Band inversion amplifies 31 P-31 P nuclear overhauser effects: Relaxation mechanism and dynamic behavior of ATP in the human brain by 31 P MRS at 7 T

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

ATP line splitting in association with reduced intracellular magnesium and pH: a brain 31 P MR spectroscopic imaging (MRSI) study of pediatric patients with myelin oligodendrocyte glycoprotein antibody-associated disorders (MOGADs)

Over the past four decades, ATP, the obligatory energy molecule for keeping all cells alive and functioning, has been thought to contribute only one set of signals in brain ³¹ P MR spectra. Here we report for the first time the observation of two separate β-ATP peaks in brain spectra acquired from patients with myelin oligodendrocyte glycoprotein antibody-associated disorders (MOGADs) using 3D MRSI at 7 T. In voxel spectra with β-ATP line splitting, these two peaks are separated by 0.46 ± 0.18 ppm (n = 6). Spectral lineshape analysis indicates that the upper field β-ATP peak is smaller in relative intensity (24 ± 11% versus 76 ± 11%), and narrower in linewidth (56.8 ± 10.3 versus 41.2 ± 10.3 Hz) than the downfield one. Data analysis also reveals a similar line splitting for the intracellular inorganic phosphate (P_i ) signal, which is characterized by two components with a smaller separation (0.16 ± 0.09 ppm) and an intensity ratio (26 ± 7%:74 ± 7%) comparable to that of β-ATP. While the major components of P_i and β-ATP correspond to a neutral intracellular pH (6.99 ± 0.01) and a free Mg²⁺ level (0.18 ± 0.02 mM, by Iotti's conversion formula) as found in healthy subjects, their minor counterparts relate to a slightly acidic pH (6.86 ± 0.07) and a 50% lower [Mg²⁺ ] (0.09 ± 0.02 mM), respectively. Data correlation between β-ATP and P_i signals appears to suggest an association between an increased [H⁺ ] and a reduced [Mg²⁺ ] in MOGAD patients.

Phosphorus transversal relaxation times and metabolite concentrations in the human brain at 9.4 T

A method to estimate phosphorus (³¹ P) transversal relaxation times (T₂ s) of coupled spin systems is demonstrated. Additionally, intracellular and extracellular pH and relaxation-corrected metabolite concentrations are reported. Echo time (TE) series of ³¹ P metabolite spectra were acquired using stimulated echo acquisition mode (STEAM) localization. Spectra were fitted using LCModel with accurately modeled Versatile Simulation, Pulses and Analysis (VeSPA) basis sets accounting for J-evolution of the coupled spin systems. T₂ s were estimated by fitting a single exponential two-parameter model across the TE series. Fitted inorganic phosphate frequencies were used to calculate pH, and estimated relaxation times were used to determine the relaxation-corrected brain metabolite concentrations on an assumption of 3 mM γ-ATP. The method was demonstrated in healthy human brain at a field strength of 9.4 T. T₂ times of ATP and nicotinamide adenine dinucleotide (NAD) were shortest between 8 and 20 ms, followed by T₂ s of inorganic phosphate between 25 and 50 ms, and phosphocreatine with a T₂ of 100 ms. Phosphomonoesters and phosphodiesters had the longest T₂ s of about 130 ms. The measured T₂ s are comparable with literature values and fit in a decreasing trend with increasing field strengths. Calculated pHs and metabolite concentrations are also comparable with literature values.

31 P-MRS of healthy human brain: Measurement of guanosine diphosphate mannose at 7 T

Guanosine diphosphate mannose (GDP-Man) is the donor substrate required for mannosylation in the synthesis of glycoproteins, glycolipids and the newly discovered glycoRNA. Normal GDP-Man biosynthesis plays a crucial role in support of a variety of cellular functions, including cell recognition, cell communication and immune responses against viruses. Here, we report the detection of GDP-Man in human brain for the first time, using ³¹ P MRS at 7 T. The presence of GDP-Man is evidenced by the detection of a weak ³¹ P doublet at -10.7 ppm that can be assigned to the phosphomannosyl group (Pβ) of the GDP-Man molecule. This weak but well-resolved signal lies 0.9 ppm upfield of UDP(G) Pβ-multiplet from a mixture of UDP-Glc, UDP-Gal, UDP-GlcNAc and UDP-GalNAc. In reference to ATP (2.8 mM), the concentration of GDP-Man in human brain was estimated to be 0.02 ± 0.01 mM, about 15-fold lower than the total concentration of UDP(G) (0.30 ± 0.04, N = 17) and consistent with previous reports of UDP-Man in cells and brain tissue extracts measured by high-performance liquid chromatography. The reproducibility of the measured GDP-Man between test and 2-week retest was 21% ± 15% compared with 5% ± 4% for UDP(G) (N = 7). The measured concentrations of GDP-Man and UDP(G) are linearly correlated ([UDP(G)] = 4.3 [GDP-Man] + 0.02, with R = 0.66 and p = 0.0043), likely reflecting the effect of shared sugar precursors, which may vary among individuals in response to variation in nutritional intake and consumption. Given that GDP-Man has another set of doublet (Pα) at -8.3 ppm that overlaps with NAD(H) and UDP(G)-Pα signals, the amount of GDP-Man could potentially interfere with the deconvolution of these mixed signals in composition analysis. Importantly, this new finding may be useful in advancing our understanding of glycosylation and its role in the development of cancer, as well as infectious and neurodegenerative diseases.

