Julius B. Lucks

Design and characterization of peptide-responsive biosensors

This study designs and characterizes peptide-responsive biosensors that regulate gene expression using intracellular peptide effectors and transcription factors in vitro and in vivo.

Transcription-induced coacervation accelerates and sensitizes cell-free biosensing

This paper demonstrates that transcription-induced coacervation accelerates and enhances cell-free biosensing by mimicking intracellular phase separation, improving sensitivity and reducing detection time.

Design and discovery of "tug-of-war" riboswitches

The paper designs and discovers a new modular transcriptional riboswitch architecture called 'tug-of-war' that suppresses intrinsic termination by ligand-stabilized RNA structures upstream of terminators.

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences

The paper develops a hybrid computational and high-throughput experimental method to identify and analyze full riboswitch sequences, generating covariation models that support previously published structural rearrangement mechanisms.

Efficient and scalable modelling of cotranscriptional RNA folding with deterministic and iterative RNA structure sampling

This paper introduces iterative sampling for RNA structure prediction, achieving faster and more comprehensive sampling than existing methods, and applies it to study cotranscriptional RNA folding.

Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing

This study introduces PRIME, a method to measure RNA structural energetics, finding that RNA base pairs and tertiary interactions dynamically open with low-energy fluctuations.

Active learning-guided optimization of cell-free biosensors for lead testing in drinking water

The paper develops a machine learning-guided workflow to optimize cell-free biosensors for detecting lead in drinking water, achieving sensitivity at the EPA action level and improved selectivity.

Design Principles for Polymerase Strand Recycling Circuits

This paper develops design principles for Polymerase Strand Recycling (PSR) circuits to enhance detection of microRNA inputs in cell-free biosensing systems.

Semi-automated Production of Cell-free Biosensors

This paper develops a semi-automated method for manufacturing cell-free biosensors using liquid handling robotics, demonstrating comparable performance to manual methods.

Ultra-sensitive water contaminant detection with transcription factor interfaced microcantilevers

The paper develops a biosensor using transcription factors and microcantilevers to detect water contaminants with high sensitivity and speed.

RNA folding kinetics control riboswitch sensitivity in vivo

The paper shows that slowing RNA folding kinetics enhances riboswitch sensitivity in vivo and identifies general principles for programming RNA folding dynamics.

Engineering a cell-free biosensor signal amplification circuit with polymerase strand recycling

The paper introduces a cell-free biosensor signal amplification circuit called polymerase strand recycling (PSR) that enhances biosensor sensitivity for small molecule detection.

Developing, characterizing and modelingCRISPR-based point-of-use pathogen diagnostics

The paper develops and optimizes a one-pot NASBA-Cas13a assay for rapid, sensitive detection of SARS-CoV-2 RNA without specialized equipment.

The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch

This study investigates how pseudoknot base pairing affects cotranscriptional structural switching in fluoride riboswitches, showing a critical wobble base pair is essential for function across different temperatures.

At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring

The paper develops four cell-free biosensing modules for synthetic biology education that enable students to explore transcriptional regulation and environmental monitoring without lab equipment.

Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles

This paper demonstrates a cell-free biosensor encapsulated in lipid vesicles that detects fluoride with tunable sensitivity and real-world applicability.

Tuning Strand Displacement Kinetics Enables Programmable ZTP Riboswitch Dynamic Range in vivo

The paper shows how mutations in a riboswitch can tune its dynamic range by altering strand displacement kinetics in E. coli.

Cotranscriptional RNA strand displacement underlies the regulatory function of the E. coli thiB TPP translational riboswitch.

The paper investigates the E. coli thiB TPP riboswitch and shows it uses cotranscriptional RNA strand displacement for translational regulation.

Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

This paper develops DNA strand displacement circuits to enhance biosensors by enabling fine-tuning of reaction kinetics and faster response times, creating binary outputs that encode target molecule concentrations.

RNA sequence and structure determinants of Pol III transcriptional termination in human cells

The paper develops an in cellulo assay to study Pol III transcription termination in human cells and identifies sequence and structural determinants for efficient termination.

Rapid, Low-Cost Detection of Water Contaminants Using Regulated In Vitro Transcription

A cell-free platform pairing T7 RNA polymerase, allosteric transcription factors and DNA templates yields fluorescent RNA output to detect antibiotics, small molecules and metals in water.

Design and optimization of a cell-free atrazine biosensor

This paper designs a cell-free biosensor for atrazine detection using a metabolic pathway and a cyanuric acid biosensor, achieving faster and tunable detection compared to whole-cell sensors.

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

This paper develops a cell-free biosensor for detecting fluoride in water using a riboswitch that produces fluorescent or colorimetric signals, demonstrating its effectiveness in both lab and field settings.

Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid

This paper designs a portable biosensor for detecting cyanuric acid using a hybrid promoter system in E. coli, enabling rapid and on-demand detection with fluorescent and colorimetric reporters.

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data

DUETT identifies RNA structural transitions from chemical probing data by using a feedback control-inspired method and linear regression to detect known and novel events.

PLANT-Dx: A Molecular Diagnostic for Point of Use Detection of Plant Pathogens

This paper develops a portable, low-cost diagnostic system for detecting plant pathogens using synthetic biology and isothermal amplification with colorimetric output.

Dynamic control of pathway expression with riboregulated switchable feedback promoters

The paper introduces a new gene expression cassette called a riboregulated switchable feedback promoter (rSFP) to dynamically control gene expression in metabolic engineering, achieving higher titers in a Taxol precursor biosynthesis pathway.

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

The paper characterizes two RNA regulators with distinct timescales and demonstrates their use in creating a genetic pulse generator through computational modeling and experimental validation.

Deconstructing cell-free extract preparation for in vitro activation of transcriptional genetic circuitry

This study identifies protocol improvements for preparing cell-free extracts to enhance transcriptional activity of bacterial genetic circuits.

De-Novo-Designed Translational Repressors for Multi-Input Cellular Logic

This paper designs de-novo RNA-based translational repressors with multi-input logic capabilities for synthetic biology applications.