstelis
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742.,Center for Biomolecular Structure & Organization, College Park, MD, 20742.,Maryland Nanocenter, College Park, MD, 20742
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11
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Giovan SM, Hanke A, Levene SD. DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation. Biopolymers 2015; 103:528-38. [PMID: 26014845 DOI: 10.1002/bip.22683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/15/2015] [Accepted: 05/15/2015] [Indexed: 01/11/2023]
Abstract
For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of J as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to J for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length, the error in J arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, kB T. For larger systems, however, the deviations between harmonic and exact J values increase approximately linearly with size.
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Affiliation(s)
- Stefan M Giovan
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX, 75083
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX, 78520
| | - Stephen D Levene
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX, 75083.,Department of Physics, University of Texas at Dallas, Richardson, TX, 75083.,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, 75083
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12
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Fujita M, Watanabe S, Yoshizawa M, Yamamoto J, Iwai S. Analysis of structural flexibility of damaged DNA using thiol-tethered oligonucleotide duplexes. PLoS One 2015; 10:e0117798. [PMID: 25679955 PMCID: PMC4332495 DOI: 10.1371/journal.pone.0117798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 12/31/2014] [Indexed: 11/18/2022] Open
Abstract
Bent structures are formed in DNA by the binding of small molecules or proteins. We developed a chemical method to detect bent DNA structures. Oligonucleotide duplexes in which two mercaptoalkyl groups were attached to the positions facing each other across the major groove were prepared. When the duplex contained the cisplatin adduct, which was proved to induce static helix bending, interstrand disulfide bond formation under an oxygen atmosphere was detected by HPLC analyses, but not in the non-adducted duplex, when the two thiol-tethered nucleosides were separated by six base pairs. When the insert was five and seven base pairs, the disulfide bond was formed and was not formed, respectively, regardless of the cisplatin adduct formation. The same reaction was observed in the duplexes containing an abasic site analog and the (6-4) photoproduct. Compared with the cisplatin case, the disulfide bond formation was slower in these duplexes, but the reaction rate was nearly independent of the linker length. These results indicate that dynamic structural changes of the abasic site- and (6-4) photoproduct-containing duplexes could be detected by our method. It is strongly suggested that the UV-damaged DNA-binding protein, which specifically binds these duplexes and functions at the first step of global-genome nucleotide excision repair, recognizes the easily bendable nature of damaged DNA.
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Affiliation(s)
- Masashi Fujita
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka, 560–8531, Japan
| | - Shun Watanabe
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka, 560–8531, Japan
| | - Mariko Yoshizawa
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka, 560–8531, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka, 560–8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka, 560–8531, Japan
- * E-mail:
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13
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Coexistence of twisted, plectonemic, and melted DNA in small topological domains. Biophys J 2014; 106:1174-81. [PMID: 24606941 DOI: 10.1016/j.bpj.2014.01.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 01/19/2023] Open
Abstract
DNA responds to small changes in force and torque by over- or undertwisting, forming plectonemes, and/or melting bubbles. Although transitions between either twisted and plectonemic conformations or twisted and melted conformations have been described as first-order phase transitions, we report here a broadening of these transitions when the size of a topological domain spans several kilobasepairs. Magnetic tweezers measurements indicate the coexistence of three conformations at subpicoNewton force and linking number densities ∼-0.06. We present a statistical physics model for DNA domains of several kilobasepairs by calculating the full partition function that describes this three-state coexistence. Real-time analysis of short DNA tethers at constant force and torque shows discrete levels of extension, representing discontinuous changes in the size of the melting bubble, which should reflect the underlying DNA sequence. Our results provide a comprehensive picture of the structure of underwound DNA at low force and torque and could have important consequences for various biological processes, in particular those that depend on local DNA melting, such as the initiation of replication and transcription.
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14
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Taranova M, Hirsh AD, Perkins NC, Andricioaei I. Role of microscopic flexibility in tightly curved DNA. J Phys Chem B 2014; 118:11028-36. [PMID: 25155114 PMCID: PMC4174995 DOI: 10.1021/jp502233u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
genetic material in living cells is organized into complex
structures in which DNA is subjected to substantial contortions. Here
we investigate the difference in structure, dynamics, and flexibility
between two topological states of a short (107 base pair) DNA sequence
in a linear form and a covalently closed, tightly curved circular
DNA form. By employing a combination of all-atom molecular dynamics
(MD) simulations and elastic rod modeling of DNA, which allows capturing
microscopic details while monitoring the global dynamics, we demonstrate
that in the highly curved regime the microscopic flexibility of the
DNA drastically increases due to the local mobility of the duplex.
By analyzing vibrational entropy and Lipari–Szabo NMR order
parameters from the simulation data, we propose a novel model for
the thermodynamic stability of high-curvature DNA states based on
vibrational untightening of the duplex. This novel view of DNA bending
provides a fundamental explanation that bridges the gap between classical
models of DNA and experimental studies on DNA cyclization, which so
far have been in substantial disagreement.
