1
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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2
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Ma X, Sun C, Boutis GS. Investigation of the effect of a variety of pulse errors on spin I=1 quadrupolar alignment echo spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 211:134-42. [PMID: 21664160 PMCID: PMC3148855 DOI: 10.1016/j.jmr.2011.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 04/22/2011] [Accepted: 05/07/2011] [Indexed: 05/30/2023]
Abstract
We report on an analysis of a well known three-pulse sequence for generating and detecting spin I=1 quadrupolar order when various pulse errors are taken into account. In the situation of a single quadrupolar frequency, such as the case found in a single crystal, we studied the potential leakage of single and/or double quantum coherence when a pulse flip error, finite pulse width effect, RF transient or a resonance offset is present. Our analysis demonstrates that the four-step phase cycling scheme studied is robust in suppressing unwanted double and single quantum coherence as well as Zeeman order that arise from the experimental artifacts, allowing for an unbiased measurement of the quadrupolar alignment relaxation time, T(1Q). This work also reports on distortions in quadrupolar alignment echo spectra in the presence of experimental artifacts in the situation of a powdered sample, by simulation. Using our simulation tool, it is demonstrated that the spectral distortions associated with the pulse artifacts may be minimized, to some extent, by optimally choosing the time between the first two pulses. We highlight experimental results acquired on perdeuterated hexamethylbenzene and polyethylene that demonstrate the efficacy of the phase cycling scheme for suppressing unwanted quantum coherence when measuring T(1Q). It is suggested that one employ two separate pulse sequences when measuring T(1Q) to properly analyze the short time behavior of quadrupolar alignment relaxation data.
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Affiliation(s)
- Xiang Ma
- Brooklyn College, Department of Physics 2900 Bedford Avenue Brooklyn NY 11210
| | - Cheng Sun
- Brooklyn College, Department of Physics 2900 Bedford Avenue Brooklyn NY 11210
| | - Gregory S. Boutis
- Brooklyn College, Department of Physics 2900 Bedford Avenue Brooklyn NY 11210
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3
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Kinde-Carson MN, Ferguson C, Oyler NA, Harbison GS, Meints GA. Solid state 2H NMR analysis of furanose ring dynamics in DNA containing uracil. J Phys Chem B 2010; 114:3285-93. [PMID: 20151717 DOI: 10.1021/jp9091656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions, such as uracil, in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Increased dynamic properties in lesion-containing DNAs have been suggested to assist recognition and specificity. Deuterium solid-state nuclear magnetic resonance (SSNMR) has been used to directly observe local dynamics of the furanose ring within a uracil:adenine (U:A) base pair and compared to a normal thymine:adenine (T:A) base pair. Quadrupole echo lineshapes, <T(1Z)>, and <T(2e)> relaxation data were collected, and computer modeling was performed. The results indicate that the relaxation times are identical within the experimental error, the solid lineshapes are essentially indistinguishable above the noise level, and our lineshapes are best fit with a model that does not have significant local motions. Therefore, U:A base pair furanose rings appear to have essentially identical dynamic properties as a normal T:A base pair, and the local dynamics of the furanose ring are unlikely to be the sole arbiter for uracil recognition and specificity in U:A base pairs.
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4
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Kahn TR, Fong KK, Jordan B, Lek JC, Levitan R, Mitchell PS, Wood C, Hatcher ME. An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites. Biochemistry 2009; 48:1315-21. [PMID: 19166330 DOI: 10.1021/bi8015235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy and a library of FTIR marker bands have been used to examine the structure and relative flexibilities conferred by different flanking sequences on the EcoRI binding site. This approach allowed us to examine unique peaks and subtle changes in the spectra of d(AAAGAATTCTTT)(2), d(TTCGAATTCGAA)(2), and d(CGCGAATTCGCG)(2) and thereby identify local changes in base pairing, base stacking, backbone conformation, glycosidic bond rotation, and sugar puckering in the studied sequences. The changes in flanking sequences induce differences in the sugar puckers, glycosidic bond rotation, and backbone conformations. Varying levels of local flexibility are observed within the sequences in agreement with previous biological activity assays. The results also provide supporting evidence for the presence of a splay in the G(4)-C(9) base pair of the EcoRI binding site and a potential pocket of flexibility at the G(4) cleavage site that have been proposed in the literature. In sum, we have demonstrated that FTIR is a powerful methodology for studying the effect of flanking sequences on DNA structure and flexibility, for it can provide information about the local structure of the nucleic acid and the overall relative flexibilities conferred by different flanking sequences.
