1
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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2
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Genthon A, Dvirnas A, Ambjörnsson T. Equilibrium melting probabilities of a DNA molecule with a defect: An exact solution of the Poland-Scheraga model. J Chem Phys 2023; 159:145102. [PMID: 37815110 DOI: 10.1063/5.0168915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023] Open
Abstract
In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson-Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland-Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct importance, for instance, for studies where fluorophore-quencher pairs are used for studying single basepair fluctuations of designed DNA molecules.
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Affiliation(s)
- Arthur Genthon
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Albertas Dvirnas
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, SE-223 62 Lund, Sweden
| | - Tobias Ambjörnsson
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, SE-223 62 Lund, Sweden
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3
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Nicy, Chakraborty D, Wales DJ. Energy Landscapes for Base-Flipping in a Model DNA Duplex. J Phys Chem B 2022; 126:3012-3028. [PMID: 35427136 PMCID: PMC9098180 DOI: 10.1021/acs.jpcb.2c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Indexed: 12/31/2022]
Abstract
We explore the process of base-flipping for four central bases, adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid (DNA) duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation spectroscopy studies have been used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the base-flipping rates obtained by the two methods implies that they are exploring different pathways and possibly different open states. Our results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5' side of the backbone. We find that bases align toward the 3' side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5' side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, we find that the equilibrium constant for opening is large compared to flipping via the major groove. We find that the estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
| | - Debayan Chakraborty
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
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4
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Pant P, Aggarwal L. Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations. Biophys Chem 2022; 282:106758. [DOI: 10.1016/j.bpc.2021.106758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/09/2021] [Accepted: 12/30/2021] [Indexed: 01/17/2023]
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5
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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6
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Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res 2020; 48:5147-5156. [PMID: 32282905 PMCID: PMC7229855 DOI: 10.1093/nar/gkaa207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.
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Affiliation(s)
- Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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7
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Basov A, Drobotenko M, Svidlov A, Gerasimenko E, Malyshko V, Elkina A, Baryshev M, Dzhimak S. Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/ 1H Replacement in DNA. Molecules 2020; 25:E3753. [PMID: 32824686 PMCID: PMC7463606 DOI: 10.3390/molecules25163753] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/04/2020] [Accepted: 08/15/2020] [Indexed: 12/15/2022] Open
Abstract
In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.
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Affiliation(s)
- Alexander Basov
- Kuban State Medical University, 350063 Krasnodar, Russia; (A.B.); (V.M.)
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
| | - Mikhail Drobotenko
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
| | - Alexandr Svidlov
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | | | - Vadim Malyshko
- Kuban State Medical University, 350063 Krasnodar, Russia; (A.B.); (V.M.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Anna Elkina
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Mikhail Baryshev
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Kuban State Technological University, 350042 Krasnodar, Russia;
| | - Stepan Dzhimak
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
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8
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Sarkar S, Rajdev P, Singh PC. Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies. Phys Chem Chem Phys 2020; 22:15582-15591. [PMID: 32613973 DOI: 10.1039/d0cp01548b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ionic liquids (ILs) have been extensively used for stabilization and long-term DNA storage. However, molecular level understanding of the role of the hydrogen bond of DNA with ILs in its stabilization is still inadequate. Two ILs, namely, 1,1,3,3-tetramethylguanidinium acetate (TMG) and 2,2-diethyl-1,1,3,3-tetramethylguanidinium acetate (DETMG), have been synthesized, of which TMG has a hydrogen bonding N-H group whereas DETMG does not contain any hydrogen bonding site. It has been found that both TMG and DETMG cations interact in the groove region of DNA; however, their mode of interaction is distinctly different, which causes the stabilization of DNA in the presence of TMG, whereas the effect is opposite in the case of DETMG. It is apparent from the data that only the accommodation of ILs in the groove region is not enough for the stabilization of DNA. MD simulation and spectroscopic studies combinedly indicate that the hydrogen bonding capability of the TMG cation enhances the hydrogen bonding between the Watson-Crick base pairs of DNA, resulting in its stabilization. In contrast, the bigger size as well as the absence of the hydrogen bonding site of the DETMG cation perturbs the minor groove width and base pair step parameters of DNA during its intrusion into the minor groove, which decreases the hydrogen bond between the Watson-Crick base pairs of DNA, leading to destabilization.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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9
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10
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Liebl K, Zacharias M. How global DNA unwinding causes non-uniform stress distribution and melting of DNA. PLoS One 2020; 15:e0232976. [PMID: 32413048 PMCID: PMC7228070 DOI: 10.1371/journal.pone.0232976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
- * E-mail:
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11
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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12
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Buckle AM, Buckle M. Ribosome Evolution and Structural Capacitance. Front Mol Biosci 2019; 6:123. [PMID: 31803754 PMCID: PMC6872460 DOI: 10.3389/fmolb.2019.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022] Open
Abstract
In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic "structural capacitance elements." Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance - that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (D→O) transition in previously disordered regions of proteins. Here we propose that the D→O transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.