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Affiliation(s)
- Maryna Taranova
- Department of Chemistry, University of California , 1102 Natural Sciences 2, Irvine, California 92697, United States
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15
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Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res 2014; 42:1857-72. [PMID: 24234453 PMCID: PMC3919604 DOI: 10.1093/nar/gkt1116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/21/2022] Open
Abstract
Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5' flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5' ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.
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Affiliation(s)
- Timothy D. Craggs
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Richard D. Hutton
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Alfonso Brenlla
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Malcolm F. White
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - J. Carlos Penedo
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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16
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Jo SD, Kim JS, Joe CO, Mok H, Nam YS. Small interfering RNA nunchucks with a hydrophobic linker for efficient intracellular delivery. Macromol Biosci 2013; 14:195-201. [PMID: 24106091 DOI: 10.1002/mabi.201300291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/22/2013] [Indexed: 12/12/2022]
Abstract
The high stiffness and low spatial charge density of siRNA limit the effectiveness of the electrostatic condensation of siRNA with cationic polyelectrolytes. Here, a facile method to stabilize nanoscale siRNA/polyelectrolyte complexes by introducing a reductively cleavable alkyl chain to siRNA as a hybrophobic linker of dimeric siRNA conjugates is reported. The increased length of the hydrophobic linker increases the intracellular translocation and gene silencing activity of the dimeric siRNA conjugates when they are complexed with linear polyethylenimine (LPEI). The results suggest that the introduction of a hydrophobic linker in the dimeric siRNA conjugates can facilitate the intracellular delivery of siRNA through effective condensation with cationic polyelectrolytes.
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Affiliation(s)
- Sung Duk Jo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea
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17
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Mapping the Transition State for DNA Bending by IHF. J Mol Biol 2012; 418:300-15. [DOI: 10.1016/j.jmb.2012.02.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 02/14/2012] [Accepted: 02/17/2012] [Indexed: 01/01/2023]
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18
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Sheinin MY, Forth S, Marko JF, Wang MD. Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors. PHYSICAL REVIEW LETTERS 2011; 107:108102. [PMID: 21981534 PMCID: PMC3201814 DOI: 10.1103/physrevlett.107.108102] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 07/18/2011] [Indexed: 05/05/2023]
Abstract
DNA melting under torsion plays an important role in a wide variety of cellular processes. In the present Letter, we have investigated DNA melting at the single-molecule level using an angular optical trap. By directly measuring force, extension, torque, and angle of DNA, we determined the structural and elastic parameters of torsionally melted DNA. Our data reveal that under moderate forces, the melted DNA assumes a left-handed structure as opposed to an open bubble conformation and is highly torsionally compliant. We have also discovered that at low forces melted DNA properties are highly dependent on DNA sequence. These results provide a more comprehensive picture of the global DNA force-torque phase diagram.
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Affiliation(s)
- Maxim Y. Sheinin
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Scott Forth
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - John F. Marko
- Department of Physics and Astronomy and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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19
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Ortiz V, de Pablo JJ. Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties. PHYSICAL REVIEW LETTERS 2011; 106:238107. [PMID: 21770550 PMCID: PMC3410732 DOI: 10.1103/physrevlett.106.238107] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Indexed: 05/31/2023]
Abstract
A central question in biophysics is whether DNA sequence affects its mechanical properties, which are thought to influence nucleosome positioning and gene expression. Previous attempts to answer this question have been hindered by an inability to resolve DNA structure and dynamics at the base-pair level. Here we use a model to measure the effects of sequence on the stability of DNA under bending. Sequence is shown to influence DNA's flexibility and its ability to form kinks, which arise when certain motifs slide past others to form non-native contacts. A mechanism for nucleosome positioning is proposed in which sequence influences DNA-histone binding by altering the local base-pair-level structure when subject to the curvature necessary for binding.
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Affiliation(s)
- Vanessa Ortiz
- University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
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20
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Abstract
A vast literature has explored the genetic interactions among the cellular components regulating gene expression in many organisms. Early on, in the absence of any biochemical definition, regulatory modules were conceived using the strict formalism of genetics to designate the modifiers of phenotype as either cis- or trans-acting depending on whether the relevant genes were embedded in the same or separate DNA molecules. This formalism distilled gene regulation down to its essence in much the same way that consideration of an ideal gas reveals essential thermodynamic and kinetic principles. Yet just as the anomalous behavior of materials may thwart an engineer who ignores their non-ideal properties, schemes to control and manipulate the genetic and epigenetic programs of cells may falter without a fuller and more quantitative elucidation of the physical and chemical characteristics of DNA and chromatin in vivo.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, National Cancer Institute, 10 Center Drive, Building 10, Room 2N106, Bethesda, MD 20892-1500, USA.
