Research Overview

Welcome to the Xie Group homepage. We are a group of scientists working at the interface of several disciplines, striving to develop new physical and chemical tools to solve compelling biological problems.

Advances in life sciences over the past sixty years can best be described as understanding life processes at the molecular level. We have now sequenced the genomes of many species, including humans, and obtained high-resolution structures of many macromolecular machines. What are the new challenges? Well, there are many. One challenge, in particular, is to study how molecular machineries actually work – how they work in real time, how they work individually, how they work together, and finally, how they work inside live cells. How does genetic information carried by DNA control cell functions?

Physical tools have always facilitated advances in biology. Notable examples are crystallography and the patch clamp techniques. In recent years, due to contributions from numerous research groups, single-molecule experiments have changed the way many biological problems are addressed. Knowledge from these experiments continues to emerge. Our group was one of the first to pioneer fluorescence studies of single molecules at room temperature in the early 1990s and has since made important advances in single molecule spectroscopy and imaging, and their application to biophysical chemistry, and molecular and cell biology. Our interest has been not only to bring about technological innovations, but to generate new insights on fundamental scientific issues as well.

There are many reasons to use the single-molecule approach in biology. First, single-molecule experiments generate movies of motions and biochemical reactions of macromolecular machineries, which are particularly helpful in elucidating their mechanisms. In establishing single molecule enzymology, we developed in vitro assays to probe enzyme activities and conformational dynamics of single molecules, statistical analyses for their stochastic kinetics, and theoretical models for fundamental understanding of the observed phenomena. We have carried out studies of DNA protein interactions; for example, the search of a target DNA sequence by a nonspecifically bound protein, allostery through DNA, and transcription bursting of RNA polymerase induced by DNA supercoiling.

Secondly, there are only one or two copies of a particular gene in an individual cell, which result in stochastic gene expression that cannot be synchronized with other cells. Recently, we achieved single-molecule sensitivity for many proteins, with millisecond time resolution and nanometer precision in a living cell. We were able to observe protein being generated one molecule at a time in E. coli cells and to describe and understand transcription and translation processes at a quantitative level. We found that a single-molecule event can be solely responsible for the life-changing decision of a cell.

On another front, since 1999, our group has led in the rapid development of Coherent anti-Stokes Raman Scattering (CARS) microscopy which was recently superseded by our advance of Stimulated Raman Scattering microscopy (SRS). These are label-free imaging techniques based on vibrational spectroscopy, and are capable of video-rate, noninvasive examination of living cells and organisms. Orders of magnitude more sensitive than conventional Raman microscopy, they allow mapping of 3D distributions of small molecules, such as metabolites and drugs, as well as tumor identification in tissues, which open exciting new possibilities for biology and medicine.

Finally, our newest single molecule experiment sequences the genome of a single human cell with >90% coverage, detects the quantized copy number variation, and calls single base mutation with no false positives. This allows unprecedented capability in fundamental research, such as direct measurements of mutation rates, as well as exciting possibilities in medicine, such as cancer diagnostics and prognostics by analyzing circulating tumor cells, comprehensive prenatal tests, and safe in vitro fertilization.

With a wealth of physical and chemical tools at our disposal, our group is excited to make both scientific and technological contributions to life science.

Sunney Xie