1
|
Pederson K, Meints GA, Drobny GP. Base Dynamics in the HhaI Protein Binding Site. J Phys Chem B 2023; 127:7266-7275. [PMID: 37561575 PMCID: PMC10461302 DOI: 10.1021/acs.jpcb.3c03687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.
Collapse
Affiliation(s)
- Kari Pederson
- Department
of Chemistry & Biochemistry, California
State University at Dominguez Hills, Carson, California 90747, United States
| | - Gary A. Meints
- Department
of Chemistry, Missouri State University, Springfield, Missouri 65897, United States
| | - Gary P. Drobny
- Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700, United
States
| |
Collapse
|
2
|
Geronimo I, Vidossich P, Donati E, Vivo M. Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Elisa Donati
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Marco Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| |
Collapse
|
3
|
Evich M, Spring-Connell AM, Germann MW. Impact of modified ribose sugars on nucleic acid conformation and function. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2017-0056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AbstractThe modification of the ribofuranose in nucleic acids is a widespread method of manipulating the activity of nucleic acids. These alterations, however, impact the local conformation and chemical reactivity of the sugar. Changes in the conformation and dynamics of the sugar moiety alter the local and potentially global structure and plasticity of nucleic acids, which in turn contributes to recognition, binding of ligands and enzymatic activity of proteins. This review article introduces the conformational properties of the (deoxy)ribofuranose ring and then explores sugar modifications and how they impact local and global structure and dynamics in nucleic acids.
Collapse
Affiliation(s)
- Marina Evich
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
| | | | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, GA 30303, USA
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, GA 30303, USA
- Georgia State University, Neuroscience Institute, P.O. 5030, Atlanta, GA 30303, USA
| |
Collapse
|
4
|
Fujitsuka M, Majima T. Charge transfer dynamics in DNA revealed by time-resolved spectroscopy. Chem Sci 2017; 8:1752-1762. [PMID: 28451299 PMCID: PMC5396511 DOI: 10.1039/c6sc03428d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023] Open
Abstract
In the past few decades, charge transfer in DNA has attracted considerable attention from researchers in a wide variety of fields, including bioscience, physical chemistry, and nanotechnology. Charge transfer in DNA has been investigated using various techniques. Among them, time-resolved spectroscopic methods have yielded valuable information on charge transfer dynamics in DNA, providing an important basis for numerical practical applications such as development of new therapy applications and nanomaterials. In DNA, holes and excess electrons act as positive and negative charge carriers, respectively. Although hole transfer dynamics have been investigated in detail, the dynamics of excess electron transfer have only become clearer relatively recently. In the present paper, we summarize studies on the dynamics of hole and excess electron transfer conducted by several groups including our own.
Collapse
Affiliation(s)
- Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan . ;
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN) , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan . ;
| |
Collapse
|
5
|
Mondal S, Chakraborty K, Bandyopadhyay S. Microscopic understanding of the conformational features of a protein–DNA complex. Phys Chem Chem Phys 2017; 19:32459-32472. [DOI: 10.1039/c7cp05161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.
Collapse
Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Kaushik Chakraborty
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| |
Collapse
|
6
|
Lin SH, Fujitsuka M, Majima T. Excess-Electron Transfer in DNA by a Fluctuation-Assisted Hopping Mechanism. J Phys Chem B 2016; 120:660-6. [DOI: 10.1021/acs.jpcb.5b10857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
7
|
Přecechtělová J, Munzarová ML, Vaara J, Novotný J, Dračínský M, Sklenář V. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations. J Chem Theory Comput 2013; 9:1641-56. [DOI: 10.1021/ct300488y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | - Juha Vaara
- NMR Research Group, Department of Physics,
University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
| | | | - Martin Dračínský
- NMR Laboratory, Institute of
Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nám.
2, CZ-16610 Prague 6, Czech Republic
- Department of Chemistry, Durham University, Durham, DH13LE, United Kingdom
| | | |
Collapse
|
8
|
Nikolova EN, Bascom GD, Andricioaei I, Al-Hashimi HM. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry 2012; 51:8654-64. [PMID: 23035755 DOI: 10.1021/bi3009517] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet few studies have experimentally explored the sequence dependence of DNA dynamics that occur on biologically relevant time scales. Here, we use nuclear magnetic resonance (NMR) carbon spin relaxation combined with molecular dynamics (MD) simulations to examine the picosecond to nanosecond dynamics in a variety of dinucleotide steps as well as in varying length homopolymeric A(n)·T(n) repeats (A(n)-tracts, where n = 2, 4, or 6) that exhibit unusual structural and mechanical properties. We extend the NMR spin relaxation time scale sensitivity deeper into the nanosecond regime by using glycerol and a longer DNA duplex to slow overall tumbling. Our studies reveal a structurally unique A-tract core (for n > 3) that is uniformly rigid, flanked by junction steps that show increasing sugar flexibility with A-tract length. High sugar mobility is observed at pyrimidine residues at the A-tract junctions, which is encoded at the dinucleotide level (CA, TG, and CG steps) and increases with A-tract length. The MD simulations reproduce many of these trends, particularly the overall rigidity of A-tract base and sugar sites, and suggest that the sugar-backbone dynamics could involve transitions in sugar pucker and phosphate backbone BI ↔ BII equilibria. Our results reinforce an emerging view that sequence-specific DNA flexibility can be imprinted in dynamics occurring deep within the nanosecond time regime that is difficult to characterize experimentally at the atomic level. Such large-amplitude sequence-dependent backbone fluctuations might flag the genome for specific DNA recognition.
