1
|
Bhanjadeo MM, Nial PS, Sathyaseelan C, Singh AK, Dutta J, Rathinavelan T, Subudhi U. Biophysical interaction between lanthanum chloride and (CG) n or (GC) n repeats: A reversible B-to-Z DNA transition. Int J Biol Macromol 2022; 216:698-709. [PMID: 35809677 DOI: 10.1016/j.ijbiomac.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022]
Abstract
The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.
Collapse
Affiliation(s)
- Madhabi M Bhanjadeo
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Ajit K Singh
- Structural Biology Laboratory, DBT-Institute of Life Sciences, Bhubaneswar 751023, India; Department of Pharmacology, University of Vermont College of Medicine, Burlington 05405, USA
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India; Homi Bhaba National Institute, Mumbai 400094, India
| | | | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| |
Collapse
|
2
|
Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
Collapse
Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| |
Collapse
|
3
|
Yang T, Low JJA, Woon ECY. A general strategy exploiting m5C duplex-remodelling effect for selective detection of RNA and DNA m5C methyltransferase activity in cells. Nucleic Acids Res 2020; 48:e5. [PMID: 31691820 PMCID: PMC7145549 DOI: 10.1093/nar/gkz1047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 01/25/2023] Open
Abstract
RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a combination of biophysical studies led us to identify distinct duplex-remodelling effects of m5C on RNA and DNA duplexes. Specifically, m5C induces a C3′-endo to C2′-endo sugar-pucker switch in CpG RNA duplex but triggers a B-to-Z transformation in CpG DNA duplex. Inspired by these different ‘structural signatures’, we developed a m5C-sensitive probe which fluoresces spontaneously in response to m5C-induced sugar-pucker switch, hence useful for sensing RNA:m5C methyltransferase activity. Through the use of this probe, we achieved real-time imaging and flow cytometry analysis of NOP2/Sun RNA methyltransferase 2 (NSUN2) activity in HeLa cells. We further applied the probe to the cell-based screening of NSUN2 inhibitors. The developed strategy could also be adapted for the detection of DNA:m5C methyltransferases. This was demonstrated by the development of DNA m5C-probe which permits the screening of DNA methyltransferase 3A inhibitors. To our knowledge, this study represents not only the first examples of m5C-responsive probes, but also a new strategy for discriminating RNA and DNA m5C methyltransferase activity in cells.
Collapse
Affiliation(s)
- Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Joanne J A Low
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| |
Collapse
|
4
|
Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory. Int J Mol Sci 2018; 19:ijms19082346. [PMID: 30096923 PMCID: PMC6122091 DOI: 10.3390/ijms19082346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
Collapse
|
5
|
Linking Temperature, Cation Concentration and Water Activity for the B to Z Conformational Transition in DNA. Molecules 2018; 23:molecules23071806. [PMID: 30037061 PMCID: PMC6099936 DOI: 10.3390/molecules23071806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/05/2022] Open
Abstract
High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models can allow a thermodynamic characterization of the transition. Both form right handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na+ at 25 °C. However, at 2.0 M Na+ or 200 μM [Co(NH3)6]3+, (dm5C-dG)4 assumes a left handed double helical structure (Z-DNA) while the unmethylated (dC-dG)4 analogue remains right handed under those conditions. We have previously demonstrated that the enthalpy of the transition at 25 °C for either inducer can be determined using isothermal titration calorimetry (ITC). Here, ITC is used to investigate the linkages between temperature, water activity and DNA conformation. We found that the determined enthalpy for each titration varied linearly with temperature allowing determination of the heat capacity change (ΔCp) between the initial and final states. As expected, the ΔCp values were dependent upon the cation (i.e., Na+ vs. [Co(NH3)6]3+) as well as the sequence of the DNA oligomer (i.e., methylated vs. unmethylated). Osmotic stress experiments were carried out to determine the gain or loss of water by the oligomer induced by the titration. The results are discussed in terms of solvent accessible surface areas, electrostatic interactions and the role of water.
Collapse
|
6
|
Miyahara T, Nakatsuji H, Sugiyama H. Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study. J Phys Chem A 2016; 120:9008-9018. [PMID: 27809523 DOI: 10.1021/acs.jpca.6b08023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.
Collapse
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| |
Collapse
|
7
|
Subramani VK, Kim D, Yun K, Kim KK. Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ. FEBS Lett 2016; 590:2275-85. [PMID: 27265117 DOI: 10.1002/1873-3468.12238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/19/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022]
Abstract
The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity.
Collapse
Affiliation(s)
- Vinod Kumar Subramani
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Doyoun Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kyunghee Yun
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| |
Collapse
|
8
|
Miyahara T, Nakatsuji H. Indicator of the Stacking Interaction in the DNA Double-Helical Structure: ChiraSac Study. J Phys Chem A 2015; 119:8269-78. [DOI: 10.1021/acs.jpca.5b02848] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute, Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute, Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| |
Collapse
|
9
|
Miyahara T, Nakatsuji H, Sugiyama H. Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study. J Phys Chem A 2012; 117:42-55. [DOI: 10.1021/jp3085556] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Sugiyama
- Department of Chemistry,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwakecho,
Sakyo-Ku, Kyoto 606-8502, Japan
| |
Collapse
|
10
|
Gomzi V. DFT study of sulfur centred radicals formed in 5-methylcytosine hemihydrate crystal doped with 5-methyl-2-thiocytosine. Mol Phys 2008. [DOI: 10.1080/00268970802238312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
11
|
Khanduri D, Collins S, Kumar A, Adhikary A, Sevilla MD. Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical. J Phys Chem B 2008; 112:2168-78. [PMID: 18225886 DOI: 10.1021/jp077429y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.