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21
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Heinicke LA, Nallagatla SR, Hull CM, Bevilacqua PC. RNA helical imperfections regulate activation of the protein kinase PKR: effects of bulge position, size, and geometry. RNA (NEW YORK, N.Y.) 2011; 17:957-966. [PMID: 21460237 PMCID: PMC3078744 DOI: 10.1261/rna.2636911] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 02/24/2011] [Indexed: 05/30/2023]
Abstract
The protein kinase, PKR, is activated by long stretches of double-stranded (ds) RNA. Viruses often make long dsRNA elements with imperfections that still activate PKR. However, due to the complexity of the RNA structure, prediction of whether a given RNA is an activator of PKR is difficult. Herein, we systematically investigated how various RNA secondary structure defects contained within model dsRNA affect PKR activation. We find that bulges increasingly disfavor activation as they are moved toward the center of a duplex and as they are increased in size. Model RNAs designed to conform to cis, trans, or bent global geometries through strategic positioning of one or more bulges decreased activation of PKR relative to perfect dsRNA, although cis-bulged RNAs activated PKR much more potently than trans-bulged RNAs. Activation studies on bulge-containing chimeric duplexes support a model wherein PKR monomers interact adjacently, rather than through-space, for activation on bulged substrates. Last, unusually low ionic strength induced substantial increases in PKR activation in the presence of bulged RNAs suggesting that discrimination against bulges is higher under biological ionic strength conditions. Overall, this study provides a set of rules for understanding how secondary structural defects affect PKR activity.
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Affiliation(s)
- Laurie A Heinicke
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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22
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Abstract
It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent 'softening' of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.
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23
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Abstract
Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23°C to 42°C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.
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Affiliation(s)
- Robert A Forties
- Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117, USA
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24
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Siegfried NA, Bevilacqua PC. Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding. Methods Enzymol 2009; 455:365-93. [PMID: 19289213 DOI: 10.1016/s0076-6879(08)04213-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Double and triple mutant thermodynamic cycles provide a means to dissect the cooperativity of RNA and DNA folding at both the secondary and tertiary structural levels through use of the thermodynamic box or cube. In this article, we describe three steps for applying thermodynamic cycles to nucleic acid folding, with considerations of both conceptual and experimental features. The first step is design of an appropriate system and development of hypotheses regarding which residues might interact. Next is implementing this design in terms of a tractable experimental strategy, with an emphasis on UV melting. The final step, and the one we emphasize the most, is interpreting mutant cycles in terms of coupling between specific residues in the RNA or DNA. Coupling free energy in the absence and presence of changes elsewhere in the molecule is discussed in terms of specific folding models, including stepwise folding and concerted changes. Last, we provide a practical section on the use of commercially available software (KaleidaGraph) to fit melting data, along with a consideration of error propagation. Along the way, specific examples are chosen from the literature to illustrate the methods. This article is intended to be accessible to the biochemist or biologist without extensive thermodynamics background.
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Affiliation(s)
- Nathan A Siegfried
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
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25
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Huo YX, Zhang YT, Xiao Y, Zhang X, Buck M, Kolb A, Wang YP. IHF-binding sites inhibit DNA loop formation and transcription initiation. Nucleic Acids Res 2009; 37:3878-86. [PMID: 19395594 PMCID: PMC2709558 DOI: 10.1093/nar/gkp258] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptional activation of enhancer and σ54-dependent promoters requires efficient interactions between enhancer-binding proteins (EBP) and promoter bound σ54-RNA polymerase (Eσ54) achieved by DNA looping, which is usually facilitated by the integration host factor (IHF). Since the lengths of the intervening region supporting DNA-loop formation are similar among IHF-dependent and IHF-independent promoters, the precise reason(s) why IHF is selectively important for the frequency of transcription initiation remain unclear. Here, using kinetic cyclization and in vitro transcription assays we show that, in the absence of IHF protein, the DNA fragments containing an IHF-binding site have much less looping-formation ability than those that lack an IHF-binding site. Furthermore, when an IHF consensus-binding site was introduced into the intervening region between promoter and enhancer of the target DNA fragments, loop formation and DNA-loop-dependent transcriptional activation are significantly reduced in a position-independent manner. DNA-looping-independent transcriptional activation was unaffected. The binding of IHF to its consensus site in the target promoters clearly restored efficient DNA looping formation and looping-dependent transcriptional activation. Our data provide evidence that one function for the IHF protein is to release a communication block set by intrinsic properties of the IHF DNA-binding site.
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Affiliation(s)
- Yi-Xin Huo
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China
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26
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Tsortos A, Papadakis G, Mitsakakis K, Melzak KA, Gizeli E. Quantitative determination of size and shape of surface-bound DNA using an acoustic wave sensor. Biophys J 2008; 94:2706-15. [PMID: 18178642 PMCID: PMC2267124 DOI: 10.1529/biophysj.107.119271] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 11/12/2007] [Indexed: 11/18/2022] Open
Abstract
DNA bending plays a significant role in many biological processes, such as gene regulation, DNA replication, and chromosomal packing. Understanding how such processes take place and how they can, in turn, be regulated by artificial agents for individual oriented therapies is of importance to both biology and medicine. In this work, we describe the application of an acoustic wave device for characterizing the conformation of DNA molecules tethered to the device surface via a biotin-neutravidin interaction. The acoustic energy dissipation per unit mass observed upon DNA binding is directly related to DNA intrinsic viscosity, providing quantitative information on the size and shape of the tethered molecules. The validity of the above approach was verified by showing that the predesigned geometries of model double-stranded and triple-helix DNA molecules could be quantitatively distinguished: the resolution of the acoustic measurements is sufficient to allow discrimination between same size DNA carrying a bent at different positions along the chain. Furthermore, the significance of this analysis to the study of biologically relevant systems is shown during the evaluation of DNA conformational change upon protein (histone) binding.