Collapse
Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
| | | | | | | |
Collapse
|
9
|
Rinnenthal J, Richter C, Nozinovic S, Fürtig B, Lopez JJ, Glaubitz C, Schwalbe H. RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis. JOURNAL OF BIOMOLECULAR NMR 2009; 45:143-55. [PMID: 19636800 DOI: 10.1007/s10858-009-9343-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/19/2009] [Indexed: 05/13/2023]
Abstract
We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample. In order to interpret the (31)P relaxation data (R (1), R (2)), we measured the (31)P chemical shift anisotropy (CSA) by solid-state NMR spectroscopy under various salt and hydration conditions. A value of 178.5 ppm for the (31)P CSA in the static state (S (2) = 1) could be determined. In order to obtain information about fast time scale dynamics we performed a modelfree analysis on the basis of our relaxation data. The results show that subnanosecond dynamics detected around the phosphodiester backbone are more pronounced than the dynamics detected for the ribofuranosyl and nucleobase moieties of the individual nucleotides (Duchardt and Schwalbe, J Biomol NMR 32:295-308, 2005; Ferner et al., Nucleic Acids Res 36:1928-1940, 2008). Furthermore, the dynamics of the individual phosphate groups seem to be correlated to the 5' neighbouring nucleobases.
Collapse
Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, Frankfurt/Main, Germany
| | | | | | | | | | | | | |
Collapse
|
10
|
KAUR INDERPREET, KULKARNI GIRISHS, AJORE RAM, BHARADWAJ RICHA, KOTAMARTHI BHANUPRAKASH, SINGH NIMAL, BHARADWAJ LALITM. ROLE OF ADENINE AND GUANINE SITES IN HOLE HOPPING IN DNA NANOWIRE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2009. [DOI: 10.1142/s0219633609004873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A) n G , n = 1, 2, …, 10; G(A) x G(A) y G , x + y = 9; and G(A) x G(A) y G(A) z G , x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A) n G sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A) 10 G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A) x G(A) y G (where x + y = 9) reduces the transfer integrals, thus explaining the hampering of A-hopping. Hence, sequences of the type G(A) n G , n > 3, are better suited for their application as molecular wire. Finally, studies on the effect of flipping of bases, i.e. flipping G:C to C:G on transfer integrals, have revealed that helical distortions and conformational changes due to sequence variations lead to changes in coupling, which is highly unpredictable.
Collapse
Affiliation(s)
- INDERPREET KAUR
- Biomolecular Electronics and Nanotechnology Division (BEND), Central Scientific Instruments Organization (CSIO), Sector-30C, Chandigarh, India
| | - GIRISH S. KULKARNI
- Biomolecular Electronics and Nanotechnology Division (BEND), Central Scientific Instruments Organization (CSIO), Sector-30C, Chandigarh, India
| | - RAM AJORE
- Biomolecular Electronics and Nanotechnology Division (BEND), Central Scientific Instruments Organization (CSIO), Sector-30C, Chandigarh, India
| | - RICHA BHARADWAJ
- Biomolecular Electronics and Nanotechnology Division (BEND), Central Scientific Instruments Organization (CSIO), Sector-30C, Chandigarh, India
| | | | - NIMAL SINGH
- Department of Physics, Panjab University, Sector-14, Chandigarh, India
| | - LALIT M. BHARADWAJ
- Biomolecular Electronics and Nanotechnology Division (BEND), Central Scientific Instruments Organization (CSIO), Sector-30C, Chandigarh, India
| |
Collapse
|
11
|
Duchardt E, Nilsson L, Schleucher J. Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucleic Acids Res 2008; 36:4211-9. [PMID: 18579564 PMCID: PMC2475628 DOI: 10.1093/nar/gkn375] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Using (13)C spin relaxation NMR in combination with molecular dynamic (MD) simulations, we characterized internal motions within double-stranded DNA on the pico- to nano-second time scale. We found that the C-H vectors in all cytosine ribose moieties within the Dickerson-Drew dodecamer (5'-CGCGAATTCGCG-3') are subject to high amplitude motions, while the other nucleotides are essentially rigid. MD simulations showed that repuckering is a likely motional model for the cytosine ribose moiety. Repuckering occurs with a time constant of around 100 ps. Knowledge of DNA dynamics will contribute to our understanding of the recognition specificity of DNA-binding proteins such as cytosine methyltransferase.
Collapse
Affiliation(s)
- Elke Duchardt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.
| | | | | |
Collapse
|
12
|
Meints GA, Miller PA, Pederson K, Shajani Z, Drobny G. Solid-state nuclear magnetic resonance spectroscopy studies of furanose ring dynamics in the DNA HhaI binding site. J Am Chem Soc 2008; 130:7305-14. [PMID: 18489097 DOI: 10.1021/ja075775n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5'-GCGC-3' moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes < 0.3 A). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5'-GCGC-3' is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the HhaI methyltransferase.
Collapse
Affiliation(s)
- Gary A Meints
- Department of Chemistry, Missouri State University, Springfield, Missouri 65897, and Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | | | | | | | | |
Collapse
|
13
|
Ferner J, Villa A, Duchardt E, Widjajakusuma E, Wöhnert J, Stock G, Schwalbe H. NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops. Nucleic Acids Res 2008; 36:1928-40. [PMID: 18272534 PMCID: PMC2346598 DOI: 10.1093/nar/gkm1183] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.
Collapse
Affiliation(s)
- Jan Ferner
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance, Frankfurt/M, Germany
| | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. The many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins or other nucleic acids, whereas local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. Although these statements make a compelling case to study the sequence dependent dynamics in nucleic acids, there are few residue-specific studies of nucleic acid dynamics. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention. The aim of this review is to provide an update of the recent progress in studies of nucleic acid dynamics by NMR based on the application of solution relaxation techniques.