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Affiliation(s)
- Talia R Kahn
- Joint Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, USA
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5
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Tian Y, Kayatta M, Shultis K, Gonzalez A, Mueller LJ, Hatcher ME. 31P NMR investigation of backbone dynamics in DNA binding sites. J Phys Chem B 2009; 113:2596-603. [PMID: 18717548 PMCID: PMC2711773 DOI: 10.1021/jp711203m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein--DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here, we use 31P dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2H NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps, but this effect is localized to only near neighbors and base-pairing partners. Last, we have been able to characterize the percent BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the noncanonical BII conformation, even at low temperatures. Our results demonstrate that 31P dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein-DNA recognition events.
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Affiliation(s)
- Ye Tian
- Department of Chemistry University of California, Riverside, CA 92521
| | | | | | | | | | - Mary E. Hatcher
- The Joint Science Department of the Claremont Colleges; Claremont McKenna, Pitzer and Scripps Colleges, Claremont CA 91711
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6
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Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage. Proc Natl Acad Sci U S A 2008; 105:10366-71. [PMID: 18653759 DOI: 10.1073/pnas.0800405105] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists of approximately 7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, S, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA-protein interface within a virus.
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7
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Shajani Z, Varani G. 13C relaxation studies of the DNA target sequence for hhai methyltransferase reveal unique motional properties. Biochemistry 2008; 47:7617-25. [PMID: 18578505 DOI: 10.1021/bi7020469] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The goal of this work was to examine if sequence-dependent conformational flexibility in DNA plays a role in base extrusion, a common conformational change induced by many DNA-modifying enzymes. We studied the dynamics of the double-stranded DNA target of the HhaI methyltransferase by recording an extensive set of (13)C NMR relaxation parameters. We observe that the cytidine furanose rings experience fast (picosecond to nanosecond) motions that are not present in other nucleotides; the methylation site experiences particularly high mobility. We also observe that the bases of guanosine and cytidine residues within the HhaI recognition sequence GCGC experience motions on a much slower (1-100 micros) time scale. We compare these observations with previous solution and solid-state NMR studies of the EcoRI nuclease target sequence, and solid-state NMR studies of a similar HhaI target construct. While an increased mobility of cytidine furanose rings compared to those of other nucleotides is observed for both sequences, the slower motions are only observed in the HhaI target DNA. We propose that this inherent flexibility lowers the energetic barriers that must occur when the DNA binds to the HhaI methyltransferase and for extrusion of the cytidine prior to its methylation.
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Affiliation(s)
- Zahra Shajani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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8
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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.
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Affiliation(s)
- Elke Duchardt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.
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9
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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.
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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
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10
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Tanaka K, Struts AV, Krane S, Fujioka N, Salgado GFJ, Martínez-Mayorga K, Brown MF, Nakanishi K. Synthesis of CD3-Labeled 11-cis-Retinals and Application to Solid-State Deuterium NMR Spectroscopy of Rhodopsin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2177] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Larsen FH. Simulations of molecular dynamics in solid-state NMR spectra of spin-1 nuclei including effects of CSA- and EFG-terms up to second order. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2007; 31:100-14. [PMID: 17418539 DOI: 10.1016/j.ssnmr.2007.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2006] [Revised: 01/28/2007] [Accepted: 02/22/2007] [Indexed: 05/14/2023]
Abstract
By numerical simulations MAS and QCPMG methods for acquiring spectra of spin-1 nuclei were compared in order to determine the most sensitive experiment for analysis of molecular dynamics. To comply with the large quadrupolar constants for 14N and the CSA reported for 6Li both of these interactions are included up to second order. For 2H and 6Li both QCPMG and single-pulse MAS experiments were suitable for dynamics studies whereas the single-pulse MAS experiment were the method of choice for investigation of 14N dynamics for C(Q)'s larger than 750kHz at 14.1T. This property prohibits excitation of the 14N lineshape using either single hard or softer composite rf-pulses. Focusing on 14N it was demonstrated that the centerband lineshape is sensitive toward both off-MAS and CSA effects. In addition, excitation by real-time pulses showed that proper lineshapes corresponding to a site with a C(Q) of 3MHz may be excited by a very short pulse.
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Affiliation(s)
- Flemming H Larsen
- Department of Food Science, Quality and Technology, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg, Denmark.