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Affiliation(s)
- Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Malcolm Buckle
- LBPA, ENS Paris-Saclay, CNRS, Université Paris-Saclay, Cachan, France
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13
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Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry. Molecules 2019; 24:molecules24101852. [PMID: 31091778 PMCID: PMC6571787 DOI: 10.3390/molecules24101852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
The clinically widely-used anticancer drug, cisplatin, binds strongly to DNA as a DNA-damaging agent. Herein, we investigated the interaction of cisplatin with a 15-mer single-stranded C,T-rich oligodeoxynucleotide, 5′-CCTT4CTT7G8C9T10TCTCC-3′ (ODN15), using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with tandem mass spectrometry (top-down MS). Top-down MS analysis with collision-induced dissociation (CID) fragmentation of the mono-platinated and di-platinated ODN15 provided abundant and informative Pt-containing or Pt-free a/[a − B], w and internal fragments, allowing the unambiguous identification of T4, T7, C9, and T10 as the platination sites on the cisplatin-ODN15 adducts. These results revealed that, in addition to the well-established guanine site, the unexpected thermodynamic binding of cisplatin to cytosine and thymine bases was also evident at the oligonucleotide level. Furthermore, the binding models of cisplatin with cytosine and thymine bases were built as the Pt coordinated to cytosine-N(3) and thymine-N(3) with displacement of the proton or tautomerization of thymine. These findings contribute to a better understanding of the mechanism of action of cisplatin and its preference for gene loci when the drug binds to cellular DNA, and also demonstrate the great potential and superiority of FT-ICR MS in studying the interactions of metallodrugs with large biomolecules.
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14
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Abstract
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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15
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Kingsland A, Maibaum L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J Phys Chem B 2018; 122:12251-12259. [DOI: 10.1021/acs.jpcb.8b06007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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16
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Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018; 193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Rukshan T Perera
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Henry S White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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17
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Zoli M. End-to-end distance and contour length distribution functions of DNA helices. J Chem Phys 2018; 148:214902. [DOI: 10.1063/1.5021639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, I-62032 Camerino, Italy
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18
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Bergamo A, Dyson PJ, Sava G. The mechanism of tumour cell death by metal-based anticancer drugs is not only a matter of DNA interactions. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.01.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Drobotenko MI, Dzhimak SS, Svidlov AA, Basov AA, Lyasota OM, Baryshev MG. A Mathematical Model for Basepair Opening in a DNA Double Helix. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918020069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Vologodskii A, Frank-Kamenetskii MD. DNA melting and energetics of the double helix. Phys Life Rev 2017; 25:1-21. [PMID: 29170011 DOI: 10.1016/j.plrev.2017.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Studying melting and energetics of the DNA double helix has been one of the major topics of molecular biophysics over the past six decades. The main objective of this article is to overview the current state of the field and to emphasize that there are still serious gaps in our understanding of the issue. We start with a concise description of the commonly accepted theoretical model of the DNA melting. We then concentrate on studies devoted to the comparison with experiment of theoretically predicted melting profiles of DNAs with known sequences. For long DNA molecules, such comparison is significant from the basic-science viewpoint while an accurate theoretical description of melting of short duplexes is necessary for various very important applications in biotechnology. Several sets of DNA melting parameters, proposed within the framework of the nearest neighbor model, are compared and analyzed. The analysis leads to a conclusion that in case of long DNA molecules the consensus set of nearest neighbor parameters describes well the experimental melting profiles. Unexpectedly, for short DNA duplexes the same set of parameters hardly yields any improvement as compared to the simplest model, which completely ignores the effect of heterogeneous stacking. Possible causes of this striking observation are discussed. We then overview the issue of separation of base-pairing and base-stacking contributions into the double helix stability. The recent experimental attempts to solve the problem are extensively analyzed. It is concluded that the double helix is essentially stabilized by stacking interaction between adjacent base pairs. Base pairing between complementary pairs does not appreciably contribute into the duplex stability. In the final section of the article, kinetic aspects of the DNA melting phenomenon are discussed. The main emphasis is made on the hysteresis effects often observed in melting of long DNA molecules. It is argued that the phenomenon can be well described via an accurate theoretical treatment of the random-walk model of melting kinetics of an isolated helical segment in DNA.
