DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly13C-Labeled Purine Nucleotides

Kojima, Chojiro; Ono, Akira; Kainosho, Masatsune; James, Thomas Leroy

doi:10.1006/jmre.1998.1584

Cited by 56 publications

(50 citation statements)

References 88 publications

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“…Previous NMR measurements have detected an increased amplitude of motion at the ends of oligonucleotides in the picosecond time range, but could not isolate a time constant for this motion. [4][5][6] X-ray, 3 NMR 4-6 and computer [7][8][9] experiments agree that fraying is largely confined to the last two base-pairs, with most of the motion on the terminal base pair. Two general types of motion can be envisioned, each of which could be detected in a TRSS experiment.…”

Section: Discussionmentioning

confidence: 79%

“…Another aspect of fraying is that the closed base-pair experiences increased mobility due to the reduced structural constraints at the end of the helix. Evidence for this increased mobility is seen by x-ray crystallography, 3 by NMR spectroscopy [4][5][6] and by computer simulation. [7][8][9] However, none of these studies have given specific rates for these extra motions.…”

Section: Introductionmentioning

confidence: 90%

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Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

et al. 2006

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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 [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.

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Section: Discussionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 90%

Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

et al. 2006

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“…The generalized order parameters measured for bond vectors in base moieties in duplex helices tend to have values of around S 2 % 0.8. [126,[139][140][141] Lower values are often observed in sugar moieties and terminal bases [142][143][144] and in nonhelical residues such as loops and bulges. [145,146] A number of studies have also provided insight into the heterogeneity of RNA dynamics.…”

Section: Fast (Ps-ns) Librational Motions By Spin Relaxationmentioning

confidence: 99%

Dynamics‐Based Amplification of RNA Function and Its Characterization by Using NMR Spectroscopy

Al‐Hashimi

2005

ChemBioChem

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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.

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“…[12][13][14] Over the next decade, a number of investigators 15,16 recorded relaxation data on natural abundance DNA duplexes for both ribose and base carbons. Low levels of random 13 C fractional enrichment were later used to study the internal dynamics of DNA 17 and RNA. 18 Although some of the limitations of 13 C relaxation studies can be overcome by reducing 13 C-13 C interactions, natural abundance and random fractional enrichment studies suffer from serious limitations in regards to sensitivity.…”

Section: Historical Contextmentioning

confidence: 99%

“…19 Several studies in RNA and DNA also incorporated R ex into the fitting parameters. 16,17,20,26,27 The Effect of Chemical Shift Anisotropy on Relaxation Rates in RNA and DNA Bases…”

Section: Model-free Analysismentioning

confidence: 99%

NMR studies of dynamics in RNA and DNA by ¹³C relaxation

Shajani

Varani

2006

Biopolymers

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T he 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. 1,2 Although structurally more conservative and therefore dynamically less diverse, 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. 3 These statements make a compelling case to study the sequence dependent dynamics in nucleic acids; yet, residue-specific studies of nucleic acid dynamics are relatively few. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention, this spectroscopy being the only way to access information on a residue-by-residue basis. The questions that are being asked are how motion contributes to the affinity and specificity of biological interactions and what trajectories lead to the remarkably large conformational changes that are sometimes observed.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. Figure 1 summarizes the NMR spectroscopic techniques commonly used to obtain information in each motional regime. Dynamics occurring on time scales that are considered ''fast'' in NMR spectroscopic studies (ps-ns) largely reflects bond librations associated with small amplitude and localized motions.

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DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly13C-Labeled Purine Nucleotides

Cited by 56 publications

References 88 publications

Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

Dynamics‐Based Amplification of RNA Function and Its Characterization by Using NMR Spectroscopy

NMR studies of dynamics in RNA and DNA by ¹³C relaxation

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DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly13C-Labeled Purine Nucleotides

Cited by 56 publications

References 88 publications

Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix

Dynamics‐Based Amplification of RNA Function and Its Characterization by Using NMR Spectroscopy

NMR studies of dynamics in RNA and DNA by 13C relaxation

Contact Info

Product

Resources

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NMR studies of dynamics in RNA and DNA by ¹³C relaxation