Collapse
Affiliation(s)
- Zahra Shajani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | | |
Collapse
|
15
|
Banerjee D, Pal SK. Direct Observation of Essential DNA Dynamics: Melting and Reformation of the DNA Minor Groove. J Phys Chem B 2007; 111:10833-8. [PMID: 17676797 DOI: 10.1021/jp074697n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.
Collapse
Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | | |
Collapse
|
16
|
Ramreddy T, Rao BJ, Krishnamoorthy G. Site-specific dynamics of strands in ss- and dsDNA as revealed by time-domain fluorescence of 2-aminopurine. J Phys Chem B 2007; 111:5757-66. [PMID: 17469866 DOI: 10.1021/jp068818f] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well recognized that structure and dynamics of DNA strands guide proteins toward their cognate sites in DNA. While the dynamics is controlled primarily by the nucleotide sequence, the context of a particular sequence in relation to an open end could also play a significant role. In this work we have used the fluorescent analogue of adenine, 2-aminopurine (2-AP), to extract information on site-specific dynamics of DNA strands associated with 30-70 nucleotides length. Measurement of fluorescence lifetime and anisotropy decay kinetics in various types of DNA strands in which 2-AP was located in specific positions revealed novel insights into the dynamics of strands. We find that in single-stranded (ss) DNA, the extent of motional dynamics of the bases falls off sharply from the very end toward the middle of the strand. In contrast, the flexibility of the backbone decreases more gradually in the same direction. In double-stranded (ds) DNA, the level of base-pair fraying increases toward the ends in a graded manner. Surprisingly, the same is countered by the presence of ss-overhangs emanating from dsDNA ends. Moreover, the extent of concerted motion of bases in duplex DNA increased from the end to the middle of the duplex, a result which is both striking and counterintuitive. Most surprisingly, the two complementary strands of a duplex that were unequal in length exhibited differential dynamics: the longer one with overhangs showed a distinctly higher level of flexibility than the recessed shorter strand in the same duplex. All these results, taken together, provoke newer insights in our understanding of how different bases in DNA strands are endowed with specific dynamic properties as a function of their positions. These properties are likely to be used in facilitating specific recognitions of DNA bases by proteins during various DNA-protein interaction systems.
Collapse
Affiliation(s)
- T Ramreddy
- Department of Chemical Science and Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | | | | |
Collapse
|
17
|
Fausti S, Penna GL, Cuniberti C, Perico A. Diffusive Dynamics in a Detailed Potential: Application to Biological Macromolecules. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
18
|
Johnson JE, Julien KR, Hoogstraten CG. Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA. JOURNAL OF BIOMOLECULAR NMR 2006; 35:261-74. [PMID: 16937241 DOI: 10.1007/s10858-006-9041-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 06/02/2006] [Indexed: 05/04/2023]
Abstract
Heteronuclear NMR spin relaxation studies of conformational dynamics are coming into increasing use to help understand the functions of ribozymes and other RNAs. Due to strong 13C-13C magnetic interactions within the ribose ring, however, these studies have thus far largely been limited to (13)C and (15)N resonances on the nucleotide base side chains. We report here the application of the alternate-site (13)C isotopic labeling scheme, pioneered by LeMaster for relaxation studies of amino acid side chains, to nucleic acid systems. We have used different strains of E. coli to prepare mononucleotides containing (13)C label in one of two patterns: Either C1' or C2' in addition to C4', termed (1'/2',4') labeling, or nearly complete labeling at the C2' and C4' sites only, termed (2',4') labeling. These patterns provide isolated 13C-1H spin systems on the labeled carbon atoms and thus allow spin relaxation studies without interference from 13C-13C scalar or dipolar coupling. Using relaxation studies of AMP dissolved in glycerol at varying temperature to produce systems with correlation times characteristic of different size RNAs, we demonstrate the removal of errors due to 13C-13C interaction in T (1) measurements of larger nucleic acids and in T (1rho) measurements in RNA molecules. By extending the applicability of spin relaxation measurements to backbone ribose groups, this technology should greatly improve the flexibility and completeness of NMR analyses of conformational dynamics in RNA.
Collapse
Affiliation(s)
- James E Johnson
- Department of Biochemistry & Molecular Biology, Michigan State University, 212 Biochemistry Building, East Lansing, MI, 48824, USA
| | | | | |
Collapse
|
19
|
Andreatta D, Sen S, Lustres JLP, Kovalenko SA, Ernsting NP, Murphy CJ, Coleman RS, Berg MA. Ultrafast dynamics in DNA: "fraying" at the end of the helix. J Am Chem Soc 2006; 128:6885-92. [PMID: 16719468 PMCID: PMC2528932 DOI: 10.1021/ja0582105] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics of the electric fields in the interior of DNA are measured by using oligonucleotides in which a native base pair is replaced by a dye molecule (coumarin 102) whose emission spectrum is sensitive to the local electric field. Time-resolved measurements of the emission spectrum have been extended to a six decade time range (40 fs to 40 ns) by combining results from time-correlated photon counting, fluorescence up-conversion, and transient absorption. Recent results showed that when the reporter is placed in the center of the oligonucleotide, the dynamics are very broadly distributed over this entire time range and do not show specific time constants associated with individual processes (Andreatta, D.; et al. J. Am. Chem. Soc. 2005, 127, 7270). This paper examines an oligonucleotide with the reporter near its end. The broadly distributed relaxation seen before remains with little attenuation. In addition, a new relaxation with a well-defined relaxation time of 5 ps appears. This process is assigned to the rapid component of "fraying" at the end of the helix.