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21
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Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. J Chem Inf Model 2017; 57:2020-2026. [PMID: 28696686 DOI: 10.1021/acs.jcim.7b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Free energy simulations are presented to probe the energetic coupling between DNA bending and the flipping of a central thymine in double stranded DNA 13mers. The energetics are shown to depend on the neighboring base pairs, and upstream C or T or downstream C tended to make flipping more costly. Flipping to the major groove side was generally preferred. Bending aids flipping, by pushing the system up in free energy, but for small and intermediate bending angles the two were uncorrelated. At higher bending angles, bending and flipping became correlated, and bending primed the system for base flipping toward the major groove. Flipping of the 6-4 pyrimidine-pyrimidone and pyrimidine dimer photoproducts is shown to be more facile than for undamaged DNA. For the damages, major groove flipping was preferred, and DNA bending was much facilitated in the 6-4 pyrimidine-pyrimidone damaged system. Aspects of the calculations were verified by structural analyses of protein-DNA complexes with flipped bases.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
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22
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Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Sci Rep 2017; 7:4071. [PMID: 28642456 PMCID: PMC5481346 DOI: 10.1038/s41598-017-03199-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/24/2022] Open
Abstract
DNA shape is emerging as an important determinant of transcription factor binding beyond just the DNA sequence. The only tool for large scale DNA shape estimates, DNAshape was derived from Monte-Carlo simulations and predicts four broad and static DNA shape features, Propeller twist, Helical twist, Minor groove width and Roll. The contributions of other shape features e.g. Shift, Slide and Opening cannot be evaluated using DNAshape. Here, we report a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustive set of DNA shape features. We compared the DNAshape and DynaSeq predictions for the common features and applied both to predict the genome-wide binding sites of 1312 TFs available from protein interaction quantification (PIQ) data. The results indicate a good agreement between the two methods for the common shape features and point to advantages in using DynaSeq. Predictive models employing ensembles from individual conformational parameters revealed that base-pair opening - known to be important in strand separation - was the best predictor of transcription factor-binding sites (TFBS) followed by features employed by DNAshape. Of note, TFBS could be predicted not only from the features at the target motif sites, but also from those as far as 200 nucleotides away from the motif.
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Affiliation(s)
- Munazah Andrabi
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan
- Faculty of Biology,Medicine and Health, Michael Smith Building, The University of Manchester, Dover Street, Manchester, M13 9PT, UK
| | - Andrew Paul Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055, China
| | - Diego Miranda-Saavedra
- World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Osaka, Japan
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Department of Computer Science, University of Oxford Wolfson Building, Parks Road, OXFORD, OX1 3QD, United Kingdom
| | - Hidetoshi Kono
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7, Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Ruth Nussinov
- National Cancer Institute, Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick, Maryland, USA
- Department of Biochemistry and Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan
| | - Shandar Ahmad
- National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan.
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
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23
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Zoli M. Twist-stretch profiles of DNA chains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:225101. [PMID: 28394255 DOI: 10.1088/1361-648x/aa6c50] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are applied to generate a large ensemble of possible configurations for the base pairs of the sequence. The model also accounts for the bending and twisting fluctuations between adjacent base pairs along the molecules stack. Simulating a broad range of twisting conformation, we compute the helix structural parameters by averaging over the ensemble of base pairs configurations. The method selects, for any applied force, the average twist angle which minimizes the molecule's free energy. It is found that the chains generally over-twist under an applied stretching and the over-twisting is physically associated to the contraction of the average helix diameter, i.e. to the damping of the base pair fluctuations. Instead, assuming that the maximum amplitude of the bending fluctuations may decrease against the external load, the DNA molecule first over-twists for weak applied forces and then untwists above a characteristic force value. Our results are discussed in relation to available experimental information albeit for kilo-base long molecules.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, I-62032 Camerino, Italy
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24
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Paston SV, Nikolaev AI, Ushkov PA. EDTA, thymidine, and Cu2+ ion complexes from mass spectrometry data. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Kilchherr F, Wachauf C, Pelz B, Rief M, Zacharias M, Dietz H. Single-molecule dissection of stacking forces in DNA. Science 2017; 353:353/6304/aaf5508. [PMID: 27609897 DOI: 10.1126/science.aaf5508] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
Abstract
We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from -0.8 to -3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.