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research & Technology Hellas, Vassilika Vouton, 71110 Heraklion, Greece
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27
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Chen H, Yan J. Effects of kink and flexible hinge defects on mechanical responses of short double-stranded DNA molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:041907. [PMID: 18517656 DOI: 10.1103/physreve.77.041907] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/07/2008] [Indexed: 05/26/2023]
Abstract
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer, plasmon resonance techniques, and the traditional biochemistry cyclization probability measurements.
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Affiliation(s)
- Hu Chen
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, Singapore.
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28
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Doss RM, Marques MA, Foister S, Chenoweth DM, Dervan PB. Programmable oligomers for minor groove DNA recognition. J Am Chem Soc 2007; 128:9074-9. [PMID: 16834381 PMCID: PMC2547997 DOI: 10.1021/ja0621795] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The four Watson-Crick base pairs of DNA can be distinguished in the minor groove by pairing side-by-side three five-membered aromatic carboxamides, imidazole (Im), pyrrole (Py), and hydroxypyrrole (Hp), four different ways. On the basis of the paradigm of unsymmetrical paired edges of aromatic rings for minor groove recognition, a second generation set of heterocycle pairs, imidazopyridine/pyrrole (Ip/Py) and hydroxybenzimidazole/pyrrole (Hz/Py), revealed that recognition elements not based on analogues of distamycin could be realized. A new set of end-cap heterocycle dimers, oxazole-hydroxybenzimidazole (No-Hz) and chlorothiophene-hydroxybenzimidazole (Ct-Hz), paired with Py-Py are shown to bind contiguous base pairs of DNA in the minor groove, specifically 5'-GT-3' and 5'-TT-3', with high affinity and selectivity. Utilizing this technology, we have developed a new class of oligomers for sequence-specific DNA minor groove recognition no longer based on the N-methyl pyrrole carboxamides of distamycin.
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Affiliation(s)
- Raymond M Doss
- The Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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29
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Yuan C, Lou XW, Rhoades E, Chen H, Archer LA. T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res 2007; 35:5294-302. [PMID: 17686784 PMCID: PMC2018621 DOI: 10.1093/nar/gkm582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.
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Affiliation(s)
- Chongli Yuan
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Xiong Wen Lou
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Rhoades
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Huimin Chen
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lynden A. Archer
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- *To whom correspondence should be addressed. +1 607 254 8825+1 607 255 9166
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30
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Wellington KW, Benner SA. A review: synthesis of aryl C-glycosides via the heck coupling reaction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 25:1309-33. [PMID: 17067955 DOI: 10.1080/15257770600917013] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.
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Affiliation(s)
- Kevin W Wellington
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, USA
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31
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32
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Fujimoto BS, Brewood GP, Schurr JM. Torsional rigidities of weakly strained DNAs. Biophys J 2006; 91:4166-79. [PMID: 16963514 PMCID: PMC1635678 DOI: 10.1529/biophysj.106.087593] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Accepted: 08/21/2006] [Indexed: 11/18/2022] Open
Abstract
Measurements on unstrained linear and weakly strained large (> or =340 bp) circular DNAs yield torsional rigidities in the range C = 170-230 fJ fm. However, larger values, in the range C = 270-420 fJ fm, are typically obtained from measurements on sufficiently small (< or =247 bp) circular DNAs, and values in the range C = 300-450 fJ fm are obtained from experiments on linear DNAs under tension. A new method is proposed to estimate torsional rigidities of weakly supercoiled circular DNAs. Monte Carlo simulations of the supercoiling free energies of solution DNAs, and also of the structures of surface-confined supercoiled plasmids, were performed using different trial values of C. The results are compared with experimental measurements of the twist energy parameter, E(T), that governs the supercoiling free energy, and also with atomic force microscopy images of surface-confined plasmids. The results clearly demonstrate that C-values in the range 170-230 fJ fm are compatible with experimental observations, whereas values in the range C > or = 269 fJ fm, are incompatible with those same measurements. These results strongly suggest that the secondary structure of DNA is altered by either sufficient coherent bending strain or sufficient tension so as to enhance its torsional rigidity.
