Biology subjects

Gandavadi, D.

Publications and source records attributed to Gandavadi, D..

8 recordsLinked to original sources

bioRxiv2026

Geometry-dependent mRNA delivery with programmable RNA-DNA nanostructures

Efficient intracellular delivery of neoantigen-encoded mRNAs is central to the development of effective cancer vaccines and immunotherapies. However, how the nanoscale geometry of delivery carriers impacts mRNA delivery remains poorly understood, largely because conventional delivery platforms do not readily permit systematic variation of carrier architecture while maintaining comparable chemical composition. Here, we develop a modular RNA-DNA hybrid nanoplatform that enables controlled investigation of geometry-dependent mRNA delivery. Guided by a unified design principle, we construct a series of two- and three-dimensional nanostructures with programmable architectures and systematically compare their delivery performance using consistent functional readouts. We further investigate how mRNA embedding strategies and aptamer-mediated functionalization influence intracellular delivery efficiency. By providing precise control over carrier geometry, this platform establishes a framework for elucidating structure-function relationships in mRNA delivery and offers a versatile strategy for engineering targeted nucleic acid delivery systems.

bioengineering↗

bioRxiv2026

Programmable DNA Assemblies Reconstitute Supramolecular Protein Function

Biological processes are often regulated through reactions involving supramolecular protein complexes organized with nanoscale precision, such as the apoptosome that activates procaspase-9 through defined stoichiometry to induce apoptosis. Here we report designer CASCAD (CARD Assembly on SCAffold DNA), a self-assembled DNA nanoplatform that spatially organizes caspase recruitment domains (CARDs), exhibiting catalytic intracellular caspase-9 activation. By functioning like a natural apoptosome, CASCAD enhances caspase-9 oligomerization and promotes valency-dependent enzymatic activation. Further, after incorporating targeting aptamers and membrane-interacting peptides for cellular uptake and cytosolic delivery, CASCAD has successfully reconstituted apoptosome function and downstream apoptotic signaling in in-vitro 2D and 3D cultures. Our molecular design paradigm establishes CASCAD as versatile and programmable DNA nanomaterial for reconstructing signaling pathways driven by diverse supramolecular complexes, including inflammasomes and myddosomes, providing a general chemical framework for engineering cellular signaling and directing cellular function and fate.

synthetic biology↗

bioRxiv2026

Multi-dimensional DNA nanostructures isothermally assembled in hydrated ionic liquids

DNA nanostructures can be tailored to perform a wide variety of functions, with continued interest in biological applications. Some aspects of DNA nanostructure assembly can hinder the ability of nanostructures to be useful in physiological environments. Typical assembly methods employ magnesium ions to stabilize the structure, which leave the structure susceptible to damage by nucleases in body fluids. Further, DNA nanostructure assembly typically involves a thermal annealing protocol in which DNA strands are heated in a specific buffer to a high temperature and cooled slowly at specific rates, preventing convenient encapsulation of temperature-sensitive guest molecules. In this work, we demonstrate the assembly of a wide variety of DNA nanostructures and 3D crystals in a hydrated ionic liquid (choline dihydrogen phosphate, CDHP) instead of magnesium at constant moderate temperatures, thus avoiding thermal annealing. CDHP-assembled structures show enhanced biostability against a variety of nucleases. Molecular dynamics simulations show that choline ions stabilize DNA nanostructures by a direct and close-range interaction in contrast to the predominantly water-mediated interactions of Mg2+, leading to enhanced nuclease resistance in CDHP-containing environments. CDHP-assembled structures do not affect the viability of HepG2 cells and show higher cell internalization. Overall, this work develops a potential method to construct more biostable DNA nanostructures and 3D crystals in a simple one pot process. Assembly of DNA nanostructures under isothermal conditions is desirable for scaffolding biomolecules and to reduce the need for thermal annealing instruments, allowing nanostructure preparation in low-resource settings.

biophysics↗

bioRxiv2026

AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

Aptamers are single-stranded oligonucleotides that bind molecular targets with high affinity and specificity. However, their discovery remains time-consuming, expensive, and susceptible to experimental biases. Here we present AptaBLE, a deep learning framework for predicting aptamer-protein binding. Additionally, we demonstrate two de novo generation methods that produce novel aptamers with desired specificity profiles and Kds as low as 31 nM to-date. AptaBLE represents a significant advance towards therapeutic and diagnostic aptamer development.

