Ulrich Krull

Academic Title: Professor

Phone: 905-828-5437

Office: SB 2035

Email:

Research Homepage: http://www.utm.utoronto.ca/index.php?id=7429&no_cache=1&tx_hisfacultyprofiles_pi1[pointer]=0&tx_hisfacultyprofiles_pi1[mode]=1&tx_hisfacultyprofiles_pi1[showUid]=164

The overall objective of my research program is the investigation of chemically-selective surfaces that are suitable for development of rapid and reversible biosensors. The progress of the Human Genome Project and the many smaller genome projects that are currently underway has generated substantial interest in the use of nucleic acid hybridization technologies to detect and identify organisms, mutations and drug interactions. The sequence information that is generated by these projects is being used to develop biochips and genetic arrays based on immobilized DNA probes, and such analytical systems are well suited for large scale genetic screening. However, there is also a clear need for reliable and reusable bioanalytical devices that are targeted to the rapid and quantitative detection of specific sequences, organisms and compounds of concern in areas such as disease, new therapies, forensics and the detection of pathogens. We are focussing our efforts in the area of such biosensor development, and the goal is ultimately to develop technology that requires minimal sample preparation, to generate a quantitative result within seconds to minutes without the need for PCR amplification.

Biosensors and biochips can determine the presence of nucleic acid in a test sample through detection of hybridization between an immobilized nucleic acid (probe) and a nucleic acid in a test sample (target). The research efforts in Krull’s group relates to fundamental investigations of surface chemistry that can ultimately be integrated to increase speed, sensitivity and selectivity of nucleic acid diagnostic devices. The various projects are components of a research program that encompass all aspects of device design, including sample processing, sample transport, selective capture of target, and high sensitivity detection.

The potential for use of polymerized oligonucleotides to form selective “solid phase extraction” media that concurrently operate by charge, size exclusion and hybridization, is being studied to determine whether such an approach can improve the speed and efficiency of sample processing.

A new molecular templating method is being developed to place probe molecules at defined locations on surfaces so that control of nearest neighbour interactions will improve the selectivity of hybridization. This research addresses the challenge of creation of an environment for immobilized oligonucleotides that offers good structural regularity and reproducibility, where nearest neighbour interactions provide for control of selectivity, yet where the degree of hybridization does not alter nearest neighbour interactions. The hypothesis is that a “matrix isolation” method will produce the desired environment for the probe molecules. DNA oligonucleotide probes are polyelectrolytes with charged backbones and significant flexibility. Various methods are being investigated to isolate the probe molecules by surrounding each on average with a sheath of immobilized polyelectrolyte that is not based on complementary nucleic acid. It should be possible in such mixed films to use polyelectrolytes (oligomers) with charged and branched backbones that are not based on nucleotide chemistry so as to tune the selectivity of ssDNA oligonucleotide probe molecules. The intention is to develop immobilization methods that enhance differences in signal magnitude generated for fully matched target nucleic acid in contrast to partially matched target nucleic acid prior to signal processing. This will significantly improve confidence in results from devices that are not designed to operate with large redundancy, and will make the task of signal processing less onerous, time consuming and complex.

One important finding is that the control of the density of immobilized single stranded probe molecules can be used to tune selectivity to facilitate detection of even single base pair mismatches. We have proposed a new approach to detection and quantitative measurement of nucleic acids. This new approach provides for a multi-dimensional distribution of selective chemistry at a surface, but in such a way that the coatings of probe molecules are continuous, and operate to provide gradients of selectivity in one or more directions. Such a Gradient Resolved Information Platform (GRIP), is based on a surface that is coated with a continuous gradient of density and/or sequence and/or orientation and structure of ssDNA. The location, extent of hybridization, and speed of hybridization on such a surface by a target sequence can be used to identify and quantitatively measure the target. This sensor platform is being embedded in a new microfluidics package that is designed to quantitatively deliver small volumes of sample and reagents to the sensing surface.

Fluorescence spectroscopy will serve as the basis for highly sensitive detection. Fluorophores that bind to hybrids are being integrated as permanent components of the immobilized probes. Fluorescence suppression (quenching) based on use of tethered fluorophore-quencher pairs is being evaluated as a method of transduction. The use of time-resolved fluorescence spectroscopy methods is being investigated for improvement of sensitivity by reduction of background.

Immobilization of probes onto indium tin oxide optical electrodes permit control of stringency and kinetics by electrochemical manipulation. All the fundamental advances will be integrated with microfluidics technologies.

A.K.Y. Wong and U. J. Krull, “Surface characterization of 3-glycidoxypropyltrimethoxysilane films on silicon-based substrates”, Analytical and Bioanalytical Chemistry, 383:187-200, 2005.

A. Chan and U.J. Krull, “Capillary electrophoresis for capture and concentrating of target nucleic acids by affinity gels modified to contain single-stranded nucleic acid probes”, Analytica Chimica Acta, 578: 31-42, 2006.

W. R. Algar, M. Massey and U.J. Krull, “Fluorescence resonance energy transfer and complex formation between thiazole orange and various dye-DNA conjugates: implications in signaling nucleic acid hybridization”, Journal of Fluorescence, 16: 555-567, 2006.

S-.H. Park and U.J. Krull, A spatially resolved DNA biochip based on a gradient of density of immobilized probe oligonucleotide, Analytica Chimica Acta, 564: 133-140, 2006.

W. Russ Algar and U.J. Krull, Adsorption and Hybridization of Oligonucleotides on Mercaptoacetic Acid-Capped CdSe/ZnS Quantum Dots and Quantum Dot-Oligonucleotide Conjugates, Langmuir, 22: 11346-11352, 2006.

W. Russ Algar and U.J Krull, Luminescence and stability of aqueous thioalkyl acid capped CdSe/ZnS quantum dots correlated to ligand ionization, ChemPhysChem, 8: 561 – 568, 2007.

Y. Kravtsova, U. Krull, S. F. Musikhin, L. Levina, H. E. Ruda and A. Shik, Polarization memory in a system of CdSe nanorods, Appl. Phys. Lett. 90: 083120, 2007.

W. Russ Algar and U.J. Krull, Towards multi-colour strategies for the detection of oligonucleotide hybridization using quantum dots as energy donors in fluorescence resonance energy transfer (FRET), Analytica Chimica Acta, 581: 193-201, 2007.