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Affiliation(s)
- Bryant S Fujimoto
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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33
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Chenoweth DM, Poposki JA, Marques MA, Dervan PB. Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-kappaB binding inhibition. Bioorg Med Chem 2006; 15:759-70. [PMID: 17095230 PMCID: PMC3208330 DOI: 10.1016/j.bmc.2006.10.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 10/23/2006] [Accepted: 10/23/2006] [Indexed: 11/24/2022]
Abstract
A series of hairpin oligomers containing benzimidazole (Bi) and imidazopyridine (Ip) rings were synthesized and screened to target 5'-WGGGGW-3', a core sequence in the DNA-binding site of NF-kappaB, a prolific transcription factor important in biology and disease. Five Bi and Ip containing oligomers bound to the 5'-WGGGGW-3' site with high affinity. One of the oligomers (Im-Im-Im-Im-gamma-Py-Bi-Py-Bi-beta-Dp) was able to inhibit DNA binding by the transcription factor NF-kappaB.
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34
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Bao Q, Chen H, Liu Y, Yan J, Dröge P, Davey CA. A divalent metal-mediated switch controlling protein-induced DNA bending. J Mol Biol 2006; 367:731-40. [PMID: 17276457 DOI: 10.1016/j.jmb.2006.09.082] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 09/26/2006] [Accepted: 09/27/2006] [Indexed: 11/24/2022]
Abstract
Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found to adopt two stable conformational states in complex with a specific DNA target. In the so-called open state, the degree of protein-induced DNA bending is reduced significantly compared with the closed state. The conformational switch between these states is controlled by divalent metal binding in two electronegative zones arising from the lysine-to-glutamate substitution in the protein body proximal to the phosphate backbone of one DNA arm. We show that this switch can be employed to control the efficiency of site-specific recombination catalyzed by lambda integrase. Introduction of acidic residues at the protein-DNA interface holds potential for the design of metal-mediated switches for the investigation of functional relationships.
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Affiliation(s)
- Qiuye Bao
- Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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35
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Yuan C, Rhoades E, Lou XW, Archer LA. Spontaneous sharp bending of DNA: role of melting bubbles. Nucleic Acids Res 2006; 34:4554-60. [PMID: 16954151 PMCID: PMC1636343 DOI: 10.1093/nar/gkl394] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The role of centrally located and distributed base pair mismatches (‘melting bubbles’) on localized bending and stiffness of short dsDNA fragments is evaluated using time-dependent fluorescence lifetime measurements. Distributed melting bubbles are found to induce larger bending angles and decreased levels of stiffness in DNA than centrally located ones of comparable overall size. Our results indicate that spontaneous local opening-up of the DNA duplex could facilitate sharp bending of short DNA strands even in the absence of DNA binding proteins. We also find that the occurrence of two closely spaced melting bubbles will generally be favored when a large energetic barrier must be overcome in forming the desired bent DNA structure.
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Affiliation(s)
| | - Elizabeth Rhoades
- Department of Applied and Engineering Physics, Cornell UniversityIthaca, NY 14853, USA
| | | | - Lynden A. Archer
- To whom correspondence should be addressed at School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA. Tel: +1 607 254 8825; Fax: +1 607 255 9166;
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36
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Kannan S, Kohlhoff K, Zacharias M. B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations. Biophys J 2006; 91:2956-65. [PMID: 16861282 PMCID: PMC1578486 DOI: 10.1529/biophysj.106.087163] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The twist flexibility of DNA is central to its many biological functions. Explicit solvent molecular dynamics simulations in combination with an umbrella sampling restraining potential have been employed to study induced twist deformations in DNA. Simulations allowed us to extract free energy profiles for twist deformations and were performed on six DNA dodecamer duplexes to cover all 10 possible DNA basepair steps. The shape of the free energy curves was similar for all duplexes. The calculated twist deformability was in good agreement with experiment and showed only modest variation for the complete duplexes. However, the response of the various basepair steps on twist stress was highly nonuniform. In particular, pyrimidine/purine steps were much more flexible than purine/purine steps followed by purine/pyrimidine steps. It was also possible to extract correlations of twist changes and other helical as well as global parameters of the DNA molecules. Twist deformations were found to significantly alter the local as well as global shape of the DNA modulating the accessibility for proteins and other ligands. Severe untwisting of DNA below an average of 25 degrees per basepair step resulted in the onset of a global structural transition with a significantly smaller twist at one end of the DNA compared to the other.
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37
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Nechaev S, Geiduschek EP. The role of an upstream promoter interaction in initiation of bacterial transcription. EMBO J 2006; 25:1700-9. [PMID: 16601684 PMCID: PMC1440836 DOI: 10.1038/sj.emboj.7601069] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 03/09/2006] [Indexed: 11/09/2022] Open
Abstract
The bacterial RNA polymerase (RNAP) recognizes promoters through sequence-specific contacts of its promoter-specificity components (sigma) with two DNA sequence motifs. Contacts with the upstream ('-35') promoter motif are made by sigma domain 4 attached to the flap domain of the RNAP beta subunit. Bacteriophage T4 late promoters consist solely of an extended downstream ('-10') motif specifically recognized by the T4 gene 55 protein (gp55). Low level basal transcription is sustained by gp55-RNAP holoenzyme. The late transcription coactivator gp33 binds to the beta flap and represses this basal transcription. Gp33 can also repress transcription by Escherichia coli sigma70-RNAP holoenzyme mutated to allow gp33 access to the beta flap. We propose that repression is due to gp33 blocking an upstream sequence-independent DNA-binding site on RNAP (as sigma70 domain 4 does) but, unlike sigma70 domain 4, providing no new DNA interaction. We show that this upstream interaction is essential only at an early step of transcription initiation, and discuss the role of this interaction in promoter recognition and transcriptional regulation.