bioinformatics↗

bioRxiv2026

APIPred Web 1.0: A Web Platform to Predict Potential Aptamer Sequences for Protein targets

Aptamers are short single-stranded nucleic acids that bind protein targets with high specificity and are increasingly used in diagnostics and therapeutics, yet experimental discovery remains slow and variable in success. This creates a demand for computational systems that not only score candidate binders but also generate experimentally usable libraries under biologically meaningful constraints. Here, we present APIPred Web 1.0, a unified web platform that integrates constraint-aware aptamer library generation, machine learning- based aptamer- protein interaction prediction, and DNA secondary-structure analysis within a user-facing workflow. Users submit a target protein aminoacid sequence and define an aptamer template in a PREFIX - [VARIABLE] - SUFFIX format with real-time validation of key biological constraints (GC content and homopolymer limits). On the backend, sequences are converted into model- compatible features via optimized k-mer encodings (aptamer) and pseudo amino acid composition (PAAC) descriptors (protein), followed by inference with a trained XGBoost predictor. APIPred Web 1.0 improves the computational efficiency by applying precomputed protein features, vectorized batch processing (hundreds of sequences per batch), optimized XGBoost DMatrix inference, and a bounded heap that retains only the top 25 candidates during generation. The platform then computes minimum free energy (MFE) structures using ViennaRNA with parallel folding and returns ranked list of the top candidates with log-transformed interaction scores, complete sequences (variable region highlighted), dot-bracket structures, MFE values, and interactive 2D visualizations via persistent result links. In a demonstration study targeting CD64 protein, the platform produced 25 putative binders from a custom 40- nucleotide library and enabled selection of structurally diverse candidates for experimental testing. Flow cytometry showed specific binding to CD64-expressing THP-1 cells with minimal signal in Ramos control cells. Collectively, APIPred Web 1.0 offers a reproducible, structure-informed, and computationally efficient pipeline for rapid generation of aptamer candidates against target proteins for downstream experimental validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/697194v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1c1ca4dorg.highwire.dtl.DTLVardef@1c8b23dorg.highwire.dtl.DTLVardef@12dfe2dorg.highwire.dtl.DTLVardef@8a7c8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Hybrid peptide DNA nanomaterials enable potent and broad-spectrum virus neutralization

The continued emergence of antigenic drift and drug-resistant viral strains highlights the need for antiviral strategies that deliver robust efficacy, broad subtype coverage, and minimal off-target toxicity. We demonstrate a potent and broad-spectrum strategy that employs hybrid biomaterials of Urumin (a host defense peptide) and a honeycomb (HC) DNA origami through spatially organized multivalent presentation for enhanced antiviral efficacy. Molecular dynamics simulations reveal that Urumin penetrates and destabilizes the hemagglutinin (HA) trimer core, disrupting influenza A viral (IAV) entry. Arranging Urumin in trimeric clusters on the HC enables potent multivalent binding to trimeric HAs on IAV, enhancing antiviral efficacy at nanomolar concentrations, [~]1,000-fold more effective than free Urumin. In vitro assays confirm HC-Urumin outperforms free Urumin in blocking viral entry and preserving cell viability in more IAV subtypes. In vivo studies show that compared to free Urumin, HC-Urumin treatment reduces disease severity, preserves physiological behavior, and decreases mortality in infected mice, while maintaining virus-specific adaptive immune responses without altering humoral immunity. Our study offers an advanced and effective materials platform and strategy for broad-spectrum, low-dose intervention against human and animal IAVs, which can be adapted to combat other viruses by patterning corresponding host defense peptides on custom designed DNA nanostructures.

bioengineering↗

bioRxiv2023

Self-assembly of DNA nanostructures in different cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg2+ and Na+). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif ([~]134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+, Ba2+, Na+, K+ and Li+ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+, K+ and Li+) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+, Ca2+ and Ba2+). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

synthetic biology↗

bioRxiv2022

Multispecies autocatalytic RNA reaction networks in coacervates

Robust and dynamic localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of an RNA system within charge-rich coacervates where catalytic RNAs are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates -- both in micron sized droplets as well as a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, these collectively autocatalytic reaction networks endow unique compositional identities to the coacervates which in turn transiently protect the identity against external perturbations, due to differential molecular transport and reaction rates. Our results establish a compartmentalised chemical system possessing a compositional identity possessing a balance between robustness and variability required for chemical evolution.

evolutionary biology↗