Collapse
Affiliation(s)
- Deepti Khanduri
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
| | | | | | | | | |
Collapse
|
12
|
Ferreira JM, Sheardy RD. Enthalpy of the B-to-Z conformational transition of a DNA oligonucleotide determined by isothermal titration calorimetry. Biophys J 2006; 91:3383-9. [PMID: 16920828 PMCID: PMC1614508 DOI: 10.1529/biophysj.106.084145] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 07/28/2006] [Indexed: 11/18/2022] Open
Abstract
The influence of high concentrations of Na(+) or [Co(NH(3))(6)](3+) on the conformation of two related DNA oligomers was investigated by circular dichroism spectropolarimetry (CD), isothermal titration calorimetry (ITC), and differential scanning calorimetry (DSC). As revealed by CD, DNA oligomers, (dC-dG)(4) and (dm(5)C-dG)(4), both form right-handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na(+) at 25 degrees C. However, at 2.0 M Na(+) or 200 microM [Co(NH(3))(6)](3+), (dm(5)C-dG)(4) assumes a left-handed double helical structure (Z-DNA), whereas the unmethylated (dC-dG)(4) analog remains right-handed under those conditions. ITC was then used to determine the enthalpy change upon increasing the concentration of either Na(+) or [Co(NH(3))(6)](3+) for both DNA oligomers at 25 degrees C. The titration with Na(+) resulted in endothermic isotherms with (dm(5)C-dG)(4) being more endothermic than (dC-dG)(4) by 700 cal/mol basepair. In contrast, titration with [Co(NH(3))(6)](3+) resulted in exothermic isotherms with (dC-dG)(4) being more exothermic than (dm(5)C-dG)(4) by 720 cal/mol basepair. We attribute the enthalpy difference to the conformational transition from B-form DNA to Z-form DNA for (dm(5)C-dG)(4), a transition which does not occur for the unmethylated (dC-dG)(4). The value of approximately 700 cal/mol basepair for the enthalpy of the B-Z transition compares favorably with previously published results obtained by different techniques. DSC was used to monitor the duplex to single strand transitions for both oligomers under the different concentrations. These results indicated that methylation of the cytidine destabilizes (dm(5)C-dG)(4) relative to (dC-dG)(4). Coupling the DSC data with the ITC data allowed construction of a thermodynamic cycle which gives insight into the influence of both temperature and ionic strength on the heat content of the two DNA systems studied. Further, this study reveals the utility of using ITC for determinations of transition enthalpies with the appropriate choice of control.
Collapse
Affiliation(s)
- Jaime M Ferreira
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, USA
| | | |
Collapse
|
13
|
Thibaudeau C, Chattopadhyaya J. The Information Transmission from the Nucleobase Drives the Sugar-Phosphate Backbone Conformation in the Nucleotide Wire. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Christophe Thibaudeau
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
| | - Jyoti Chattopadhyaya
- a Department of Bioorganic Chemistry , University of Uppsala , Box 581, Biomedical Centre, S-751 23 , Uppsala , Sweden
| |
Collapse
|
14
|
Thibaudeau C, Chattopadhyaya J. The Discovery of Intramolecular Stereoelectronic Forces That Drive The Sugar Conformation in Nucleosides and Nucleotides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002912] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- C. Thibaudeau
- a Department of Bioorganic Chemistry , Box 581 Biomedical Center, Uppsala University , Uppsala , S-751 23 , Sweden
| | - J. Chattopadhyaya
- a Department of Bioorganic Chemistry , Box 581 Biomedical Center, Uppsala University , Uppsala , S-751 23 , Sweden
| |
Collapse
|
15
|
Boudreau EA, Pelczer I, Borer PN, Heffron GJ, LaPlante SR. Changes in drug 13C NMR chemical shifts as a tool for monitoring interactions with DNA. Biophys Chem 2004; 109:333-44. [PMID: 15110931 DOI: 10.1016/j.bpc.2003.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 11/11/2003] [Accepted: 12/11/2003] [Indexed: 10/26/2022]
Abstract
The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to monitor drug 13C NMR chemical shifts changes. The binding mode of netropsin to the minor groove of DNA is well-known, and served as a good model for evaluating the relative sensitivity of 13C chemical shifts to hydrogen bonding. Large downfield shifts were observed for four resonances of carbons that neighbor sites which are known to form hydrogen bond interactions with the DNA minor groove. Many of the remaining resonances of netropsin exhibit shielding or relatively smaller deshielding changes. Based on the model system presented here, large deshielding NMR shift changes of a ligand upon macromolecule binding can likely be attributed to hydrogen bond formation at nearby sites.