Comparison of four 31P single-voxel MRS sequences in the human brain at 9.4 T

PURPOSE

In this study, different single-voxel localization sequences were implemented and systematically compared for the first time for phosphorous MRS (³¹ P-MRS) in the human brain at 9.4 T.

METHODS

Two multishot sequences, image-selected in vivo spectroscopy (ISIS) and a conventional slice-selective excitation combined with localization by adiabatic selective refocusing (semiLASER) variant of the spin-echo full intensity-acquired localized spectroscopy (SPECIAL-semiLASER), and two single-shot sequences, semiLASER and stimulated echo acquisition mode (STEAM), were implemented and optimized for ³¹ P-MRS in the human brain at 9.4 T. Pulses and coil setup were optimized, localization accuracy was tested in phantom experiments, and absolute SNR of the sequences was compared in vivo. The SNR per unit time (SNR/t) was derived and compared for all four sequences and verified experimentally for ISIS in two different voxel sizes (3 × 3 × 3 cm³ , 5 × 5 × 5 cm³ , 10-minute measurement time). Metabolite signals obtained with ISIS were quantified. The possible spectral quality in vivo acquired in clinically feasible time (3:30 minutes, 3 × 3 × 3 cm³ ) was explored for two different coil setups.

RESULTS

All evaluated sequences performed with good localization accuracy in phantom experiments and provided well-resolved spectra in vivo. However, ISIS has the lowest chemical shift displacement error, the best localization accuracy, the highest SNR/t for most metabolites, provides metabolite concentrations comparable to literature values, and is the only one of the sequences that allows for the detection of the whole ³¹ P spectrum, including β-adenosine triphosphate, with the used setup. The SNR/t of STEAM is comparable to the SNR/t of ISIS. The semiLASER and SPECIAL-semiLASER sequences provide good results for metabolites with long T₂ .

CONCLUSION

At 9.4 T, high-quality single-voxel localized ³¹ P-MRS can be performed in the human brain with different localization methods, each with inherent characteristics suitable for different research issues.

Quantitative measurement of redox state in human brain by 31 P MRS at 7T with spectral simplification and inclusion of multiple nucleotide sugar components in data analysis

PURPOSE

To develop a simplified method for quantitative measurement of NAD⁺ /NADH (nicotinamide adenine dinucleotides) levels in human brain by ³¹ P MRS without interference from the α-ATP signal and with inclusion of multiple UDP-sugar components.

METHODS

Simple pulse-acquire ³¹ P MR spectra were collected at 7T with and without a frequency-selective inversion pulse to remove the dominant α-ATP signal from the underlying NAD(H) signal. Careful inspection of the ³¹ P signal at -9.8 ppm previously assigned to UDP-glucose revealed multiple UDP-sugar components that must also be considered when deconvoluting the NAD(H) signal to quantify NAD⁺ and NADH. Finally, the overlapping NAD(H) and UDP(G) resonances were deconvoluted into individual components using Voigt lineshape analysis and UDP(G) modeling.

RESULTS

The inversion-based spectral editing method enabled clean separation of the NAD(H) signal from the otherwise dominant α-ATP signal. In addition, the upfield signal near -9.8 ppm appears more "quartet-like" than a simple doublet consistent with contributions from other nucleotide sugars such as UDP-galactose, UDP-N-acetyl-galactosamine, and UDP-N-acetyl-glucosamine in addition to UDP-glucose. Deconvolution of the combined NAD(H) and UDP(G) signals showed that the measured NAD⁺ /NAD ratio was heavily influenced by UDP(G) modeling (7.5 ± 1.8 when the UDP(G) signal was fitted as multiple doublets versus 5.3 ± 0.6 when a simplified pseudo doublet model was used). In a test/re-test experiments separated by 2 weeks, consistent NAD⁺ /NADH ratios were measured in the brain of seven human subjects.