Collapse
|
20
|
Nielsen KE, Spielmann HP. The structure of a mixed LNA/DNA:RNA duplex is driven by conformational coupling between LNA and deoxyribose residues as determined from 13C relaxation measurements. J Am Chem Soc 2006; 127:15273-82. [PMID: 16248670 DOI: 10.1021/ja051026z] [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] [Indexed: 11/29/2022]
Abstract
A study of the internal dynamics of an LNA/DNA:RNA duplex has been performed to further characterize the conformational changes associated with the incorporation of locked nucleic acid (LNA) nucleotides in a DNA:RNA duplex. In general, it was demonstrated that the LNA/DNA:RNA duplex has a very high degree of order compared to dsDNA and dsRNA duplexes. The order parameters of the aromatic carbon atoms in the LNA/DNA strand are uniformly high, whereas a sharp drop in the degree of order was seen in the RNA strand in the beginning of the AUAU stretch in the middle of the strand. This can be related to a return to normal dsRNA dynamics for the central A:U base pair. The high order of the heteroduplex is consistent with preorganization of the chimera strand for an A-form duplex conformation. These results partly explain the dramatic increase in T(m) of the chimeric heteroduplex over dsDNA and DNA:RNA hybrids of the same sequence.
Collapse
Affiliation(s)
- Katrine E Nielsen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | | |
Collapse
|
21
|
Al-Hashimi HM. Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. Chembiochem 2006; 6:1506-19. [PMID: 16138302 DOI: 10.1002/cbic.200500002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ever-increasing cellular roles ascribed to RNA raise fundamental questions regarding how a biopolymer composed of only four chemically similar building-block nucleotides achieves such functional diversity. Here, I discuss how RNA achieves added mechanistic and chemical complexity by undergoing highly controlled conformational changes in response to a variety of cellular signals. I examine pathways for achieving selectivity in these conformational changes that rely to different extents on the structure and dynamics of RNA. Finally, I review solution-state NMR techniques that can be used to characterize RNA structural dynamics and its relationship to function.
Collapse
Affiliation(s)
- Hashim M Al-Hashimi
- Department of Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
22
|
Duchardt E, Schwalbe H. Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR 13C relaxation. JOURNAL OF BIOMOLECULAR NMR 2005; 32:295-308. [PMID: 16211483 DOI: 10.1007/s10858-005-0659-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with 13C and 15N were studied by 13C spin relaxation experiments. R1, R1rho and the 13C-[1H] steady-state NOE of C6 and C1' in pyrimidine and C8 and C1' in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time tau(c) of 2.31 +/- 0.13 ns and an axial ratio of 1.35 +/- 0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported 13C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539-10551; Fiala et al., 2000 J. Biomol. NMR 16, 291-302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165-190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82 < S2 < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S2 = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of 13C relaxation rates were found to be in agreement with 15N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702-709).
Collapse
Affiliation(s)
- Elke Duchardt
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Marie-Curie Str. 11, D-60439, Frankfurt/Main, Germany
| | | |
Collapse
|
23
|
Vallurupalli P, Kay LE. A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics. J Am Chem Soc 2005; 127:6893-901. [PMID: 15869313 DOI: 10.1021/ja0427799] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A suite of (2)H-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly (13)C, randomly fractionally deuterated ( approximately 50%) RNA molecules. The experiments quantify (2)H R(1) and R(2) relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity permitting, the consistency of the data can be evaluated by measuring all five rates that are accessible for a spin 1 particle and establishing that the rates obey relations that are predicted from theory. The utility of the methodology is demonstrated with studies of the dynamics of a 14-mer RNA containing the UUCG tetraloop at temperatures of 25 and 5 degrees C. The high quality of the data, even at 5 degrees C, suggests that the experiments will be of use for the study of RNA molecules that are as large as 30 nucleotides.
Collapse
Affiliation(s)
- Pramodh Vallurupalli
- Protein Engineering Network Centers of Excellence and the Departments of Medical Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | | |
Collapse
|
24
|
Shajani Z, Varani G. 13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein. J Mol Biol 2005; 349:699-715. [PMID: 15890361 DOI: 10.1016/j.jmb.2005.04.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Revised: 03/25/2005] [Accepted: 04/06/2005] [Indexed: 11/22/2022]
Abstract
The widespread importance of induced fit and order-disorder transition in RNA recognition by proteins and small molecules makes it imperative that RNA motional properties are characterized quantitatively. Until now, however, very few studies have been dedicated to the systematic characterization of RNA motion and to their changes upon protein or small-molecule binding. The U1A protein-RNA complexes provide some of the best-studied examples of the role of RNA motional changes upon protein binding. Here, we report (13)C NMR relaxation studies of base and ribose dynamics for the RNA internal loop target of human U1A protein located within the 3'-untranslated region (3'-UTR) of the mRNA coding for U1A itself. We also report the semi-quantitative analysis of both fast (nano- to picosecond) and intermediate (micro- to millisecond) motions for this paradigmatic RNA system. We measure (13)C T(1), T(1rho) and heteronuclear nuclear Overhauser effects (NOEs) for sugar and base nuclei, as well as the power dependence of T(1rho) at 500 MHz and 750 MHz, and analyze these results using the model-free formalism. The results provide a much clearer picture of the type of motions experienced by this RNA in the absence of the protein than was provided by the analysis of the structure based solely on NOEs and scalar couplings. They define a model where the RNA internal loop region "breathes" on a micro- to millisecond timescale with respect to the double-helical regions. Superimposed on this slower motion, the residues at the very tip of the loop undergo faster (nano- to picosecond) motions. We hypothesize that these motions allow the RNA to sample multiple conformations so that the protein can select a structure within the ensemble that optimizes intermolecular contacts.