Collapse
Affiliation(s)
- Eilis A Boudreau
- Health Science Research and Development Program, Portland VA Medical Center, Portland, OR 97239, USA
| | | | | | | | | |
Collapse
|
16
|
LaPlante SR, Borer PN. Changes in 13C NMR chemical shifts of DNA as a tool for monitoring drug interactions. Biophys Chem 2001; 90:219-32. [PMID: 11407640 DOI: 10.1016/s0301-4622(01)00143-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to explore the effects of ligand binding on the 13C NMR chemical shifts of the DNA base and sugar carbons. The binding mode of netrospin to TA-rich tracts of DNA has been well documented and served as an attractive model system. For the base carbons, four large changes in resonance chemical shifts were observed upon complex formation: -0.64 ppm for carbon 4 of either Ado4 or Ado6, 1.36 ppm for carbon 2 of Thd5, 1.33 ppm for carbon 5 of Thd5 and 0.94 for carbon 6 of Thd5. AdoC4 is covalently bonded to a heteroatom that is hydrogen bonded to netropsin; this relatively large deshielding is consistent with the known hydrogen bond formed at AdoN3. The three large shielding increases are consistent with hydrogen bonds to water in the minor groove being disrupted upon netropsin binding. For the DNA sugar resonances, large changes in chemical shifts were observed upon netropsin complexation. The 2', 3' and 5' 13C resonances of Thd3 and Thd5 were shielded whereas those of Ado4 and Ado6 were deshielded; the 13C resonances of 1' and 4' could not be assigned. These changes are consistent with alteration of the dynamic pseudorotational states occupied by the DNA sugars. A significant alteration in the pseudorotational states of Ado4 or Ado6 must occur as suggested by the large change in chemical shift of -1.65 ppm of the C3' carbon. In conclusion, 13C NMR may serve as a practical tool for analyzing structural changes in DNA-ligand complexes.
Collapse
Affiliation(s)
- S R LaPlante
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, PQ.
| | | |
Collapse
|
17
|
|
18
|
Thibaudeau C, Kumar A, Bekiroglu S, Matsuda A, Marquez VE, Chattopadhyaya J. NMR Conformation of (−)-β-d-Aristeromycin and Its 2‘-Deoxy and 3‘-Deoxy Counterparts in Aqueous Solution. J Org Chem 1998. [DOI: 10.1021/jo980364y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Thibaudeau
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - A. Kumar
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - S. Bekiroglu
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - A. Matsuda
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - V. E. Marquez
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| | - J. Chattopadhyaya
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, Laboratory of Medicinal Chemistry, DPT, DCT, National Cancer Institute, NIH, Bethesda, Maryland 20892, and Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060, Japan
| |
Collapse
|
19
|
Thibaudeau C, Plavec J, Chattopadhyaya J. A New Generalized Karplus-Type Equation Relating Vicinal Proton-Fluorine Coupling Constants to H−C−C−F Torsion Angles. J Org Chem 1998. [DOI: 10.1021/jo980144k] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christophe Thibaudeau
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
| | - Janez Plavec
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
| | - Jyoti Chattopadhyaya
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden, and National Institute of Chemistry, Hajdrihova 19, SI-1115 Ljubljana, Slovenia
| |
Collapse
|
20
|
Thibaudeau C, Földesi A, Chattopadhyaya J. The quantitation of the competing energetics of the stereoelectronic and steric effects of the 3′-OH and the aglycone in the α-versus & by 1H-NMR. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(97)10403-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Thibaudeau C, Földesi A, Chattopadhyaya J. The first experimental evidence for a larger medium-dependent flexibility of natural β--nucleosides compared to the α--nucleosides. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)00909-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Sugiyama H, Kawai K, Matsunaga A, Fujimoto K, Saito I, Robinson H, Wang AH. Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions. Nucleic Acids Res 1996; 24:1272-8. [PMID: 8614630 PMCID: PMC145791 DOI: 10.1093/nar/24.7.1272] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of the Z conformation under physiological salt conditions. The NOE-restrained refinement unequivocally demonstrated that d(CGC[m8G]CG)2 adopts a Z structure with all guanines in the syn conformation. The refined NMR structure is very similar to the Z form crystal structure of d(CGCGCG)2, with a root mean square deviation of 0.6 between the two structures. The contribution of m8G to the stabilization of Z-DNA has been estimated from the mid-point NaCl concentrations for the B-Z transition of various m8G-containing oligomers. The presence of m8G in d(CGC[m8G]CG)2 stabilizes the Z conformation by at least deltaG = -0.8 kcal/mol relative to the unmodified hexamer. The Z conformation was further stabilized by increasing the number of m8Gs incorporated and destabilized by incorporating syn-A or syn-T, found respectively in the (A,T)-containing alternating and non-alternating pyrimidine-purine sequences. The results suggest that the chemically less reactive m8G base is a useful agent for studying molecular interactions of Z-DNA or other DNA structures that incorporate syn-G conformation.
