Guojia:Research

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(Fluorescent Hybridization Probes for Nucleic Acid Detection)
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[[Guojia:Home| <font face="trebuchet ms" style="color:#ffffff"> '''Home''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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==Research Overview==
 
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My research focuses on the design and synthesis of novel molecular tags for biological imaging and DNA sequencing applications. The objective is to systematically investigate all the important biological molecules involved in a pathway at the single molecule level in single cells. I am pursuing these research objectives by using chemical science, engineering principles and experimental biological approaches.
 
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==The Novel Comet-FISH Approach to Study Genome Integrity==
 
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By combing single cell gel electrophoresis (Comet) with fluorescence in situ hybridization (FISH) using novel fluorescent probes, we can study the induction and removal of various DNA lesions and modifications (including epigenetic modifications) in respective DNA strands in defined DNA sequences at the single molecule level and in the genome overall in individual cells.
 
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[[Image:Comet-FISH2.png|center|700px|]]
 
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*'''J. Guo''', P. C. Hanawalt and G. Spivak. “Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells” Submitted.
 
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==Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems==
 
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To understand the complexity and dynamics of the molecular interactions in biological systems, the parallel analysis of multiple species, such as different proteins in a cell or cells in a tissue specimen, is often needed. Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. To address this issue, we have developed multispectral oligodeoxyfluoroside (ODF) and coupled them to DNA, RNA, peptides and proteins. This approach enables the monitoring of multiple biological species simultaneously in real-time.
 
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[[Image:ODF.png|center|800px|]]
 
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*'''J. Guo''', S. Wang, N. Dai, Y. N. Teo and E. T. Kool. “Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging” '''PNAS''', 2011, 108: 3493-3498.
 
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*N. Dai, '''J. Guo''', Y. N. Teo and E. T. Kool. “Protease Probes Built from DNA: Multispectral Fluorescent DNA–peptide Conjugates as Caspase Sensors” '''Angew Chem Int Ed''', 2011, 50:5105-5109.
 
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*S. Wang,''' J. Guo''', T. Ono and E. T. Kool. "DNA Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems" '''Angew Chem Int Ed''', 2012, in press.
 
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==Next Generation DNA Sequencing with Chemically Modified Nucleotides==
 
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By integrating the advantages of the Sanger sequencing methodology and the sequencing by synthesis (SBS) approach, we developed a novel high-throughput DNA sequencing method, which allows hundreds of millions of different DNA/RNA fragments immobilized on a chip to be deciphered simultaneously. The conventional SBS approach leaves chemical tails on the bases after each sequencing cycle, which may interfere with the subsequent sequencing reactions. To tackle this issue, we utilized nucleotide reversible terminators combined with fluorescent permanent terminators to generate primers only composed of natural nucleotides. With the enhanced sequencing accuracy and read-length, this methodology together with other next-generation sequencing technologies enables the genome-wide studies of DNA sequence variations, transcriptome analysis, DNA/RNA-protein interactions, chromosome 3-D structures, RNA secondary structures, among others. 
 
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[[Image:SBS2.png|center|800px|]]
 
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*'''J. Guo''', N. Xu, Z. Li, S. Zhang, J. Wu, D. H. Kim, M. S. Marma, Q. Meng, H. Cao, X. Li, S. Shi, L. Yu, S. Kalachikov, J. Russo, N. J. Turro and J. Ju. “Four-color DNA sequencing with 3’-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides” '''PNAS''', 2008, 105: 9145-9150.
 
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*'''J. Guo''', L. Yu, N. J. Turro and J. Ju. “An integrated system for DNA sequencing by synthesis using novel nucleotide analogues” '''Acc Chem Res''', 2010, 43: 551-563.
 
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==Fluorescent Hybridization Probes for Nucleic Acid Detection==
 
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To understand the expression and transportation of mRNA from transcription through degradation and their effect on health, we developed oligonucleotide-based fluorescent hybridization probes. These probes enables the monitoring of mRNA in individual living cells.
 
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[[Image:Hybridization probes.png|center|700px|]]
 
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*  '''J. Guo''', J. Ju and N. J. Turro. "Fluorescent hybridization probes for nucleic acid detection"  '''Anal Bioanal Chem''', 2012, 402:3115-3125.
 
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Last Updated: September, 2012
 
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Revision as of 13:27, 25 August 2013

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