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Affiliation(s)
- Fabian Kilchherr
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Christian Wachauf
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany
| | - Benjamin Pelz
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany
| | - Matthias Rief
- Lehrstuhl für Molekulare Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Martin Zacharias
- Lehrstuhl für Theoretische Biophysik, Physik Department, Technische Universität München, James-Franck-Strasse 1, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany
| | - Hendrik Dietz
- Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany. Institute for Advanced Study, TUM, Germany.
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26
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Wang Y, Gong S, Wang Z, Zhang W. The thermodynamics and kinetics of a nucleotide base pair. J Chem Phys 2017; 144:115101. [PMID: 27004898 DOI: 10.1063/1.4944067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.
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Affiliation(s)
- Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China
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27
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Tian L, Zhang Z, Wang H, Zhao M, Dong Y, Gong Y. Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea. PLoS One 2016; 11:e0163361. [PMID: 27685992 PMCID: PMC5042384 DOI: 10.1371/journal.pone.0163361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/07/2016] [Indexed: 12/26/2022] Open
Abstract
T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this phylum lack the protein homologues responsible for the recognition of the mismatch in the DNA repair pathways. To investigate whether Cren7, a highly conserved chromatin protein in Crenarchaea, serves a role in the repair of T:G mispairs, the crystal structures of Cren7-GTAATTGC and Cren7-GTGATCGC complexes were solved at 2.0 Å and 2.1 Å. In our structures, binding of Cren7 to the AT-rich DNA duplex (GTAATTGC) induces opening of T2:G15 but not T10:G7 base pair. By contrast, both T:G mispairs in the GC-rich DNA duplex (GTGATCGC) retain the classic wobble type. Structural analysis also showed DNA helical changes of GTAATTGC, especially in the steps around the open T:G base pair, as compared to GTGATCGC or the matched DNAs. Surface plasmon resonance assays revealed a 4-fold lower binding affinity of Cren7 for GTAATTGC than that for GTGATCGC, which was dominantly contributed by the decrease of association rate. These results suggested that binding of Cren7 to DNA leads to T:G mispair opening in a sequence dependent manner, and therefore propose the potential roles of Cren7 in DNA repair.
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Affiliation(s)
- Lei Tian
- Department of general surgery, Navy General Hospital, Beijing 100048, China
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hanqian Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Mohan Zhao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
- * E-mail:
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28
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29
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Maity A, Singh A, Singh N. Differential stability of DNA based on salt concentration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:33-40. [DOI: 10.1007/s00249-016-1132-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/28/2023]
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30
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McCarty J, Valsson O, Parrinello M. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling. J Chem Theory Comput 2016; 12:2162-9. [PMID: 27057791 DOI: 10.1021/acs.jctc.6b00125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence determining free energy differences is central for understanding many important phenomena. Here we present a new biasing strategy, which employs the recent variationally enhanced sampling approach (Valsson and Parrinello Phys. Rev. Lett. 2014, 113, 090601). The bias is constructed from an intuitive model of the local free energy surface describing fluctuations around metastable minima and depends on only a few parameters which are determined variationally such that efficient sampling between states is obtained. The bias constructed in this manner largely reduces the need of finding a set of collective variables that completely spans the conformational space of interest, as they only need to be a locally valid descriptor of the system about its local minimum. We introduce the method and demonstrate its power on two representative examples.
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Affiliation(s)
- James McCarty
- Department of Chemistry and Applied Biosciences, ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland.,Facoltà di Informatica, Instituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI) , Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
| | - Omar Valsson
- Department of Chemistry and Applied Biosciences, ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland.,Facoltà di Informatica, Instituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI) , Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland.,Facoltà di Informatica, Instituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI) , Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
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31
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Abstract
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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32
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Reiter-Schad M, Werner E, Tegenfeldt JO, Mehlig B, Ambjörnsson T. How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model. J Chem Phys 2015; 143:115101. [DOI: 10.1063/1.4930220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Michaela Reiter-Schad
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Erik Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Jonas O. Tegenfeldt
- Division of Solid State Physics, Department of Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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33
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Zrimec J, Lapanje A. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1137-1145. [PMID: 26451825 DOI: 10.1109/tcbb.2015.2396057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.