Collapse
Affiliation(s)
- H Sugiyama
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan
| | | | | | | | | | | | | |
Collapse
|
23
|
Thibaudeau C, Plavec J, Chattopadhyaya J. Quantitation of the pD Dependent Thermodynamics of the N ⇄ S Pseudorotational Equilibrium of the Pentofuranose Moiety in Nucleosides Gives a Direct Measurement of the Strength of the Tunable Anomeric Effect and the pKa of the Nucleobase†. J Org Chem 1996. [DOI: 10.1021/jo951124a] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Thibaudeau
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
| | - J. Plavec
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
| | - J. Chattopadhyaya
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
| |
Collapse
|
24
|
|
25
|
Plavec J, Thibaudeau C, Viswanadham G, Sund C, Chattopadhyaya J. How does the 3′-phosphate drive the sugar conformation in DNA? ACTA ACUST UNITED AC 1994. [DOI: 10.1039/c39940000781] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
26
|
Rousse B, Puri N, Viswanadham G, Agback P, Glemarec C, Sandström A, Sund C, Chattopadhyaya J. Solution conformation of hexameric & heptameric lariat-RNAs and their self-cleavage reactions which give products mimicking those from some catalytic RNAs (ribozymes). Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)80852-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
27
|
Rousse B, Sund C, Glemarec C, Sandström A, Agback P, Chattopadhyaya J. Remarkable conformational change promoted by 3′-ethylphosphate at the branch-point of a tetrameric lariat-RNA dictates its self-cleavage reaction modelling some catalytic RNAs (ribozymes). Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)85346-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
28
|
Affiliation(s)
- R E Dickerson
- Molecular Biology Institute, University of California, Los Angeles 90024
| |
Collapse
|
29
|
Ansevin AT, Wang AH. Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA. Nucleic Acids Res 1990; 18:6119-26. [PMID: 2235494 PMCID: PMC332415 DOI: 10.1093/nar/18.20.6119] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The structure of Z-DNA, currently accepted as a model for all left-handed DNAs, fails to provide convincing explanations for at least four well established properties of left-handed DNA polymers in solution. However, the major discrepancies between theory and experiment are resolved by the structure presently proposed for Z[WC]-DNA, a new left-handed, zig-zag double helix with Watson-Crick-type backbone directions. Structural features of Z[WC]-DNA include the presence of an additional H-bond between each guanine N2-amino group and an adjacent phosphate oxygen, the capacity to form four-stranded, base-matched complexes that should readily precipitate from solution, and backbone progressions that are the same as B-DNA (opposite to Z-DNA). However, since Z[WC]-DNA and Z-DNA have many parameters in common, they could be difficult to distinguish in a majority of existing experiments. In view of the close relationship of the new helix to B-DNA, which allows a relatively unhindered right-to-left transition in handedness, Z[WC]-DNA is theorized to be the left-handed structure preferentially generated in vivo by the torque available in naturally occurring DNA supercoils.
Collapse
Affiliation(s)
- A T Ansevin
- Genetics Center, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston 77225
| | | |
Collapse
|
30
|
Sanford DG, Stollar BD. Characterization of anti-Z-DNA antibody binding sites on Z-DNA by nuclear magnetic resonance spectroscopy. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)44795-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
31
|
Thomas GA, Peticolas WL. A temperature-dependent Z to B to single-strand transition in d(CGCG). Biopolymers 1989; 28:1625-36. [PMID: 2775852 DOI: 10.1002/bip.360280911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A thermally induced left- to right-handed helical interconversion for the self-complementary tetradeoxynucleotide d(CGCG) has been observed in the presence of NaCl at concentrations from 1.5 to 2.25M. Analysis of the Raman spectrum of d(CGCG) in aqueous solution as a function of temperature indicates that at low temperature a left-handed Z-helical form is the predominant species. An increase in temperature results in a decrease in the population of the left-handed form and an increase in the population of the right-handed form. Further elevation in temperature results in extensive disruption of base stacking and a loss of secondary structure. This unstacking presumably represents dissociation to a single-stranded structure. The data suggest that a temperature-dependent Z to B to single-strand transition occurs under the conditions employed. A direct Z to single-strand conversion was not identified. In contrast to previous examples, the thermally induced left- to right-handed helical conversion for d(CGCG) can occur in the absence of chemically modified nucleic acid bases, alcohol solutions, or divalent ions.
Collapse
|
32
|
Bloch G, Ceolin F, Macquaire F, Neumann JM, Babin F, Huynh-Dinh T. Proton and phosphorus NMR study of RNA self-complementary hexamers: influence of the 5-methylcytidine on the conformational transitions and the molecular motions. J Biomol Struct Dyn 1989; 6:1151-75. [PMID: 2479395 DOI: 10.1080/07391102.1989.10506542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present proton and phosphorus NMR data, which contribute to explain why the 5-methylcytidine (m5C) differently affects the conformational transitions of CGUAm5CG (Bloch et al., FEBS Letters 219, 464 (1987)) and CGm5CGCG (Ceolin et al., J. Am. Chem. Soc. 109, 2539 (1987)). The atypical intermediate form observed in the random coil to A-like duplex transition of CGm5CGCG is determined: this original duplex structure exhibits a frame-shift pairing of the two strands, with a partial conservation of the A-type structure. In the case of CGUAm5CG such a pairing process would lead to a complete mismatch pairing. This feature probably explains that the NMR data of CGUACG and CGUAm5CG are similar and consistent with a random coil to A-type helix transition. Nevertheless a significant difference between the correlation times observed for the molecular motions of the two duplexes is detected. Another example of unusual conformational transition of methylated RNA oligomers is given by CAm5CGUG.
Collapse
Affiliation(s)
- G Bloch
- Département de Biologie, Service de Biophysique, Gif-sur-Yvette Cedex, France
| | | | | | | | | | | |
Collapse
|
33
|
Benight AS, Wang YS, Amaratunga M, Chattopadhyaya R, Henderson J, Hanlon S, Ikuta S. Conformation and dynamics of a left-handed Z-DNA hairpin: studies of d(CGCGCGTTTTCGCGCG) in solution. Biochemistry 1989; 28:3323-32. [PMID: 2545256 DOI: 10.1021/bi00434a030] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The physical properties of the DNA oligomer d(CGCGCGTTTTCGCGCG) in solvents containing 4 M NaClO4 and 0.1 M NaCl were investigated by proton NMR, optical melting, and circular dichroism spectroscopy. Results of these investigations are as follows: (i) The DNA hexadecamer exists as a unimolecular hairpin in either high or low salt. (ii) In high salt the stem region of the hairpin is in the left-handed Z conformation. (iii) In either high or low salt, the duplex stem of the hairpin is stabilized against melting by approximately 40 degrees C compared to the linear core duplex. The added stability of the hairpin is entropic in origin. (iv) In high salt, as the temperature is elevated, the equilibrium structure of the duplex stem of the hairpin shifts from the Z to the B conformation before melting. (v) In low salt, when the DNA duplex exists in the B conformation, attachment of a T4 single-strand loop to one end only slightly decreases (by 14%) the correlation time of the CH5-CH6 interproton vector. In high salt, when the DNA duplex exists in the Z conformation, the correlation time of the CH5-CH6 interproton vector decreases by 51%. Since these viscosity-corrected correlation times are taken to be indicators of duplex motions on the nanosecond time scale, this result directly suggests a larger amplitude of these motions is present in the duplex stem of the hairpin when it exists in the Z conformation.
