Theoretical study of R1ρ rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange

Trott, Oleg; Palmer, Arthur G.

doi:10.1016/j.jmr.2004.06.005

Cited by 81 publications

(102 citation statements)

References 18 publications

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“…Similar deviations are observed here for both RNA and DNA (Supplementary Table 4). We postulated that ‘minor’ exchange 36 between ES1 and ES2 could ‘mix’ their chemical shifts and give rise to such deviations (Extended Data Fig. 6a,b and Supplementary Table 4).…”

Section: Sequence-dependent Anion Equilibriamentioning

confidence: 99%

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

Kimsey

Szymanski

Zahurancik

et al. 2018

Nature

134

183

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Tautomeric and anionic Watson-Crick-like mismatches play important roles in replication and translation errors through mechanisms that are not fully understood. Using NMR relaxation dispersion, we resolved a sequence-dependent kinetic network connecting G•T/U wobbles with three distinct Watson-Crick mismatches consisting of two rapidly exchanging tautomeric species (Genol•T/U⇌G•Tenol/Uenol; population <0.4%) and one anionic species (G•T−/U−; population ≈0.001% at neutral pH). Inserting the sequence-dependent tautomerization/ionization step into a minimal kinetic mechanism for correct incorporation during replication following initial nucleotide binding leads to accurate predictions of dG•dT misincorporation probability across different polymerases, pH conditions, and for a chemically modified nucleotide, and provides mechanisms for sequence-dependent misincorporation. Our results indicate that the energetic penalty for tautomerization/ionization accounts for ≈10−2−10−3–fold discrimination against misincorporation, which proceeds primarily via tautomeric dGenol•dT and dG•dTenol with contributions from anionic dG•dT− dominating at pH ≥8.4 or for some mutagenic nucleotides.

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Section: Sequence-dependent Anion Equilibriamentioning

confidence: 99%

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

Kimsey

Szymanski

Zahurancik

et al. 2018

Nature

134

183

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“…Recently, R 1q relaxation dispersion experiments have been extended to describe systems using weak radiofrequency (rf) fields and slow chemical exchange kinetics [2][3][4]. As noted by Trott and Palmer [5], the R 1q relaxation dispersion technique becomes more sensitive, compared to other techniques such as Carr-Purcell-Meiboom-Gill relaxation dispersion [6,7], to parameters characterizing chemical exchange processes at the extremes of slow exchange or weak rf fields. Characterizing such processes requires accurate analytical expressions for the R 1q relaxation rate constant that are not limited to the fast-exchange regime and do not assume special experimental conditions, such as on-resonance irradiation [8,9].…”

Section: Introductionmentioning

confidence: 99%

R1ρ relaxation for two-site chemical exchange: General approximations and some exact solutions

Miloushev

Palmer

2005

Journal of Magnetic Resonance

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“…A long pulse or a short pulse recycle delay may not affect the magnetization for the paramagnetic agent compartment due to the relaxation enhancement effect, but it can reduce the magnetization for the tissue compartment substantially due to the magnetization transfer and spin saturation effect. Studies on the exchange kinetics in the off-resonance rotating frame have been reported for spins in aqueous media [23][24][25], but no appropriate mathematic model has been established for the water diffusion-exchange between dynamically heterogeneous compartments yet.…”

Section: Introductionmentioning

confidence: 99%

Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

Zhang

Xie

2007

Journal of Magnetic Resonance

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The off-resonance rotating frame technique based on the spin relaxation properties of off-resonance T 1ρ can significantly increase the sensitivity of detecting paramagnetic labeling at high magnetic fields. However, the in vivo detectable dimension for labeled cell clusters/tissues in T 1ρ -weighted images is limited by the water diffusion-exchange between mesoscopic scale compartments. An experimental investigation of the effect of water diffusion-exchange between compartments on the paramagnetic relaxation enhancement of paramagnetic agent compartment is presented for in vitro/ in vivo models. In these models, the size of paramagnetic agent compartment is comparable to the mean diffusion displacement of water molecules during the long RF pulses that are used to generate the off-resonance rotating frame. The three main objectives of this study were: (1) to qualitatively correlate the effect of water diffusion-exchange with the RF parameters of the long pulse and the rates of water diffusion, (2) to explore the effect of water diffusion-exchange on the paramagnetic relaxation enhancement in vitro, and (3) to demonstrate the paramagnetic relaxation enhancement in vivo. The in vitro models include the water permeable dialysis tubes or water permeable hollow fibers embedded in cross-linked proteins gels. The MWCO of the dialysis tubes was chosen from 0.1 to 15 kDa to control the water diffusion rate. Thin hollow fibers were chosen to provide submillimeter scale compartments for the paramagnetic agents. The in vivo model utilized the rat cerebral vasculatures as a paramagnetic agent compartment, and intravascular agents (Gd-DTPA) 30 -BSA were administrated into the compartment via bolus injections. Both in vitro and in vivo results demonstrate that the paramagnetic relaxation enhancement is predominant in the T 1ρ -weighted imaging in the presence of water diffusion exchange. The T 1ρ contrast has substantially higher sensitivity than the conventional T 1 contrast in detecting paramagnetic agents, especially at low paramagnetic agent volumetric fractions, low paramagnetic agent concentrations, and low RF amplitudes. Short pulse duration, short pulse recycle delay and efficient paramagnetic relaxation can reduce the influence of water diffusion-exchange on the paramagnetic enhancement. This study paves the way for the design of off-resonance rotating experiments to detect labeled cell clusters/tissue compartments in vivo at a sub-millimeter scale.

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Theoretical study of R1ρ rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange

Cited by 81 publications

References 18 publications

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

R1ρ relaxation for two-site chemical exchange: General approximations and some exact solutions

Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

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