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12
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Okonogi TM, Alley SC, Reese AW, Hopkins PB, Robinson BH. Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model. Biophys J 2002; 83:3446-59. [PMID: 12496111 PMCID: PMC1302419 DOI: 10.1016/s0006-3495(02)75344-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The short-time (submicrosecond) bending dynamics of duplex DNA were measured to determine the effect of sequence on dynamics. All measurements were obtained from a single site on duplex DNA, using a single, site-specific modified base containing a rigidly tethered, electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of single-step sequence-dependent bending force constants, determined from the mean squared amplitude of bending relative to the end-to-end vector using the modified weakly bending rod model. The bending dynamics at a single site are a function of the sequence of the nucleotides constituting the duplex DNA. We developed and examined several dinucleotide-based models for flexibility. The models indicate that the dominant feature of the dynamics is best explained in terms of purine- and pyrimidine-type steps, although distinction is made among all 10 unique steps: It was found that purine-purine steps (which are the same as pyrimidine-pyrimidine steps) were near average in flexibility, but the pyrimidine-purine steps (5' to 3') were nearly twice as flexible, whereas purine-pyrimidine steps were more than half as flexible as average DNA. Therefore, the range of stepwise flexibility is approximately fourfold and is characterized by both the type of base pair step (pyrimidine/purine combination) and the identity of the bases within the pair (G, A, T, or C). All of the four models considered here underscore the complexity of the dependence of dynamics on DNA sequence with certain sequences not satisfactorily explainable in terms of any dinucleotide model. These findings provide a quantitative basis for interpreting the dynamics and kinetics of DNA-sequence-dependent biological processes, including protein recognition and chromatin packaging.
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Affiliation(s)
- T M Okonogi
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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13
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Pichler A, Rüdisser S, Rauch C, Flader W, Wellenzohn B, Winger RH, Liedl KR, Hallbrucker A, Mayer E. Restructuring of Hydration Shells Rules the Low-Temperature Dynamics of B-DNA via Its Two Conformer Substates. J Phys Chem B 2002. [DOI: 10.1021/jp013121+] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Abstract
We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility, assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methylation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides.
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Affiliation(s)
- Dafna Nathan
- Departments of Chemistry, Yale University, New Haven, CT 06520, USA
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15
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Abstract
Determination of the conformational flexibility of the furanose ring is of vital importance in understanding the structure of DNA. In this work we have applied a model of furanose ring motion to the analysis of deuterium line shape data obtained from sugar rings in solid hydrated DNA. The model describes the angular trajectories of the atoms in the furanose ring in terms of pseudorotation puckering amplitude (q) and the pseudorotation puckering phase phi. Fixing q, the motion is thus treated as Brownian diffusion through an angular-dependent potential U(phi). We have simulated numerous line shapes varying the adjustable parameters, including the diffusion coefficient D, pseudorotation puckering amplitude q, and the form of the potential U(phi). We have used several forms of the potential, including equal double-well potentials, unequal double-well potentials, and a potential truncated to "second order" in the Fourier series. To date, we have obtained best simulations for both equilibrium and nonequilibrium (partially relaxed) solid-state deuterium NMR line shapes for the sample [2' '-2H]-2'-deoxycytidine at the position C3 (underlined) in the DNA sequence [d(CGCGAATTCGCG)]2, using a double-well potential with an equal barrier height of U(0) = 5.5k(B)T ( approximately 3.3 kcal/mol), a puckering amplitude of q = 0.4 A, and a diffusion coefficient characterizing the underlying stochastic jump rate D = 9.9 x 10(8) Hz. Then the rate of flux for the C-D bond over the barrier, i.e., the escape velocity or the overall rate of puckering between modes, was found to be 0.7 x 10(7) Hz.
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Affiliation(s)
- G A Meints
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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16
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Meints GA, Drobny GP. Dynamic impact of methylation at the M. Hhai target site: a solid-state deuterium NMR study. Biochemistry 2001; 40:12436-43. [PMID: 11591165 DOI: 10.1021/bi0102555] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Base methylation plays an important role in numerous biological functions of DNA, from inhibition of cleavage by endonucleases to inhibition of transcription factor binding. Studies of nucleic acid structure have shown little differences in unmethylated DNAs and the identical sequence containing methylated analogues. We have investigated changes in the local dynamics of DNA upon substitution of a methylated cytosine analogue for cytosine using solid-state deuterium NMR. In particular, we have observed changes in the local dynamics at the target site of the M. HhaI restriction system. These studies observe changes in the amplitudes of the local backbone dynamics at the actual target site of the HhaI methyltransferase. This conclusion is another indication that the significant result of base methylation is to perturb the local dynamics, and therefore the local conformational flexibility, of the DNA helix, inhibiting or restricting the protein's ability to manipulate the DNA helix in order to perform its chemical alterations.