Collapse
Affiliation(s)
- A S Benight
- Department of Chemistry, University of Illinois, Chicago 60680
| | | | | | | | | | | | | |
Collapse
|
34
|
Topping RJ, Stone MP, Brush CK, Harris TM. Non-Watson-Crick structures in oligodeoxynucleotides: self-association of d(TpCpGpA) stabilized at acidic pH. Biochemistry 1988; 27:7216-22. [PMID: 3207671 DOI: 10.1021/bi00419a008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The 1H NMR spectrum of the tetradeoxynucleotide d(TpCpGpA) was examined as a function of temperature, pH, and concentration. At pH 7 and above the solution conformation for this oligodeoxynucleotide appears to be a mixture of random coil and Watson-Crick duplex. At 25 degrees C, a pH titration of d(TpCpGpA) shows that distinct conformational changes occur as the pH is lowered below 7.0. These conformational changes are reversible upon readjusting the pH to neutrality, indicating the presence of a pH-dependent set of conformational equilibria. At 25 degrees C, the various conformational states in the mixture are in rapid exchange on the NMR time scale. Examination of the titration curve shows the presence of distinct conformational states at pH greater than 7, and between pH 4 and pH 5. At pH less than 4, a third conformational state is present. When the pH titration is repeated at 5 degrees C, the conformational equilibria are in slow exchange on the NMR time scale; distinct signals from each conformational state are observable. The stable conformational state present between pH 4 and pH 5 represents an ordered conformation of d(TpCpGpA) which dissociates to a less ordered structure upon raising the temperature. This ordered conformation does not result from an intramolecular rearrangement, as is shown by by spectra obtained by varying oligodeoxynucleotide concentration at constant pH. The ordered conformation differs from the Watson-Crick helix, as is shown from nuclear Overhauser enhancement experiments, as well as chemical shift data. An ordered conformation for d(TpCpGpA) was previously reported [Reid, D. G., Salisbury, S. A., Brown, T., & Williams, D. H. (1985) Biochemistry 24, 4325-4332].(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- R J Topping
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | | | | | | |
Collapse
|
35
|
Xodo LE, Manzini G, Quadrifoglio F, van der Marel GA, van Boom JH. The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins. Biochemistry 1988; 27:6327-31. [PMID: 3219338 DOI: 10.1021/bi00417a019] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The capacity to assume a left-handed conformation and the thermodynamics of loop formation in concentrated aqueous NaClO4 have been investigated for the following palindromic sequences: d-(CGCGCGAAAAACGCGCG) (A5), d(CGCGCGTTTTTCGCGCG) (T5), d(CGCGCGTACGCGCG) (TA), and d(CGCGCGATCGCGCG) (AT). The results show that (a) each oligomer assumes a Z conformation upon exposure to increasing NaClO4 concentrations; the salt concentration at the transition midpoint is 1.8 M for both A5 and T5 and 3 and 3.5 M for TA and AT, respectively; (b) in high salt the four oligomers exist, over a wide range of nucleotide concentrations (up to 10(-3) M) and of temperature (greater than 0 degrees C), as unimolecular hairpin structures; (c) hairpins TA and AT exhibit, in buffer A, a lower thermal stability with respect to A5 and T5 (delta T about 16 degrees C), contrary to what is observed at low ionic strength; (d) on hairpin formation, the enthalpic term is about -52 kcal/mol for the two 17-mers and -38 kcal/mol for the two 14-mers, while the change in entropy is found to be around -150 eu for A5 and T5 and -115 eu for TA and AT. This thermodynamic picture suggests that a two-residue loop for TA and AT, found at low ionic strength [see preceding paper (Xodo, L.E., Manzini, G., Quadrifoglio, F., van der Marel, G.A., & van Boom, J.H. (1988) Biochemistry (preceding paper in this issue)], is substituted by a longer one including two additional residues from a missing dC.dG base pairing at the top of the stem.
Collapse
Affiliation(s)
- L E Xodo
- Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy
| | | | | | | | | |
Collapse
|
36
|
Shindo H, Okhubo S, Matsumoto U, Giessner-Prettre C, Zon G. Nuclear magnetic spectra of self complementary decanucleotides in solution; base sequence effect on the chemical shifts of nonexchangeable protons. J Biomol Struct Dyn 1988; 5:913-31. [PMID: 2856030 DOI: 10.1080/07391102.1988.10506434] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The aim of this study was to attempt to determine the extent to which the chemical shifts of the nonexchangeable base protons of a DNA helix depend upon the base sequence. We measured the proton NMR spectra of twelve decadeoxynucleotides in order to carry out a "statistical" treatment. In the helices, the chemical shifts were found to be determined within +/- 0.04 ppm, largely by the nearest neighbor residues on the 5'-side, and to a smaller extent by the residue on the 3'-side. The theoretical chemical shift calculations reproduced very well the polymerization shifts measured for H2 protons of adenosines if the electrostatic field effect was taken into account. A fair agreement was also obtained for H8 protons of the adenosine and guanosine residues. However, theory underestimates the polarization effects of the base protons of cytidine. This discrepancy suggests that the conformation of this residue is different in the mononucleotides relative to double helices.