CONCLUSIONS

The NAD⁺ /NADH ratio in human brain can be measured using ³¹ P MR spectra simplified by spectral editing and with inclusion of multiple UDP-sugar components in the data analysis.

Modular 31 P wideband inversion transfer for integrative analysis of adenosine triphosphate metabolism, T1 relaxation and molecular dynamics in skeletal muscle at 7T

PURPOSE

For efficient and integrative analysis of de novo adenosine triphosphate (ATP) synthesis, creatine-kinase-mediated ATP synthesis, T₁ relaxation time, and ATP molecular motion dynamics in human skeletal muscle at rest.

METHODS

Four inversion-transfer modules differing in center inversion frequency were combined to generate amplified magnetization transfer (MT) effects in targeted MT pathways, including Pi ↔ γ-ATP, PCr ↔ γ-ATP, and ³¹ P_γ(α)ATP ↔ ³¹ P_βATP . MT effects from both forward and reverse exchange kinetic pathways were acquired to reduce potential bias and confounding factors in integrated data analysis.

RESULTS

Kinetic data collected using 4 wideband inversion modules (8 minutes each) yielded the forward exchange rate constants, k_{PCr →γ ATP} = 0.31 ± 0.05 s^-1 and k_{Pi →γ ATP} = 0.064 ± 0.012 s^-1 , and the reverse exchange rate constants, k_γATP→Pi = 0.034 ± 0.006 s^-1 and k_γATP→PCr = 1.37 ± 0.22 s^-1 , respectively. The cross-relaxation rate constant, σ_{γ(α) ↔ βATP} was -0.20 ± 0.03 s^-1 , corresponding to ATP rotational correlation time τ_c of 0.8 ± 0.1 × 10^-7 seconds. The intrinsic T₁ relaxation times were Pi (9.2 ± 1.4 seconds), PCr (6.2 ± 0.4 seconds), γ-ATP (1.8 ± 0.1 seconds), α-ATP (1.4 ± 0.1 seconds), and β-ATP (1.1 ± 0.1 seconds). Muscle ATP T₁ values were found to be significantly longer than those previously measured in the brain using a similar method.

CONCLUSION

A combination of multiple inversion transfer modules provides a comprehensive and integrated analysis of ATP metabolism and molecular motion dynamics. This relatively fast technique could be potentially useful for studying metabolic disorders in skeletal muscle.

Efficient 31 P band inversion transfer approach for measuring creatine kinase activity, ATP synthesis, and molecular dynamics in the human brain at 7 T

PURPOSE

To develop an efficient ³¹ P magnetic resonance spectroscopy (MRS) method for measuring creatine kinase (CK) activity, adenosine triphosphate (ATP) synthesis, and motion dynamics in the human brain at 7 Tesla (T).

METHODS

Three band inversion modules differing in center frequency were used to induce magnetization transfer (MT) effect in three exchange pathways: (i) CK-mediated reaction PCr → γ-ATP; (ii) de novo ATP synthesis Pi → γ-ATP; and (iii) ATP intramolecular ³¹ P-³¹ P cross-relaxation γ-(α-) ↔ β-ATP. The resultant MT data were analyzed using a 5-pool model in the format of magnetization matrix according to Bloch-McConnell-Solomon formalism.

RESULTS

With a repetition time (TR) of 4 s, the scan time for each module was approximately 8 min. The rate constants were k_{PCr → γATP} 0.38 ± 0.02 s^-1 , k_{Pi → γATP} 0.19 ± 0.02 s^-1 , and σ_{γ(α) ↔ βATP} 0.19 ± 0.04 s^-1 , corresponding to ATP rotation correlation time τ_c (0.8 ± 0.2) ·10^-7 s. The T₁ relaxation times were Pi 7.26 ± 1.76 s, PCr 5.99 ± 0.58 s, γ-ATP 0.98 ± 0.07 s, α-ATP 0.95 ± 0.04 s, and β-ATP 0.68 ± 0.03 s.

CONCLUSION

Short-TR band inversion modules provide a time-efficient way of measuring brain ATP metabolism and could be useful in studying metabolic disorders in brain diseases. Magn Reson Med 78:1657-1666, 2017. © 2016 International Society for Magnetic Resonance in Medicine.