Collapse
Affiliation(s)
- Zahra Shajani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | | |
Collapse
|
25
|
Abstract
The paper examines thedynamical behavior of a radical cation(G(+*)) generated in adouble stranded DNA for differentoligonucleotide sequences. The resonancehole tunneling through an oligonucleotidesequence is studied by the method ofnumerical integration of self-consistentquantum-mechanical equations. The holemotion is considered quantum mechanicallyand nucleotide base oscillations aretreated classically. The results obtaineddemonstrate a strong dependence of chargetransfer on the type of nucleotidesequence. The rates of the hole transferare calculated for different nucleotidesequences and compared with experimentaldata on the transfer from (G(+*))to a GGG unit.
Collapse
Affiliation(s)
- V D Lakhno
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow region 142290 Russian Federation
| |
Collapse
|
26
|
Isaacs RJ, Rayens WS, Spielmann HP. Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics. J Mol Biol 2002; 319:191-207. [PMID: 12051946 DOI: 10.1016/s0022-2836(02)00265-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detailed description of the characteristics of mismatched DNA that are distinct from normal DNA is vital to the understanding of how mismatch repair proteins are able to recognize and repair these DNA lesions. To this end, we have used nuclear Overhauser effect spectroscopy (NOESY)-based distance restraints and (13)C relaxation measurements to solve the solution structures and measure some of the internal dynamics of the G-T mismatched DNA oligomer d(CCATGCGTGG)(2) (GT) and its parent DNA sequence d(CCACGCGTGG)(2) (GC). In GT, the mismatched G7 is structurally perturbed much more than the mismatched T4 relative to their corresponding bases in GC. The degree of G7 displacement differs from previous high-resolution structures of G-T mismatch-containing B-DNA, suggesting a dependence of G-T mismatch-induced structural perturbation on sequence context. The internal dynamics of GC and GT differ on multiple timescales. The mismatched G7 of GT contains spins that decrease significantly in order in GT compared to GC, while spins in C6, T8, and A3 have significantly higher order in GT compared to GC. Linear correlations between helical parameters of GC and GT and the order of C-1' and aromatic methine carbon atoms relate differences in internal dynamics to the structures quantitatively. The dynamic differences between the normal and mismatched DNA signify changes in local flexibility that may be exploited by the mismatch repair system to bind mismatched DNA preferentially while ignoring normal DNA.
Collapse
Affiliation(s)
- Richard J Isaacs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536-0084, USA
| | | | | |
Collapse
|
27
|
Affiliation(s)
- A N Lane
- Division of Molecular Structure, National Institute for Medical Research, London NW7 1AA, United Kingdom
| |
Collapse
|
28
|
Isaacs RJ, Spielmann HP. NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA. J Mol Biol 2001; 311:149-60. [PMID: 11469864 DOI: 10.1006/jmbi.2001.4855] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)(2) and d(CGCTAGCG)(2) have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate B(I) and B(II) conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %B(I) or %S. Sequence context-dependent variations in %B(I) and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %B(I), %S, and previously calculated model free (13)C order parameters (S(2)) were observed. The %B(I) of the phosphates were found to be correlated to the S(2) of the flanking C3' and C4' atoms. The %B(I) was also found to be correlated with the %S and C1' S(2) of the deoxyribose ring 5' of the phosphates. The %B(I) of opposing phosphates is correlated, while the %B(I) of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.
Collapse
Affiliation(s)
- R J Isaacs
- Department of Molecular and Cellular Biochemistry Department of Chemistry, & Kentucky Center for Structural Biology, University of Kentucky, Lexington, KY 40536-0084, USA
| | | |
Collapse
|
29
|
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
|
30
|
Hayes MP, Hatala PJ, Sherer BA, Tong X, Zanatta N, Borer PN, Kallmerten J. Regioselective synthesis of 13C1-labeled 2-deoxyribonolactones. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)01148-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
31
|
LaPlante SR, Aubry N, Déziel R, Ni F, Xu P. Transferred 13C T1 Relaxation at Natural Isotopic Abundance: A Practical Method for Determining Site-Specific Changes in Ligand Flexibility upon Binding to a Macromolecule. J Am Chem Soc 2000. [DOI: 10.1021/ja0017817] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven R. LaPlante
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Norman Aubry
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Robert Déziel
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Feng Ni
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Ping Xu
- Contribution from Research and Development, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada, and Biomolecular NMR Laboratory, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| |
Collapse
|
32
|
Abstract
Long-range interactions are known to play an important role in highly polar biomolecules like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate treatment of the long-range interactions are crucial for achieving stable nanosecond trajectories. In this report, we evaluate the structural and dynamic effects on a highly charged oligonucleotide in aqueous solution from different long-range truncation methods. Two group-based truncation methods, one with a switching function and one with a force-switching function were found to fail to give accurate stable trajectories close to the crystal structure. For these group-based truncation methods, large root mean square (rms) deviations from the initial structure were obtained and severe distortions of the oligonucleotide were observed. Another group-based truncation scheme, which used an abrupt truncation at 8. 0 A or at 12.0 A was also investigated. For the short cutoff distance, the conformations deviated far away from the initial structure and were significantly distorted. However, for the longer cutoff, where all necessary electrostatic interactions were included, the trajectory was quite stable. For the particle mesh Ewald (PME) truncation method, a stable DNA simulation with a heavy atom rms deviation of 1.5 A was obtained. The atom-based truncation methods also resulted in stable trajectories, according to the rms deviation from the initial B-DNA structure, of between 1.5 and 1.7 A for the heavy atoms. In these stable simulations, the heavy atom rms deviations were approximately 0.6-1.0 A lower for the bases than for the backbone. An increase of the cutoff radius from 8 to 12 A decreased the rms deviation by approximately 0.2 A for the atom-based truncation method with a force-shifting function, but increased the computational time by a factor of 2. Increasing the cutoff from 12 to 18 A for the atom-based truncation method with a force-shifting function requires 2-3 times more computational time, but did not significantly change the rms deviation. Similar rms deviations from the initial structure were found for the atom-based method with a force-shifting function and for the PME method. The computational cost was longer for the PME method with a cutoff of 12. 0 A for the direct space nonbonded calculations than for the atom-based truncation method with a force-shifting function and a cutoff of 12.0 A. If a nonperiodic boundary, e.g., a spherical boundary, was used, a considerable speedup could be achieved. From the rms fluctuations, the terminal nucleotides and especially the cytidines were found to be more flexible than the nonterminal nucleotides. The B-DNA form of the oligonucleotide was maintained throughout the simulations and is judged to depend on the parameters of the energy function and not on the truncation method used to handle the long-range electrostatic interactions. To perform accurate and stable simulations of highly charged biological macromolecules, we recommend that the atom-based force-shift method or the PME method should be used for the long-range electrostatics interactions.