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34
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Freitag C, Noble C, Fritzsche J, Persson F, Reiter-Schad M, Nilsson AN, Granéli A, Ambjörnsson T, Mir KU, Tegenfeldt JO. Visualizing the entire DNA from a chromosome in a single frame. BIOMICROFLUIDICS 2015; 9:044114. [PMID: 26392826 PMCID: PMC4570469 DOI: 10.1063/1.4923262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/18/2015] [Indexed: 05/16/2023]
Abstract
The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1 mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.
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Affiliation(s)
| | - C Noble
- Department of Astronomy and Theoretical Physics, Lund University , Lund, Sweden
| | | | | | - M Reiter-Schad
- Department of Astronomy and Theoretical Physics, Lund University , Lund, Sweden
| | - A N Nilsson
- Department of Astronomy and Theoretical Physics, Lund University , Lund, Sweden
| | - A Granéli
- Department of Physics, University of Gothenburg , Gothenburg, Sweden
| | - T Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University , Lund, Sweden
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35
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Chua EYD, Davey GE, Chin CF, Dröge P, Ang WH, Davey CA. Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents. Nucleic Acids Res 2015; 43:5284-96. [PMID: 25916851 PMCID: PMC4477649 DOI: 10.1093/nar/gkv356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/02/2015] [Indexed: 11/15/2022] Open
Abstract
Platinum-based anticancer drugs act therapeutically by forming DNA adducts, but suffer from severe toxicity and resistance problems, which have not been overcome in spite of decades of research. And yet defined chromatin targets have generally not been considered in the drug development process. Here we designed novel platinum-intercalator species to target a highly deformed DNA site near the nucleosome center. Between two seemingly similar structural isomers, we find a striking difference in DNA site selectivity in vitro, which comes about from stereochemical constraints that limit the reactivity of the trans isomer to special DNA sequence elements while still allowing the cis isomer to efficiently form adducts at internal sites in the nucleosome core. This gives the potential for controlling nucleosome site targeting in vivo, which would engender sensitivity to epigenetic distinctions and in particular cell type/status-dependent differences in nucleosome positioning. Moreover, while both compounds yield very similar DNA-adduct structures and display antitumor cell activity rivalling that of cisplatin, the cis isomer, relative to the trans, has a much more rapid cytotoxic effect and distinct impact on cell function. The novel stereochemical principles for controlling DNA site selectivity we discovered could aid in the design of improved site discriminating agents.
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Affiliation(s)
- Eugene Y D Chua
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Gabriela E Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chee Fei Chin
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Curt A Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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36
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Affiliation(s)
- Jaeoh Shin
- Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - O-Chul Lee
- Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Wokyung Sung
- Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea
- IBS Center for Self-assembly and Complexity, Pohang 790-784, South Korea
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37
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Ding Y, Fleming AM, White HS, Burrows CJ. Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore. J Phys Chem B 2014; 118:12873-82. [PMID: 25333648 PMCID: PMC4234443 DOI: 10.1021/jp5101413] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Studies
on the interaction of hairpin DNA with the α-hemolysin
(α-HL) nanopore have determined hairpin unzipping kinetics,
thermodynamics, and sequence-dependent DNA/protein interactions. Missing
from these results is a systematic study comparing the unzipping process
for fishhook (one-tail) vs internal (two-tail) hairpins when they
are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail.
