Biology subjects

Donahue, S.

Publications and source records attributed to Donahue, S..

4 recordsLinked to original sources

bioRxiv2026

Simple Feedback for Complex Movement: Capturing Whole-Limb Reorganization during Single-IMU Gait Retraining

Clinical gait retraining typically relies on multi-sensor arrays and high-dimensional feedback displays, imposing setup and interpretation burdens that limit routine clinical deployment. We developed a single-IMU visual biofeedback system that delivers real-time feedback of Lower Limb Trajectory Error (LLTE), a composite kinematic error metric integrating knee position and shank angle across the stance phase. Twenty able-bodied adults walked on a treadmill under two visual biofeedback targets (flexed-knee, extended-knee) while receiving either corrected (n=10) or uncorrected (n=8) feedback, where the correction accounted for limb orientation at initial contact. LLTE and stance-phase knee kinematics adapted consistently under the flexed-knee target for both feedback groups, with feedback formulation moderating the temporal trajectory of change. Adaptation toward the extended-knee target was limited, likely because participants were already operating near terminal knee extension and because the scalar error metric provided limited directional information for correction. Ankle range of motion (ROM) changed significantly across the stance phase under both target conditions, while hip ROM did not. Multiscale multivariate sample entropy (MSMVSE) increased monotonically with time scale across all conditions, with no statistically distinguishable difference between corrected and uncorrected feedback. These results suggest that single-IMU LLTE biofeedback can modify gait mechanics and that adaptation was expressed across multiple lower-limb segments rather than through changes at a single joint.

bioengineering↗

bioRxiv2026

QuadCleave: Enzymatic cleavage and analysis of DNA G-quadruplexes.

Prediction of G-quadruplexes (G4), noncanonical DNA secondary structures containing guanine tetrads, can have profound relevance across cancer, neurodegenerative and other genetic diseases, but require experimental validation by instrument intensive methods including CD spectroscopy, fluorescence, NMR, or crystallography. We report a novel, inexpensive, efficient and scalable 2-enzyme system for confirmation of G4 formation and copy number repeat count. First, QuadCleave, in which Mismatch Endonuclease I was used to repeatably, site-specifically and selectively cleave oligodeoxynucleotides containing exclusively G4-forming sequences. Second, HaeIII enzyme identified G4-forming sequences that can also generate GG/CC base pairs, and a sequences cleavage by both established it in C9ORF72, the most mutated gene in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These findings establish ubiquitously accessible experimental validation of G4 forming sequences and their copy number repeat assessment, with specificity to C9ORF72 oligodeoxynucleotides whose repeat expansion has critical clinical implications in a subpopulation of ALS and FTD patients.

molecular biology↗

bioRxiv2025

Thermally activated irreversible homogenization of G-quadruplexes in an ALS/FTD-associated nucleotide expansion

A significant proportion of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases exhibit a substantial copy number expansion of the hexanucleotide GGGGCC/GGCCCC sequence in the C9ORF72 gene. The GGGGCC sequence forms a non-canonical DNA structure called a G-quadruplex (G4) which has been associated with the disease states and with nucleic acid condensate formation. G4s can fold into various topologies, which can differentially impact fidelity of DNA synthesis. However, how G4 conformational heterogeneity and its regulation impact hexanucleotide repeat expansion is unclear, and important clues may lie in the thermodynamic properties of different G4 topologies. Here, we use temperature-swept CD spectroscopy to observe configurational homogenization of an initially heterogeneous population of G4s over a small range of temperatures, demonstrating thermally activated behavior. We further show that this reaction is irreversible, since subsequent temperature sweeps do not show CD shifts from non-parallel to parallel G4 topologies. Finally, we provide an analytical theory based on a two-state thermodynamic model which is compatible with experimental evidence, and we discuss alternate mechanisms for the homogenization transition. These findings suggest that kinetic regulation of non-canonical DNA structures may play a role in cellular homeostasis or disease pathogenesis. SIGNIFICANCEThe GGGGCC repeats in the C9ORF72 gene expand in copy number in certain neurodegenerative diseases, forming non-canonical DNA structures called G-quadruplexes (G4) which are associated with the pathological state. However, why the repeat expansion occurs is not known, and a key may lie in the thermodynamic stability of certain G4 conformations. Here, we use CD spectroscopy to experimentally report thermally activated heat-induced G4 conformation homogenization, from a heterogeneous population to the parallel configuration. We derive an analytical biophysical theory which is compatible with this experimental observation, which is shown to be irreversible. Our in vitro tuning of the free energy landscape that modulates G4 conformational fidelity motivates a search for possible in vivo enzymatic regulators.

biophysics↗

bioRxiv2024

Multiple factors regulate i-motif and G-quadruplex structures in vitro: analysis of repeated and non-repeated polyG/polyC clusters by circular dichroism

The B-form of DNA in the genome contains thousands of sequences that can form various noncanonical structures. Of particular interest are two structures namely G-quadruplex (G4), formed by two or more stacks of four guanine residues in a plane, and intercalating-motif (i-motif, iM) formed by alternately arranged C-C+ pairs. Circular dichroism (CD) spectroscopy is a fast biophysical technique to analyze G4s and iMs. We conducted a CD analysis of two types of DNA sequences, one containing tandem repeats and one without, for the generation of G4s and iMs under various environmental conditions, which include pH, buffer composition, boiling, with flanking sequences, complimentary DNA strands, and single-stranded DNA binding protein (SSB). Changes in pH and boiling caused drastic variations in the CD spectra of DNA containing tandem repeats of GGGGCC and GGCCCC from the C9ORF72 gene, although some changes in G4/iM-forming DNA from promoter-proximal regions of several oncogenes also occur. An increase in the number of hexanucleotide repeats generated complex CD patterns at specific pH due to the presence of both G and C bases. The presence of flanking sequences affects CD pattern of a mixture of G4- and iM-forming sequences of the c-MYC promoter-proximal region. SSB disassembled G4 and iMs of all sequences suggesting an in vivo role for SSBs in disassembly of G4s and iMs during various DNA transactions.

biophysics↗