Search bioRxiv⌕ Search

bioRxiv · 10.64898/2026.10.21.760866

Improved 1H NMR and ATR-FTIR approaches for structural characterization of high-G-block and high-M-block alginic acids isolated from sugar kelp by a two-step gelation method

Abstract

Two low-molecular-weight alginic acid fractions, G-block-rich SKP-G1 and M-block-rich SKP-G2, were sequentially isolated from a hot-water extract of sugar kelp (Saccharina latissima) alcohol-insoluble residue by acetic acid-induced and subsequent freeze-thaw-induced gelation. High-field (700 MHz) 2D 1H-1H COSY and TOCSY spectroscopy enabled comprehensive cross-peak assignments for selected alginate diad and triad sequences, supporting interpretation of 1D 1H NMR spectra. Sequence frequencies were combined with previously established inequalities [1] to calculate constrained frequency ranges for homoblocks beyond the triad level. For selected homoblock lengths up to a degree of polymerization of 18, comparison of the experimentally derived frequency ranges with frequencies predicted by chain-growth statistical models ruled out the Bernoulli model for both fractions and the first-order Markov model for SKP-G1. Applying the recently developed logarithmic cosine transformation (LCT) algorithm [2] to first- and second-derivative ATR-FTIR spectra enhanced the visualization of subtle spectral features and produced distinct fingerprints for the two fractions. As a proof of concept, LCT-transformed derivative ATR-FTIR spectra yielded distinct score distributions for the fractions in principal component analysis, suggesting their potential for chemometric differentiation of alginates with different block structures. In conclusion, extending 1H NMR-based sequence analysis to calculate constrained frequency ranges for homoblock polyads beyond the triad level, together with LCT-transformed derivative ATR-FTIR fingerprinting, expands the analytical toolkit for alginate block structure characterization.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Xing, X., Bajwa, B., Low, K. E., Tingley, J. P., Weiler, V., Montina, T., Serin, S. C., Abbott, W.. 2026-10-22. Improved 1H NMR and ATR-FTIR approaches for structural characterization of high-G-block and high-M-block alginic acids isolated from sugar kelp by a two-step gelation method. https://doi.org/10.64898/2026.10.21.760866

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Standardisation Challenges in ELISA-Based Quantification of Equine Chorionic Gonadotropin (eCG/PMSG)

Equine chorionic gonadotropin (eCG/PMSG) is widely used for female-cycle synchronization and estrus induction in livestock and in biomedical research, where reliable quantitative assessment is increasingly important. However, its structural and glycosylation heterogeneity complicates antibody-based measurement and assay standardization. This Technical Note evaluated six commercially available quantitative PMSG ELISA kits representing three distinct analytical profile groups. Kit-provided calibration standards were characterized by Western blotting, Coomassie staining, and LC-MS/MS, while quantitative performance was assessed using serial dilutions of two commercial PMSG preparations. DRG, Creative Diagnostics, and Demeditec showed similar calibration-standard profiles and concentration-dependent responses, although measured concentrations were consistently below nominal values. Biomatik and MyBiosource displayed closely related analytical profiles but little meaningful concentration-dependent response, whereas Krishgen measurements remained within a narrow range despite changes in nominal PMSG input. The calibration standards differed substantially in protein composition, and no eCG-derived peptides were identified by LC-MS/MS under the conditions used. These findings demonstrate that quantitative results obtained with commercially available PMSG ELISAs are not necessarily comparable and may be strongly influenced by calibration-material composition, assay format, and matrix effects. The findings highlight the limitations of current quantitative PMSG assays and the need for a well-characterized, commutable reference material, together with assay-specific validation of dilution parallelism and analyte recovery, to improve the reliability and comparability of eCG/PMSG measurements.

biochemistry↗

Optimization of the NFκB-DNA ensemble leads to high affinity binding of partial consensus sites

Our ability to respond to a myriad of external stressors is dependent on the activity of specific transcription factors that precisely regulate gene expression. While some transcription factors have high specificity for their consensus DNA binding site, others such as NF{kappa}B (RelA/p50) readily bind to partial and nonconsensus sites. In fact, ChIP-Seq data shows that nearly half of the DNA-bound RelA occupies sequences that do not match the consensus. Here we explore how NF{kappa}B (RelA/p50) binds to alternative sequences that differ subtly from the consensus. The two subunits of the NF{kappa}B heterodimer, RelA and p50, form an extensive pocket where DNA binding is mediated by both base-specific contacts and nonspecific interactions with the DNA backbone. RelA and p50 each form sequence-specific contacts with DNA at different 4-nucleotide sequences separated by two nucleotides, together forming a 10-base pair consensus binding sequence. Partial consensus sequences, known as half-sites, match the consensus sequence at only one of these two 4-nucleotide interaction sites. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations to investigate protein structural dynamics, we observe that rearranging nucleotides at the RelA-interacting end of a consensus DNA sequence to form a half-site induces dynamic structural changes through both subunits of RelA/p50. MD simulations reveal a shift in the position of DNA within the RelA/p50 binding pocket that allows optimal interaction with the half-site sequence. Our results demonstrate how RelA/p50 fine-tunes its interactions to achieve high-affinity binding with multiple different target DNA sequences.

biochemistry↗

A High-Sensitivity and High-Throughput LC-MS Workflow for Low-Input and Single-Cell Proteomics

Single-cell proteomics (SCP) requires sample preparation that minimizes sample loss and highly sensitive LC-MS analysis because the amount of protein available from a single cell is extremely limited. Here, we developed an integrated workflow for low-input and single-cell proteomics based on single-cell proteomics by LMNG-assisted sample preparation (scpLASP), which enables microliter-scale sample preparation using standard laboratory consumables. Systematic optimization of peptide reconstitution conditions identified 0.01% n-dodecyl-{beta}-D-maltoside (DDM) combined with 0.01% lauryl maltose neopentyl glycol (LMNG) as the condition yielding the highest number of identified peptides among those tested for low-input samples. Optimization of the LC mobile-phase composition identified 0.5% acetic acid with 1% dimethyl sulfoxide (DMSO) as the optimal condition, increasing the mean number of identified protein groups from 6,767 with 0.1% formic acid to 7,409 for 250 pg HeLa digests analyzed using an Orbitrap Astral Zoom. Shortening the LC gradient from 11 to 5.5 min enabled higher analytical throughput while maintaining mean identification counts of 6,558 and 7,088 protein groups from 100 and 250 pg HeLa digests, respectively, with median protein-level coefficients of variation of 9.20% and 6.99%. When the optimized workflow was applied to HEK293-derived Expi293F single cells using the same 5.5-min LC gradient, an effective analytical throughput of 135 samples per day was achieved with an injection volume of 4.5 {micro}L, accounting for sample-loading time. This workflow identified a median of 5,655 protein groups per cell using an empirical spectral library generated from 20-cell samples. Overall, this study establishes a sensitive and high-throughput workflow for low-input and single-cell proteomics that combines low-loss microliter-scale sample preparation with optimized LC-MS analysis, achieving high proteome depth and analytical throughput without requiring specialized nanoliter-scale sample-preparation devices.

biochemistry↗