Collapse
Affiliation(s)
- J Norberg
- Center for Structural Biochemistry, Department of Bioscience at Novum, Karolinska Institutet, S-141 57 Huddinge, Sweden.
| | | |
Collapse
|
33
|
Liang Z, Freed JH, Keyes RS, Bobst AM. An Electron Spin Resonance Study of DNA Dynamics Using the Slowly Relaxing Local Structure Model. J Phys Chem B 2000. [DOI: 10.1021/jp994219f] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
34
|
Schuster GB. Long-range charge transfer in DNA: transient structural distortions control the distance dependence. Acc Chem Res 2000; 33:253-60. [PMID: 10775318 DOI: 10.1021/ar980059z] [Citation(s) in RCA: 590] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Damage to DNA is often caused by oxidative reactions. In one such process, an electron is lost from a base, forming its radical cation. Further reaction of the radical cation can lead to permanent change, which results in mutation. This Account is a report on oxidative damage to DNA caused by irradiation of anthraquinone derivatives, which are either randomly bound to the DNA or attached to it covalently at specific locations. Radical cations introduced in the DNA by the excited quinone cause damage both near to it and far away. We describe a mechanism for long-range charge transport in DNA that depends on its spontaneous structural distortion, which we call phonon-assisted polaron hopping. This mechanism, and its extension, provides a framework for understanding the reactions and charge-transport properties of DNA.
Collapse
Affiliation(s)
- G B Schuster
- School of Chemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| |
Collapse
|
35
|
Cahen P, Luhmer M, Fontaine C, Morat C, Reisse J, Bartik K. Study by (23)Na-NMR, (1)H-NMR, and ultraviolet spectroscopy of the thermal stability of an 11-basepair oligonucleotide. Biophys J 2000; 78:1059-69. [PMID: 10653819 PMCID: PMC1300709 DOI: 10.1016/s0006-3495(00)76664-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
23Na-NMR, (1)H-NMR, and ultraviolet (UV) spectroscopy have been used to study the thermal stability of the double helix structure of an 11-basepair oligonucleotide. The denaturation curves obtained by (23)Na-NMR and UV are analyzed using a two-state model. The melting temperature and DeltaH(0) obtained are identical within experimental error, suggesting that modifications in the ionic atmosphere, probed by (23)Na-NMR, and the modifications in the basepair stacking, probed by UV, occur at the same temperature. Additional dynamical information on the denaturation process has been obtained by (1)H-NMR: slow exchange is observed between the thymine methyl resonances, and the disappearance of imino protons shows that a single basepair opening does not contribute significantly to proton exchange.
Collapse
Affiliation(s)
- P Cahen
- Laboratoire de Chimie Organique E.P. (CP165/64), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | | | | | | | | | | |
Collapse
|
36
|
Brauns EB, Madaras ML, Coleman RS, Murphy CJ, Berg MA. Measurement of Local DNA Reorganization on the Picosecond and Nanosecond Time Scales. J Am Chem Soc 1999. [DOI: 10.1021/ja992456q] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric B. Brauns
- Contribution from the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Mihaela L. Madaras
- Contribution from the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Robert S. Coleman
- Contribution from the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Catherine J. Murphy
- Contribution from the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Mark A. Berg
- Contribution from the Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| |
Collapse
|
37
|
Rundlöf T, Venable RM, Pastor RW, Kowalewski J, Widmalm G. Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling. J Am Chem Soc 1999. [DOI: 10.1021/ja992675b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Torgny Rundlöf
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard M. Venable
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard W. Pastor
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Jozef Kowalewski
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Göran Widmalm
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| |
Collapse
|
38
|
Abstract
The local dynamics of a double-stranded DNA d(TpCpGpCpG)(2) is obtained to second order in the mode-coupling expansion of the Smoluchowski diffusion theory. The time correlation functions of bond variables are derived and the (13)C-nmr spin-lattice relaxation times T(1) of different (13)C along the chains are calculated and compared to experimental data from the literature at three frequencies. The DNA is considered as a fluctuating three-dimensional structure undergoing rotational diffusion. The fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1 ns. Any technique for sampling the configurational space can be used as an alternative. For a fluctuating three-dimensional (3D) structure using the three first-order vector modes of lower rates, higher order basis sets of second-rank tensor are built to give the required mode coupling dynamics. Second- and even first-order theories are found to be in close agreement with the experimental results, especially at high frequency, where the differences in T(1) for (13)C in the base pairs, sugar, and backbone are well described. These atomistic calculations are of general application for studying, on a molecular basis, the local dynamics of fluctuating 3D structures such as double-helix DNA fragments, proteins, and protein-DNA complexes. Copyright 1999 John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- S Fausti
- Istituto di Studi Chimico-Fisici di Macromolecole Sintetiche e Naturali, National Research Council, Via De Marini 6, 16149 Genova, Italy
| | | | | |
Collapse
|
39
|
Ly D, Sanii L, Schuster GB. Mechanism of Charge Transport in DNA: Internally-Linked Anthraquinone Conjugates Support Phonon-Assisted Polaron Hopping. J Am Chem Soc 1999. [DOI: 10.1021/ja991753s] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
40
|
Henderson PT, Jones D, Hampikian G, Kan Y, Schuster GB. Long-distance charge transport in duplex DNA: the phonon-assisted polaron-like hopping mechanism. Proc Natl Acad Sci U S A 1999; 96:8353-8. [PMID: 10411879 PMCID: PMC17521 DOI: 10.1073/pnas.96.15.8353] [Citation(s) in RCA: 367] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anthraquinone-linked duplex DNA oligomer containing 60 base pairs was synthesized by PCR. The strand complementary to the quinone-containing strand has four isolated GG steps, which serve as traps for a migrating radical cation. Irradiation of the quinone leads to electron transfer from the DNA to the quinone forming the anthraquinone radical anion and a base radical cation. The radical cation migrates through the DNA, causing reaction at GG steps revealed as strand breaks. The efficiency of strand cleavage falls off exponentially with distance from the quinone (slope = -0.02 A(-1)). This finding necessitates reinterpretation of mechanisms proposed for radical cation migration in DNA. We propose that radical cations form self-trapped polarons that migrate by thermally activated hopping.