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Affiliation(s)
- Sergei Nechaev
- Division of Biological Sciences and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA.
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38
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Zhou Y, Chirikjian GS. Conformational Statistics of Semi-Flexible Macromolecular Chains with Internal Joints. Macromolecules 2006; 39:1950-1960. [PMID: 21243113 DOI: 10.1021/ma0512556] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semi-flexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities.
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Affiliation(s)
- Yu Zhou
- Department of Mechanical Engineering, State University of New York at Stony Brook, Stony Brook, New York 11794
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39
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Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006; 34:564-74. [PMID: 16449200 PMCID: PMC1360284 DOI: 10.1093/nar/gkj454] [Citation(s) in RCA: 622] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.
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40
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Bae SH, Yun SH, Sun D, Lim HM, Choi BS. Structural and dynamic basis of a supercoiling-responsive DNA element. Nucleic Acids Res 2006; 34:254-61. [PMID: 16414956 PMCID: PMC1326020 DOI: 10.1093/nar/gkj428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In both eukaryotes and prokaryotes, negative supercoiling of chromosomal DNA acts locally to regulate a variety of cellular processes, such as transcription, replication, recombination and response to environmental stresses. While studying the interaction between the Hin recombinase and mutated versions of its cognate DNA-binding site, we identified a mutated DNA site that binds Hin only when the DNA is supercoiled. To understand the mechanism of this supercoiling-responsive DNA site, we used NMR spectroscopy and fluorescence resonance energy transfer to determine the solution structures and dynamics of three related DNA oligonucleotides. The supercoiling-responsive DNA site formed a partially unwound and stretched helix and showed significant flexibility and base pair opening kinetics. The single CAG/CTG triplet contained in this DNA sequence displayed the same characteristics as do multiple CAG/CTG repeats, which are associated with several hereditary neuromuscular diseases. It is known that short DNA sequence motifs that have either very high or low bending flexibility occur preferentially at supercoiling-sensitive bacterial and eukaryotic promoters. From our results and these previous data, we propose a model in which supercoiling utilizes the intrinsic flexibility of a short DNA site to switch the local DNA structure from an inefficient conformation for protein binding to an efficient one, or vice versa.
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Affiliation(s)
| | - Sang Hoon Yun
- Department of Biology, School of Biological Science and Biotechnology, Chungnam National UniversityDaejeon 305-764, Republic of Korea
| | | | - Heon M. Lim
- Department of Biology, School of Biological Science and Biotechnology, Chungnam National UniversityDaejeon 305-764, Republic of Korea
| | - Byong-Seok Choi
- To whom correspondence should be addressed. Tel: +82 42 869 2828; Fax: +82 42 869 8120;
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41
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Bharanidharan D, Gautham N. Principal component analysis of DNA oligonucleotide structural data. Biochem Biophys Res Commun 2006; 340:1229-37. [PMID: 16414352 DOI: 10.1016/j.bbrc.2005.12.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 12/17/2005] [Indexed: 10/25/2022]
Abstract
The microstructure of a DNA helix is characterized by several base pair and base step parameters such as twist, rise, roll, propeller twist, etc., in addition to conformational parameters such as the backbone and the glycosidic torsion angles. Among these only a few, which are independent of all others and of each other, may be used to precisely characterize the helix. The problem however is to identify these independent parameters. We have used principal component analysis to identify a relatively small set of independent parameters, with which to characterize each DNA helix. We show that these principal components clearly discriminate between A and B DNA helical types. The calculations further suggest that the microstructure of a DNA helix is better characterized using dinucleotides.
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Affiliation(s)
- D Bharanidharan
- Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India
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42
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Abstract
Myc regulates to some degree every major process in the cell. Proliferation, growth, differentiation, apoptosis, and metabolism are all under myc control. In turn, these processes feed back to adjust the level of c-myc expression. Although Myc is regulated at every level from RNA synthesis to protein degradation, c-myc transcription is particularly responsive to multiple diverse physiological and pathological signals. These signals are delivered to the c-myc promoter by a wide variety of transcription factors and chromatin remodeling complexes. How these diverse and sometimes disparate signals are processed to manage the output of the c-myc promoter involves chromatin, recruitment of the transcription machinery, post-initiation transcriptional regulation, and mechanisms to provide dynamic feedback. Understanding these mechanisms promises to add new dimensions to models of transcriptional control and to reveal new strategies to manipulate Myc levels.