In the current studies, fishhook hairpins showed long unzipping times
with one deep blockage current level. In contrast, the internal hairpins
demonstrated relatively fast unzipping and a characteristic pulse-like
current pattern. These differences were further explored with respect
to stem length and sequence context. Further, a series of internal
hairpins with asymmetric tails were studied, for which it was determined
that a second tail longer than 12 nucleotides results in internal
hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved
like fishhook hairpins. Interestingly, these studies were able to
resolve a current difference of ∼6% between hairpin DNA immobilized
in the nanopore waiting to unzip vs the translocating unzipped DNA,
with the latter showing a deeper current blockage level. This demonstration
of different currents for immobilized and translocating DNA has not
been described previously. These results were interpreted as fishhook
hairpins unzipping inside the vestibule, while the internal hairpins
unzip outside the vestibule of α-HL. Lastly, we used this knowledge
to study the unzipping of a long double-stranded DNA (>50 base
pairs)
outside the vestibule of α-HL. The conclusions drawn from these
studies are anticipated to be beneficial in future application of
nanopore analysis of nucleic acids.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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38
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Frank-Kamenetskii MD. DNA breathes Hoogsteen. ARTIFICIAL DNA, PNA & XNA 2014; 2:1-3. [PMID: 21686245 DOI: 10.4161/adna.2.1.15509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 03/17/2011] [Indexed: 11/19/2022]
Abstract
A recent claim is discussed that Watson-Crick pairs in the naked duplex DNA spontaneously flip into Hoogsteen pairs under ordinary conditions. The claim is considered within the historical retrospective and is put into the broader context of DNA biophysics.
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39
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Esguerra M, Nilsson L, Villa A. Triple helical DNA in a duplex context and base pair opening. Nucleic Acids Res 2014; 42:11329-38. [PMID: 25228466 PMCID: PMC4191418 DOI: 10.1093/nar/gku848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region.
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Affiliation(s)
- Mauricio Esguerra
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
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40
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Abstract
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology - CNISM, Università di Camerino, I-62032 Camerino, Italy.
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41
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Ivchenko O, Bachert P, Imhof P. Umbrella sampling of proton transfer in a creatine–water system. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Talukder S, Sen S, Chakraborti P, Metzler R, Banik SK, Chaudhury P. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA. J Chem Phys 2014; 140:125101. [PMID: 24697480 DOI: 10.1063/1.4869112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε(hb)(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.
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Affiliation(s)
- Srijeeta Talukder
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Shrabani Sen
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Prantik Chakraborti
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Physics Department, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Suman K Banik
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
| | - Pinaki Chaudhury
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
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43
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Fluctuations in the DNA double helix: A critical review. Phys Life Rev 2014; 11:153-70. [PMID: 24560595 DOI: 10.1016/j.plrev.2014.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022]
Abstract
A critical overview of the extensive literature on fluctuations in the DNA double helix is presented. Both theory and experiment are comprehensively reviewed and analyzed. Fluctuations, which open up the DNA double helix making bases accessible for hydrogen exchange and chemical modification, are the main focus of the review. Theoretical descriptions of the DNA fluctuations are discussed with special emphasis on most popular among them: the nonlinear-dynamic Peyrard-Bishop-Dauxois (PBD) model and the empirical two-state (or helix-coil) model. The experimental data on the issue are comprehensibly overviewed in the historical retrospective with main emphasis on the hydrogen exchange data and formaldehyde kinetics. The theoretical descriptions are critically evaluated from the viewpoint of their applicability to describe DNA in water environment and from the viewpoint of agreement of their predictions with the reliable experimental data. The presented analysis makes it possible to conclude that, while the two-state model is most adequate from theoretical viewpoint and its predictions, based on an empirical parametrization, agree with experimental data very well, the PBD model is inapplicable to DNA in water from theoretical viewpoint on one hand and it makes predictions totally incompatible with reliable experimental data on the other. In particular, it is argued that any oscillation movements of nucleotides, assumed by the PBD model, are severely damped in water, that no "bubbles", which the PBD model predicts, exist in reality in linear DNA well below the melting range and the lifetime of an open state in DNA is actually 5 orders of magnitude longer than the value predicted by the PBD model.
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44
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Jeon JH, Sung W. An effective mesoscopic model of double-stranded DNA. J Biol Phys 2014; 40:1-14. [PMID: 24306264 PMCID: PMC3923960 DOI: 10.1007/s10867-013-9333-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/11/2013] [Indexed: 11/26/2022] Open
Abstract
Watson and Crick's epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA's vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.