Collapse
Affiliation(s)
- H Shindo
- Tokyo College of Pharmacy, Japan
| | | | | | | | | |
Collapse
|
37
|
Bloch G, Neumann JM, Babin F, Huynh-Dinh T. Sequence-dependence of the conformational changes induced by the 5-methyl cytosine in synthetic RNA oligomers. FEBS Lett 1987; 219:464-8. [PMID: 2440719 DOI: 10.1016/0014-5793(87)80273-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The RNA hexamer containing a 5-methyl cytosine (m5C) r(CGUAm5CG) was studied by 1H and 31P NMR at 500 MHz and 121 MHz, respectively. In contrast to r(CGm5CGCG) which exhibits an atypic duplex structure [(1987) J. Am. Chem. Soc. 109, 2539-2541], r(CGUAm5CG) adopts a classical A-type conformation. This result demonstrates that the influence of the m5C on the conformation of RNA hexamers is sequence-dependent.
Collapse
|
38
|
Manzini G, Xodo LE, Quadrifoglio F, van Boom JH, van der Marel GA. dC-dG alternating oligonucleotides: thermodynamic and kinetic aspects of the B-Z transformation. J Biomol Struct Dyn 1987; 4:651-62. [PMID: 3271458 DOI: 10.1080/07391102.1987.10507666] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The alternating cytosine-guanine oligodeoxyribonucleotides (dCdG)n, (dGdC)n, (dCdG)ndC (n = 3,4), (dGdC)7 and dG(dCdG)3 have been studied by UV and CD spectroscopy at different temperatures and NaCl concentrations. The analysis of the melting data, assuming an all-or-none model, reveals that in the B-conformation the 5'G/C3' stacking interactions are enthalpically favoured with respect to the 5'C/G3' one. The CD investigation of the B-Z equilibrium shows that the Z-conformation is enthalpically stabilized, while the B-conformation is entropically favoured, in the range of NaCl concentration considered (1 to 5 M). The kinetic data for the B-Z transformation, obtained with a salt-jump technique for the hexamer (dCdG)3, support a mechanism by which the Watson-Crick hydrogen bonds are broken before the bases flip over separately and eventually stack, reforming the H-bonds, in the new helix.
Collapse
Affiliation(s)
- G Manzini
- Dept. of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy
| | | | | | | | | |
Collapse
|
39
|
|
40
|
Orbons LP, van der Marel GA, van Boom JH, Altona C. The B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz two-dimensional NMR study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 160:131-9. [PMID: 3021446 DOI: 10.1111/j.1432-1033.1986.tb09949.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The non-exchangeable proton resonances of the hexadeoxynucleoside pentakisphosphates d(m5C-G)3 and d(br5C-G)3 in the B form as well as in the Z form were assigned by means of two-dimensional correlated spectroscopy and two-dimensional nuclear Overhauser enhancement spectroscopy. The complete proton NMR spectrum of the B form of the methylated compound was assigned in a pure 2H2O solution as well as in a 2H2O/C2H3O2H mixed solvent, containing 5 mM MgCl2. In the latter solvent the B form occurs in slow equilibrium (on the NMR time scale) with the Z form, the resonances of which also were fully assigned. The proton resonances of the B and Z forms of the brominated fragment were assigned in a 2H2O/C2H3O2H solution containing 5 mM MgCl2. A new and general method is described for the sequential assignment of the non-exchangeable proton resonances of oligonucleotides in the Z form.
Collapse
|
41
|
Hartmann B, Genest D, Thuong NT, Ptak M, Leng M. Thermal stability of the Z conformation of the hexanucleoside pentaphosphate d(br5CGbr5CGbr5CG): evidence for a conformational transition before melting. Biochimie 1986; 68:739-43. [PMID: 3089332 DOI: 10.1016/s0300-9084(86)80168-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The thermal stability of the hexanucleoside pentaphosphate d(br5CGbr5CGbr5CG) has been studied at two nucleotide concentrations, in the presence of 1 M NaClO4. At low nucleotide concentration (7 X 10(-5) M), circular dichroism experiments show a conformational transition from the Z conformation to another conformation, named X, which is not the B conformation, as the temperature is increased from 0 to 35 degrees C. Between 40 and 65 degrees C, another transition is observed which corresponds to the melting of the X conformation. At higher nucleotide concentration (2 X 10(-3) M), circular dichroism and 31P nuclear magnetic resonance experiments show that at low temperature (br5dC-dG)3 adopts the Z conformation. There are associations between the oligonucleotides which progressively disappear as the temperature increases. In the range 35-60 degrees C a transition from the Z conformation to another conformation is observed. This new conformation is the X conformation detected at low nucleotide concentration.