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Affiliation(s)
- J Liu
- Gene Regulation Section, Laboratory of Pathology, NCI, DCS, Bldg. 10, Rm 2N106, Bethesda, MD 20892-1500, USA
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43
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Chuang YK, Cheng WC, Goodman SD, Chang YT, Kao JT, Lee CN, Tsai KS, Fang WH. Nick-directed repair of palindromic loop mismatches in human cell extracts. J Biomed Sci 2005; 12:659-69. [PMID: 16078003 DOI: 10.1007/s11373-005-7891-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 05/25/2005] [Indexed: 11/28/2022] Open
Abstract
Palindromic sequences present in DNA may form secondary structures that block DNA replication and transcription causing adverse effects on genome stability. It has been suggested that hairpin structures containing mispaired bases could stimulate the repair systems in human cells. In this study, processing of variable length of palindromic loops in the presence or absence of single-base mismatches was investigated in human cell extracts. Our results showed that hairpin structures were efficiently processed through a nick-directed mechanism. In a similar sequence context, mismatch-containing hairpins have higher repair efficiencies. We also found that shorter hairpins are generally better repaired. A strand break located either 3' or 5' to the loop is sufficient to activate hairpin repair on the nicked strand. The reaction requires Mg(2+), the four dNTPs and hydrolysis of ATP for efficient repair on both palindromic loop insertions and deletions. Correction of each of these heteroduplexes was abolished by aphidicolin but was relatively insensitive to the presence of ddTTP, suggesting involvement of polymerase(s) alpha and/or delta. These findings are most consistent with the nick-directed loop repair pathway being responsible for processing hairpin heterologies in human cells.
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Affiliation(s)
- Yi-Kuang Chuang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, 7, Chung-Shan South Road, 100-63, Taipei, Taiwan, ROC
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Suswam EA, Li YY, Mahtani H, King PH. Novel DNA-binding properties of the RNA-binding protein TIAR. Nucleic Acids Res 2005; 33:4507-18. [PMID: 16091628 PMCID: PMC1184220 DOI: 10.1093/nar/gki763] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
TIA-1 related protein binds avidly to uridine-rich elements in mRNA and pre-mRNAs of a wide range of genes, including interleukin (IL)-8 and vascular endothelial growth factor (VEGF). The protein has diverse regulatory roles, which in part depend on the locus of binding within the transcript, including translational control, splicing and apoptosis. Here, we observed selective and potent inhibition of TIAR–RNP complex formation with IL-8 and VEGF 3′-untranslated regions (3′-UTRs) using thymidine-rich deoxyoligonucleotide (ODN) sequences derived from the VEFG 3′-UTR. We show by ultraviolet crosslinking and electrophoretic mobility shift assays that TIAR can bind directly to single-stranded, thymidine-rich ODNs but not to double-stranded ODNs containing the same sequence. TIAR had a nearly 6-fold greater affinity for DNA than RNA (Kdapp=1.6×10−9M versus 9.4 × 10−9 M). Truncation of TIAR indicated that the high affinity DNA-binding site overlaps with the RNA-binding site involving RNA recognition motif 2 (RRM2). However, RRM1 alone could also bind to DNA. Finally, we show that TIAR can be displaced from single-stranded DNA by active transcription through the binding site. These results provide a potential mechanism by which TIAR can shuttle between RNA and DNA ligands.
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Affiliation(s)
- Esther A. Suswam
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Yan Yan Li
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Harry Mahtani
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Peter H. King
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Department of Physiology and Biophysics, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
- To whom correspondence should be addressed. Tel: +1 205 975 8116; Fax: +1 205 934 0928;
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45
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Abstract
Proton exchange and nuclear magnetic resonance spectroscopy are being used to characterize the energetics of opening of AT/TA basepairs in the DNA dodecamer 5'-d(GCTATAAAAGGG)-3'/5'-d(CCCTTTTATAGC)-3'. The dodecamer contains the TATA box of the adenovirus major late promoter. The equilibrium constants for opening of each basepair are measured from the dependence of the exchange rates of imino protons on ammonia concentration. The enthalpy, entropy, and free energy changes in the opening reaction of each basepair are determined from the temperature dependence of the exchange rates. The results reveal that the opening enthalpy changes encompass a wide range of values, namely, from 17 to 29 kcal/mol. The largest values are observed for the AT basepairs in 7th and 8th positions. These values, and the exchange rates of the corresponding imino protons, suggest that these two basepairs open in a single concerted reaction. The enthalpy changes for opening of the central six basepairs are correlated to the opening entropy changes. This enthalpy-entropy compensation minimizes the variations in the opening free energies among these central basepairs. Deviations from the enthalpy-entropy compensation pattern are observed for basepairs located close to the ends of the duplex structure, suggesting a different mode of opening for these basepairs.