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Affiliation(s)
- Jae-Hyung Jeon
- />Department of Physics and PCTP, Pohang University of Science and Technology, Pohang, 790-784 Republic of Korea
| | - Wokyung Sung
- />Department of Physics and PCTP, Pohang University of Science and Technology, Pohang, 790-784 Republic of Korea
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45
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Mekler V, Severinov K. Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase. Nucleic Acids Res 2013; 41:7276-85. [PMID: 23771146 PMCID: PMC3753650 DOI: 10.1093/nar/gkt541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (RNAP) melts promoter DNA to form transcription-competent open promoter complex (RPo). Interaction of the RNAP σ subunit with non-template strand bases of a conserved -10 element (consensus sequence T-12A-11T-10A-9A-8T-7) is an important source of energy-driving localized promoter melting. Here, we used an RNAP molecular beacon assay to investigate interdependencies of RNAP interactions with -10 element nucleotides. The results reveal a strong cooperation between RNAP interactions with individual -10 element non-template strand nucleotides and indicate that recognition of the -10 element bases occurs only when free energy of the overall RNAP -10 element binding reaches a certain threshold level. The threshold-like mode of the -10 element recognition may be related to the energetic cost of attaining a conformation of the -10 element that is recognizable by RNAP. The RNAP interaction with T/A-12 base pair was found to be strongly stimulated by RNAP interactions with other -10 element bases and with promoter spacer between the -10 and -35 promoter elements. The data also indicate that unmelted -10 promoter element can impair RNAP interactions with promoter DNA upstream of the -11 position. We suggest that cooperativity and threshold effects are important factors guiding the dynamics and selectivity of RPo formation.
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Affiliation(s)
- Vladimir Mekler
- Department of Molecular Biology and Biochemistry, Waksman Institute of Microbiology Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA and Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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46
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47
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de Oliveira Guerra JC. Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models. Biopolymers 2013; 99:538-47. [DOI: 10.1002/bip.22214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 01/19/2013] [Indexed: 11/08/2022]
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48
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Abstract
During the past decade, the issue of strong bending of the double helix has attracted a lot of attention. Here, we overview the major experimental and theoretical developments in the field sorting out reliably established facts from speculations and unsubstantiated claims. Theoretical analysis shows that sharp bends or kinks have to facilitate strong bending of the double helix. It remains to be determined what is the critical curvature of DNA that prompts the appearance of the kinks. Different experimental and computational approaches to the problem are analyzed. We conclude that there is no reliable evidence that any anomalous behavior of the double helix happens when DNA fragments in the range of 100 bp are circularized without torsional stress. The anomaly starts at the fragment length of about 70 bp when sharp bends or kinks emerge in essentially every molecule. Experimental data and theoretical analysis suggest that kinks may represent openings of isolated base pairs, which had been experimentally detected in linear DNA molecules. The calculation suggests that although the probability of these openings in unstressed DNA is close to 10−5, it increases sharply in small DNA circles reaching 1 open bp per circle of 70 bp.
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49
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Oberstrass FC, Fernandes LE, Lebel P, Bryant Z. Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics. PHYSICAL REVIEW LETTERS 2013; 110:178103. [PMID: 23679785 PMCID: PMC3696636 DOI: 10.1103/physrevlett.110.178103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 05/16/2023]
Abstract
Changes in global DNA linking number can be accommodated by localized changes in helical structure. We have used single-molecule torque measurements to investigate sequence-specific strand separation and Z-DNA formation. By controlling the boundary conditions at the edges of sequences of interest, we have confirmed theoretical predictions of distinctive boundary-dependent backbending patterns in torque-twist relationships. Abrupt torque jumps are associated with the formation and collapse of DNA bubbles, permitting direct observations of DNA breathing dynamics.
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Affiliation(s)
| | | | - Paul Lebel
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA 94305, USA
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50
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Moreno PMD, Geny S, Pabon YV, Bergquist H, Zaghloul EM, Rocha CSJ, Oprea II, Bestas B, Andaloussi SE, Jørgensen PT, Pedersen EB, Lundin KE, Zain R, Wengel J, Smith CIE. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA. Nucleic Acids Res 2013; 41:3257-73. [PMID: 23345620 PMCID: PMC3597675 DOI: 10.1093/nar/gkt007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DSI). We thus report on the development of a clamp type of LNA ON—bisLNA—with capacity to bind and invade into supercoiled double-stranded DNA. The bisLNA links a triplex-forming, Hoogsteen-binding, targeting arm with a strand-invading Watson–Crick binding arm. Optimization was carried out by varying the number and location of LNA nucleotides and the length of the triplex-forming versus strand-invading arms. Single-strand regions in target duplex DNA were mapped using chemical probing. By combining design and increase in LNA content, it was possible to achieve a 100-fold increase in potency with 30% DSI at 450 nM using a bisLNA to plasmid ratio of only 21:1. Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes.
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Affiliation(s)
- Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, 141 86 Huddinge, Stockholm, Sweden
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