Collapse
|
42
|
Laigle A, Chinsky L, Turpin PY, Hartmann B, Thuong NT, Leng M. A study of the thermal stability of the Z form of (m5dC-dG)3 by resonance Raman spectroscopy. Nucleic Acids Res 1986; 14:3425-34. [PMID: 3703678 PMCID: PMC339782 DOI: 10.1093/nar/14.8.3425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The thermal stability of the hexanucleoside pentaphosphate m5dCpdGpm5dCpdGpm5 dCpdG has been studied by resonance Raman spectroscopy with 257 nm excitation wavelength. At low temperature and in 3M NaClO4, the Raman spectrum resembles that of poly(dG-dC).poly(dG-dC) in the Z conformation. As the temperature is increased, the position and the intensity of several bands (1312 cm-1, 1482 cm-1, 1584 cm-1 and 1632 cm-1) are modified. The variation of intensity versus temperature is biphasic. Analysis of the results suggests that the increase of temperature induces first a transition from the Z form to an intermediate stable form which then melts. These results and those previously obtained by circular dichroism and 31P nuclear magnetic resonance suggest that the intermediate form belongs to the left family but with changes in the stacking of the bases and the geometry of the phosphate groups as compared to the canonical Z form.
Collapse
|
43
|
Adam S, Taboury JA, Taillandier E, Popinel A, Huynh-Dinh T, Igolen J. Infrared spectral studies of the non regularly alternating purine-pyrimidine hexamers d(m5CGGCM5CG), d(CBr8GGCCBr8G) and d(CGCGGC). J Biomol Struct Dyn 1986; 3:873-85. [PMID: 3271415 DOI: 10.1080/07391102.1986.10508470] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The oligonucleotides d(m5CGGCm5CG), d(CBr8GGCCBr8G) and d(CGCGGC) have been prepared and studied by infrared spectroscopy. The three sequences contain two GC pairs which are out of purine-pyrimidine alternation with the rest of the sequence. From the IR data of the d(m5CGGCm5CG) hexamer, it is shown that all of the dG residues adopt a syn conformation. The marker IR bands for the C3' endo syn conformation are at 1410, 1354, 1320 and 925 cm-1 whereas those for the C2' endo anti conformation at 1420, 1374 and 890 cm-1 are clearly absent. This result implies that the two adjacent guanines of the d(m5CGGCm5CG) sequence are in syn conformation. It is suggested that duplex formation occurs in d(CGCGGC) films and that all of the guanines are in syn conformation. In contrast, the central non-brominated guanine of the d(CBr8GGCCBr8G) hexamer is found in anti conformation, as expected in a Z type structure of the non-alternating region.
Collapse
Affiliation(s)
- S Adam
- Laboratoire de Spectroscopie Biomoléculaire, UER Santé-Médecine Biologie Humaine, Bobigny, France
| | | | | | | | | | | |
Collapse
|
44
|
Davis PW, Hall K, Cruz P, Tinoco I, Neilson T. The tetraribonucleotide rCpGpCpG forms a left-handed Z-RNA double-helix. Nucleic Acids Res 1986; 14:1279-91. [PMID: 3951987 PMCID: PMC339503 DOI: 10.1093/nar/14.3.1279] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
NMR and circular dichroism studies show that the RNA tetranucleotide rCpGpCpG can form a Z-RNA left-handed double-helix. In 1.0 M NaClO4, circular dichroism measurements indicate that the tetramer is in the A-form. In 6.0 M NaClO4, there is a characteristic change in the circular dichroism, indicating that the tetramer adopts a left-handed Z-form. This conformation is verified by phosphorus and proton NMR studies. The 31P spectrum shows a large downfield shift in one of the resonances upon an increase in salt concentration. Proton nuclear Overhauser effect (NOE) experiments indicate that the guanosines are in the syn conformation. These results are consistent with the formation of a Z-form double-helix.
Collapse
|
45
|
Pochet S, Huynh-Dinh T, Neumann JM, Tran-Dinh S, Adam S, Taboury J, Taillandier E, Igolen J. NMR, CD and IR spectroscopies of a tridecanucleotide containing a no-base residue: coexistence of B and Z conformations. Nucleic Acids Res 1986; 14:1107-26. [PMID: 3945553 PMCID: PMC339486 DOI: 10.1093/nar/14.2.1107] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The synthesis of the tridecadeoxynucleotide d(CGm5CGCGxACATGT), where x is the 1-cyano-2-deoxy-beta-D-erythropentofuranose, is described. The NMR, IR, CD studies at various salt concentrations and temperatures of this oligomer show that the B and Z conformations are simultaneously present in the same short DNA fragment. A single apurinic residue is sufficient for the coexistence of the B and Z helices on this oligomer.
Collapse
|
46
|
Sharma M, Box HC. Synthesis, modification with N-acetoxy-2-acetylaminofluorene and physicochemical studies of DNA model compound d(TACGTA). Chem Biol Interact 1985; 56:73-88. [PMID: 4075447 DOI: 10.1016/0009-2797(85)90040-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The deoxyhexanucleotide d(TACGTA) was synthesized by a modified phosphotriester method. The modified procedure made rapid synthesis of deoxyoligonucleotide possible in gram quantity. N-Acetoxy-2-acetylaminofluorene (AAAF) modified d(TACGTA). Thin layer chromatography and UV analysis of the acid treated AAF modified hexanucleotide showed that the covalent modification with AAF took place exclusively at C(8) of guanine in d(TACGTA). d(TACGTA) and AAF modified d(TACGTA) were purified by preparative high performance liquid chromatography (HPLC). The pure products were characterized by 1H and 31P-NMR. The circular dichroism (CD) spectrum of d(TACGTA) was consistent with DNA in the B form even in the presence of 4 M NaCl whereas the modified hexamer had nearly inverted spectrum in the absence of any added salt. Both NMR and CD analyses indicated profound alteration of conformation of d(TACGTA) upon covalent modification with AAF. The stabilization of the Z-like conformation in the modified hexamer under physiological conditions of salt and temperature suggests biological relevance.