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Affiliation(s)
- G A Meints
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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17
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Hatcher ME, LeTrong I, Stenkamp R, Drobny GP. Local dynamics of the CpG step in a DNA crystal. J Am Chem Soc 2001; 123:8874-5. [PMID: 11535104 DOI: 10.1021/ja005771h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M E Hatcher
- The W. M. Keck Science Center of the Claremont Colleges, Claremont California 91711, USA
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18
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Winger RH, Liedl KR, Pichler A, Hallbrucker A, Mayer E. B-DNA's BII Conformer Substate Population Increases with Decreasing Water Activity. 1. A Molecular Dynamics Study of d(CGCGAATTCGCG)2. J Phys Chem B 2000. [DOI: 10.1021/jp001842n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rudolf H. Winger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Arthur Pichler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Andreas Hallbrucker
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Erwin Mayer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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19
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Shaw WJ, Long JR, Campbell AA, Stayton PS, Drobny GP. A Solid State NMR Study of Dynamics in a Hydrated Salivary Peptide Adsorbed to Hydroxyapatite. J Am Chem Soc 2000. [DOI: 10.1021/ja000878q] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wendy J. Shaw
- Department of Bioengineering Department of Chemistry University of Washington, Seattle, Washington 98195 Pacific Northwest National Laboratory Richland, Washington 99352
| | - Joanna R. Long
- Department of Bioengineering Department of Chemistry University of Washington, Seattle, Washington 98195 Pacific Northwest National Laboratory Richland, Washington 99352
| | - Allison A. Campbell
- Department of Bioengineering Department of Chemistry University of Washington, Seattle, Washington 98195 Pacific Northwest National Laboratory Richland, Washington 99352
| | - Patrick S. Stayton
- Department of Bioengineering Department of Chemistry University of Washington, Seattle, Washington 98195 Pacific Northwest National Laboratory Richland, Washington 99352
| | - Gary P. Drobny
- Department of Bioengineering Department of Chemistry University of Washington, Seattle, Washington 98195 Pacific Northwest National Laboratory Richland, Washington 99352
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20
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Stevensson B, Höög C, Ulfstedt-Jäkel K, Huang Z, Widmalm G, Maliniak A. Solid-State Deuterium NMR and Molecular Modeling Studies of Conformational Dynamics in Carbohydrates. J Phys Chem B 2000. [DOI: 10.1021/jp0002805] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Baltzar Stevensson
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Christer Höög
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Kai Ulfstedt-Jäkel
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Zhi Huang
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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21
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B-DNA's dynamics and conformational substates revealed by calorimetric enthalpy relaxation and fourier transform infrared spectroscopy. J Mol Liq 2000. [DOI: 10.1016/s0167-7322(99)00135-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Geahigan KB, Meints GA, Hatcher ME, Orban J, Drobny GP. The dynamic impact of CpG methylation in DNA. Biochemistry 2000; 39:4939-46. [PMID: 10769153 DOI: 10.1021/bi9917636] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes of motions of the phosphate-sugar backbone. These observations suggest a direct link between suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone of the DNA and inhibition of restriction enzyme cleavage.
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Affiliation(s)
- K B Geahigan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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23
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Pichler A, Rüdisser S, Winger RH, Liedl KR, Hallbrucker A, Mayer E. Nonoriented d(CGCGAATTCGCG)2 Dodecamer Persists in the B-Form Even at Low Water Activity. J Am Chem Soc 2000. [DOI: 10.1021/ja993010c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Arthur Pichler
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
| | - Simon Rüdisser
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
| | - Rudolf H. Winger
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
| | - Andreas Hallbrucker
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
| | - Erwin Mayer
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck A-6020 Innsbruck, Austria
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Winger RH, Liedl KR, Pichler A, Hallbrucker A, Mayer E. Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion. J Biomol Struct Dyn 1999; 17:223-35. [PMID: 10563572 DOI: 10.1080/07391102.1999.10508355] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations. Analysis of the resulting transition processes with respect to the backbone angles reveals concerted changes not only for backbone angles epsilon, zeta, and beta, but also for the 5'-delta and 5'-chi angles. For alpha and delta inside the interconverting base step, a change is seen in short lived B(II) conformers. With respect to base morphology distinct changes are observed for buckle, propeller twist, shift, roll and twist, as well as x-displacement and tip. The base mainly involved in the changes is identified as the base preceding the interconverting phosphate. Altogether single B(I)<==>B(II) interconversions result only in local distortions represented by the larger spread of most parameters. Comparison of the atomic positional fluctuations derived from the simulation with those obtained from the static X-ray structure results in striking similarities.
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Affiliation(s)
- R H Winger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria
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