Collapse
Affiliation(s)
- P T Henderson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | | | | | | |
Collapse
|
41
|
Sun YC, Yang SF, Hwang IL, Wu TH. A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(19990415)20:5<546::aid-jcc6>3.0.co;2-l] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
42
|
Bouchemal-Chibani N, du Penhoat CH, Abdelkafi M, Ghomi M, Turpin PY. Characterization of the dynamic behavior of r(ACC) and r(AAC) with NMR relaxation data and both metropolis monte carlo and molecular dynamics simulations. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199610)39:4<549::aid-bip7>3.0.co;2-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
43
|
Kojima C, Ono A, Kainosho M, James TL. DNA duplex dynamics: NMR relaxation studies of a decamer with uniformly 13C-labeled purine nucleotides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 135:310-333. [PMID: 9878461 DOI: 10.1006/jmre.1998.1584] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dynamics in a DNA decamer duplex, d(CATTTGCATC). d(GATGCAAATG), were investigated via a detailed 13C NMR relaxation study. Every 2'-deoxyadenosine and 2'-deoxyguanidine was chemically enriched with 15% 13C and 98% 15N isotopes. Six nuclear relaxation parameters [R(13Cz), R(1Hz), R(2(1)Hz13Cz), R(13Cx), R(2(1)Hz13Cx) and steady-state 13C¿1H¿ NOE] were measured at 600 MHz and three were measured at 500 MHz (1H frequency) for the CH spin systems of sugar 1', 3', and 4' as well as base 8 and 2 positions. A dependence of relaxation parameter values on chemical position was clearly observed; however, no sequence-specific variation was readily evident within our experimental error of approximately 5-10%, except for 3' and 5' termini. It was demonstrated that the random 15% 13C enrichment effectively suppressed both scalar and dipolar contributions of the neighboring carbons and protons on the relaxation parameters. To analyze dynamics via all observed relaxation parameters, full spectral density mapping (1992, J. W. Peng and G. Wagner, J. Magn. Reson. 98, 308) and the "model-free" approach (1982, Lipari and Szabo, J. Am. Chem. Soc. 104, 4546) were applied complementarily. A linear correlation between three spectral density values, J(omegaC), J(omegaH - omegaC), and J(omegaH + omegaC) was observed in plots containing all measured values, but not for the other spectral density terms including J(0). These linear correlations reflect the effect of overall motion and similar internal motions for each CH vector in the decamer. The correlations yielded two correlation times, 3-4 ns and 10-200 ps. One value, 3-4 ns, corresponds to the value of 3.3 ns obtained for the overall isotropic tumbling correlation time determined from analysis of 13C T1/T2 ratios. The possibility of overall anisotropic tumbling was examined, but statistical analysis showed no advantage over the assumption of simple isotropic tumbling. Lack of correlations entailing J(0) implies that a relatively slow chemical exchange contributes to yielding of effective Jeff(0) values. Based on spectral density mapping and the T1/T2 ratio analysis, three basic assumptions were initially employed (and subsequently justified) for the model-free calculation: isotropic overall tumbling, one internal motion, and the presence of chemical exchange terms. Except for terminal residues, the order parameter S2 and the corresponding fast internal motion correlation time were determined to be about 0.8 +/- 0.1 and 20 +/- 20 ps, respectively, for the various CH vectors. Only a few differences were observed between or within sugars and bases. The internal motion is very fast (ps-ns time scale) and its amplitude restricted; e.g., assuming a simple wobble-in-a-cone model, the internal motion is restricted to an angular amplitude of +/-22. 5 degrees for each of the 1', 3', 4', 2, and 8 positions in the purine nucleotides in the entire duplex.