Collapse
|
47
|
Abstract
Since the Watson-Crick proposal of right-handed B-DNA, numerous studies have been devoted to the conformation of DNA. Both natural DNAs of heterogeneous sequences and synthetic DNAs are capable of adopting more than one conformation. The specific conformation a DNA adopts appears to depend mainly on its base sequence and its environmental conditions. For a given DNA, changes in environmental conditions can induce conformational transitions which occur according to cooperative or non-cooperative processes (for general reviews see Ref. 1a, b). Despite many results, molecular biologists did not put much emphasis on the polymorphism of DNA. The discovery of the intraconversion in helical sense between the right-handed B and left-handed Z conformers of DNA has brought a new interest in the polymorphism of DNA. It is now proposed that this polymorphism has important functions in biological reactions. A recent review, 'The Chemistry and Biology of Left-handed Z-DNA', by Rich et al. has just been published. We here report some of the results published in 1984 on Z-DNA.
Collapse
|
48
|
Taboury JA, Taillandier E, Lumbroso P, Neumann JM, Tran-Dinh S, d'Estaintot BL, Huynh-Dinh T, Igolen J. Z helix-coil transition of d(C-Br8G-C-G-C-Br8G) studied by CD, 1H-NMR and IR spectroscopies. J Biomol Struct Dyn 1985; 2:1185-203. [PMID: 2855786 DOI: 10.1080/07391102.1985.10507632] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The conformation of d(C-Br8G-C-G-C-Br8G) in aqueous solution was studied by CD and 1H-NMR spectroscopy and in condensed phase by IR spectroscopy. Whether in 0.1 M or 3 M NaCl solution or in film the only double helical structure adopted by brominated d(C-G)3 oligomer is the Z form. The IR spectrum of the film presents all the characteristic absorptions of the Z conformation and in particular is indicative of a syn conformation for the central guanosine as well as for the brominated one. Imino proton resonances of d(C-Br8G-C-G-C-Br8G) demonstrating the duplex formation were observed up to 60 degrees C. It is interesting to note that the significant highfield shifts of the dC H5" exocyclic sugar protons characteristic of the non exchangeable proton spectra of d(C-G)3 containing 5-methyl dC residues in the Z form were also detected in the proton spectrum of brominated oligomer. Whereas formation of the Z helix of methylated d(C-G)3 oligomers dependent on the salt concentration was found to occur via the preliminary formation of a B helix even in 4 M NaCl solution, the Z helix of d(C-Br8G-C-G-C-Br8G) is obtained directly from the coil form. However, IR data suggest that in the Z form of d(C-Br8G-C-G-C-Br8G), the overlapping of the base planes should be slightly different in comparison with the stacking observed in d(C-G)3 crystals. The kinetic data (activation energy and lifetime) of the Z helix-coil transition of brominated d(C-G)3 are compared to those of the B helix-coil transition observed for methylated d(C-G)3 in 0.1 M NaCl solution while the thermodynamic data of these two reactions (enthalpy and midpoint temperature) are slightly different.
Collapse
Affiliation(s)
- J A Taboury
- Laboratoire de Spectroscopie Biomoléculaire, UER Santé-Médecine Biologie Humaine, Bobigny, France
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Wemmer DE, Chou SH, Hare DR, Reid BR. Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res 1985; 13:3755-72. [PMID: 4011441 PMCID: PMC341271 DOI: 10.1093/nar/13.10.3755] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two dimensional NMR methods have been used to assign proton resonances in the high salt (greater than or equal to 100mM Na+), low temperature duplex form of the self-complementary DNA dodecamer d(CGCGTATACGCG). At low salt (less than or equal to 10mM Na+) and higher temperature marked changes in the two-dimensional spectrum, and in the one-dimensional spectrum reported by others, indicate that the molecule converts to an alternate conformation. Using saturation transfer methods, many of the resonances of this new conformation have been assigned, and the kinetics of the interconversion of the two forms has been studied. The linewidth, correlation time, and concentration dependence of the formation of this alternate conformation support the idea that it is a unimolecular hairpin. Observation of chemical shifts and NOEs in the hairpin conformation allow some preliminary structural characterization. Examination of the energetics of the interconversion suggests that the exchange between forms does not proceed through a single stranded intermediate, but rather through another pathway, probably involving a cruciform structure.
Collapse
|
50
|
Neumann JM, Cavailles JA, Herve M, Tran-Dinh S, Langlois d'Estaintot B, Huynh-Dinh T, Igolen J. 500 MHz 1H-NMR study of the interaction of daunomycin with B and Z helices of d(CGm5CGCG). FEBS Lett 1985; 182:360-4. [PMID: 3979558 DOI: 10.1016/0014-5793(85)80333-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The interaction of daunomycin with B and Z helices of a self-complementary DNA fragment d(CGm5CGCG) in solution was studied by 1H-NMR spectroscopy at 500 MHz. The results show that the B-Z transition kinetics is not affected by addition of daunomycin. Daunomycin binds exclusively to the B form of d(CGm5CGCG). Z exchanges with B while the latter also exchanges with the B duplex-daunomycin complexes.
Collapse
|