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Affiliation(s)
- Congju Chen
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
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46
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Chen C, Ghosh S, Grove A. Substrate specificity of Helicobacter pylori histone-like HU protein is determined by insufficient stabilization of DNA flexure points. Biochem J 2005; 383:343-51. [PMID: 15255779 PMCID: PMC1134076 DOI: 10.1042/bj20040938] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The histone-like HU protein is ubiquitous in the eubacteria. A role for Escherichia coli HU in compaction of the bacterial genome has been reported, along with regulatory roles in DNA replication, transposition, repair and transcription. We show here that HU from the human pathogen Helicobacter pylori, which has been implicated in the development of ulcers and gastric cancer, exhibits enhanced thermal stability and distinct DNA substrate specificity. Thermal denaturation of HpyHU (H. pylori HU) measured by CD spectroscopy yields a melting temperature (T(m)) of 56.4+/-0.1 degrees C. HpyHU binds linear duplex DNA with a site size of approximately 19 bp and with low affinity, but in striking contrast to E. coli HU, HpyHU has only modest preference for DNA with mismatches, nicks or gaps. Instead, HpyHU binds stably to four-way DNA junctions with half-maximal saturation of 5 nM. Substitution of two residues adjacent to the DNA-intercalating prolines attenuates both the preference for flexible DNA and the ability to bend and supercoil DNA. These observations suggest that proline intercalation generates hinges that must be stabilized by adjacent residues; insufficient stabilization leads to reduced bending and a failure to bind preferably to DNA with flexure points, such as gaps and mismatches.
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Affiliation(s)
- Christina Chen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, U.S.A
| | - Sharmistha Ghosh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, U.S.A
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, U.S.A
- To whom correspondence should be addressed (email )
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47
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Cloutier TE, Widom J. DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proc Natl Acad Sci U S A 2005; 102:3645-50. [PMID: 15718281 PMCID: PMC553319 DOI: 10.1073/pnas.0409059102] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene-regulatory complexes often require that pairs of DNA-bound proteins interact by looping-out short (often approximately 100-bp) stretches of DNA. The loops can vary in detailed length and sequence and, thus, in total helical twist, which radically alters their geometry. How this variability is accommodated structurally is not known. Here we show that the inherent twistability of 89- to 105-bp DNA circles exceeds theoretical expectation by up to 400-fold. These results can be explained only by greatly enhanced DNA flexibility, not by permanent bends. They invalidate the use of classic theories of flexibility for understanding sharp DNA looping but support predictions of two recent theories. Our findings imply an active role for DNA flexibility in loop formation and suggest that variability in the detailed helical twist of regulatory loops is accommodated naturally by the inherent twistability of the DNA.
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Affiliation(s)
- T E Cloutier
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208-3500, USA
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48
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Chen CC, Wu HY. LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome. J Biol Chem 2005; 280:15111-21. [PMID: 15711009 DOI: 10.1074/jbc.m414544200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
LeuO protein relieves bacterial gene silencer AT8-mediated transcriptional repression as part of a promoter relay mechanism found in the ilvIH-leuO-leuABCD gene cluster. The gene silencing activity has recently been characterized as a nucleoprotein filament initiated at the gene silencer. In this gene locus, the nucleoprotein filament cis-spreads toward the target leuO promoter and results in the repression of the leuO gene. Although the cis-spreading nature of the transcriptionally repressive nucleoprotein filament has been revealed, the mechanism underlying LeuO-mediated gene silencing relief remains unknown. We have demonstrated here that LeuO functions analogously to the eukaryotic boundary element that delimits the transcriptionally active and repressive domains on the chromosome by blocking the cis-spreading pathway of the transcriptionally repressive heterochromatin. Given that one LeuO-binding site is positioned between the gene silencer and the target promoter, the simultaneous presence of a second LeuO-binding site synergistically enhances the blockade, resulting in a cooperative increase in LeuO-mediated gene silencing relief. A known DNA loop-forming protein, the lac repressor (LacI), was used to confirm that cooperative protein binding via DNA looping is responsible for the blocking synergy. Indeed, a distal LeuO site located downstream cooperates with the LeuO sites located upstream of the leuO gene, resulting in synergistic relief for the repressed leuO gene via looping out the intervening DNA between LeuO sites in the ilvIH-leuO-leuABCD gene cluster.
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Affiliation(s)
- Chien-Chung Chen
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
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Desveaux D, Maréchal A, Brisson N. Whirly transcription factors: defense gene regulation and beyond. TRENDS IN PLANT SCIENCE 2005; 10:95-102. [PMID: 15708347 DOI: 10.1016/j.tplants.2004.12.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Members of the Whirly family of proteins are found throughout the plant kingdom and are predicted to share the ability to bind to single-stranded DNA. Arabidopsis and potato Whirly orthologs act as transcription factors that regulate defense gene expression; the Arabidopsis Whirly protein AtWhy1 contributes to both basal and specific defense responses. Analysis of the crystal structure of potato StWhy1 has provided insight into the DNA-binding mechanism of this family of proteins, their mode of action and possible autoregulation. There is evidence to suggest that Whirly proteins might play roles in processes other than defense responses and could function in the chloroplast as well as in the nucleus.
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Affiliation(s)
- Darrell Desveaux
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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50
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Abstract
The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.
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Affiliation(s)
- Bruno Samorì
- Department of Biochemistry G. Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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