Collapse
Affiliation(s)
- C Kojima
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143-0446, USA
| | | | | | | |
Collapse
|
44
|
Hatcher ME, Mattiello DL, Meints GA, Orban J, Drobny GP. A Solid-State Deuterium NMR Study of the Localized Dynamics at the C9pG10 Step in the DNA Dodecamer [d(CGCGAATTCGCG)]2. J Am Chem Soc 1998. [DOI: 10.1021/ja971266h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mary E. Hatcher
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Debra L. Mattiello
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Gary A. Meints
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - John Orban
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| | - Gary P. Drobny
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195, and Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, Maryland 20850
| |
Collapse
|
45
|
Hall KB, Tang C. 13C relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin. Biochemistry 1998; 37:9323-32. [PMID: 9649313 DOI: 10.1021/bi9805285] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The iron responsive element (IRE) RNA hairpin contains a conserved six-nucleotide loop. The NMR structure of this loop showed that the positions of four of its bases are not tightly constrained, while the remaining two are hydrogen-bonded [Laing, L. G., and Hall, K. B. (1996) Biochemistry 35, 13586]. To investigate the flexibility of the RNA in the loop and in the stem, 13C NMR relaxation methods have been used to describe the dynamics of the purine bases. IRE hairpins containing [13C]guanosine and [13C]adenosine are used in NMR experiments to measure T1, T1rho, and NOE values of the bases as a function of temperature (20-37 degreesC). Data are analyzed using the Lipari-Szabo model-free formalism [Lipari, G., and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546] to determine order parameters and time scales of the motion. Results indicate that the purine bases in the stem have order parameters that are independent of temperature, although they show evidence of both fast (6-40 ps) motions and slower motions at 37 degreesC. The three purines in the loop exhibit increasingly complex motions with long (nanoseconds) correlation times as the temperature increases, suggesting that the loop structure has become disordered.
Collapse
Affiliation(s)
- K B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
| | | |
Collapse
|
46
|
Brauns EB, Murphy CJ, Berg MA. Local Dynamics in DNA by Temperature-Dependent Stokes Shifts of an Intercalated Dye. J Am Chem Soc 1998. [DOI: 10.1021/ja973207+] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
47
|
Kjellberg A, Torgny Rundlöf,, Kowalewski J, Widmalm G. Motional Properties of Two Vicinally Disubstituted Trisaccharides As Studied by Multiple-Field Carbon-13 NMR Relaxation. J Phys Chem B 1998. [DOI: 10.1021/jp971542e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra Kjellberg
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Torgny Rundlöf,
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jozef Kowalewski
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
48
|
Abdelkafi M, Leulliot N, Ghomi M, du Penhoat C, Namane A, Gouyette C, Huynh-Dinh T, Baumruk V, Turpin PY. UNCG tetraloops in short oligoribonucleotides reveal high thermodynamic stability and unusual structural properties in aqueous phase as confirmed by optical and NMR spectroscopies. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09536-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
49
|
Abstract
The hydration of the d(CGCGAATTCGCG) B-DNA duplex in solution was studied by nuclear magnetic relaxation dispersion (NMRD) of the water nuclei 1H, 2H, and 17O, and by nuclear Overhauser effects (NOEs) in high-resolution two-dimensional 1H NMR spectra. By comparing results from the free duplex with those from its complex with netropsin, water molecules in the "spine of hydration" in the AATT region of the minor groove could be distinguished from hydration water elsewhere in the duplex. The 2H and 17O relaxation dispersions yield a model-independent residence time of 0.9(+/-0.1) ns at 4 degrees C for five highly ordered water molecules in the spine. When corrected for frequency offset effects, the NOE data yield the same residence time as the NMRD data, giving credence to both methods. At 27 degrees C, the residence time is estimated to 0.2 ns, a factor of 40 shorter than the tumbling time of the duplex. The NMRD data show that all water molecules associated with the duplex, except the five molecules in the spine, have residence times significantly shorter than 1 ns at 4 degrees C. There is thus no long-lived hydration structure associated with the phosphate backbone. In contrast to 2H and 17O, the 1H relaxation dispersion is dominated by labile DNA protons and therefore provides little information about DNA hydration.
Collapse
Affiliation(s)
- V P Denisov
- Condensed Matter Magnetic Resonance Group, Lund University, Sweden
| | | | | | | |
Collapse
|
50
|
Abdelkafi M, Ghomi M, Turpin PY, Baumruk V, Hervé du Penhoat C, Lampire O, Bouchemal-Chibani N, Goyer P, Namane A, Gouyette C, Huynh-Dinh T, Bednárová L. Common structural features of UUCG and UACG tetraloops in very short hairpins determined by UV absorption, Raman, IR and NMR spectroscopies. J Biomol Struct Dyn 1997; 14:579-93. [PMID: 9130080 DOI: 10.1080/07391102.1997.10508158] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Thermodynamic and structural properties of two UNCG tetraloops in very short hairpin octamers, 5'-r(GCUUCGGC)-3' and 5'-r(GCUACGGC)-3', have been studied by means of various physical techniques. Melting profiles of both octamers, obtained from UV absorption spectra taken as a function of temperature, are consistent with a monophasic, progressive and completely reversible order-to-disorder transition and confirm their unusual structural stability (Tm > 51 degrees C). The 1H, 13C and 31P NMR chemical shifts and coupling constants of the UACG loop nucleotides are comparable with those reported previously for UUCG loops, i.e. 2'-endo/anti conformation of the second and third nucleotide of the loop as well as the syn orientation of the ultimate guanine base and the A-type double helical conformation of the hairpin stem. Simulation of quantitative NOESY volumes shows that the UACG octamer adopts a very rigid compact structure which is well represented by an average order parameter of 0.9. Three base-pairs and four additional strong hydrogen bonds are undoubtedly responsible for such limited flexibility. Raman and infrared spectra as a function of temperature reflect the order-to-disorder transition, as well. Vibrational conformational markers in low temperature spectra of both octamers indicate the hairpin structure as the major conformer in aqueous phase. These spectra further support the structural features of most of the nucleotides involved in the tetraloops and clearly demonstrate the structural similarities of the phosphodiester backbone in both hairpins. Consequently, on the basis of all present results, one can deduce that the conformational features of the UUCG and UACG tetraloops seem to be inherent to the UNCG type tetraloops, regardless of either the nature of the tetraloop second base or the stem length.
Collapse
Affiliation(s)
- M Abdelkafi
- Laboratoire de Physicochimie, Biomoléculaire et Cellulaire, URA CNRS 2056, Université Pierre et Marie Curie, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|