Project information
In vitro and in silico identification of non-canonical DNA structures in genomic sequences
- Project Identification
- GA204/08/1560
- Project Period
- 4/2008 - 12/2010
- Investor / Pogramme / Project type
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Czech Science Foundation
- Standard Projects
- MU Faculty or unit
- Faculty of Informatics
- Keywords
- non-canonical DNA structure, palindrome, repeat, duplex, triplex, cruciform DNA, approximate pattern search, bioinformatics, FPGA
- Cooperating Organization
-
Institute of Biophysics
- Responsible person Mgr. Marie Brázdová, Ph.D.
Genomic sequencing generated an increased interest in non-coding DNA. This applies also to non-canonical DNA structures and their possible biological functions. Here we propose to combine molecular biology, bioinformatics and the latest computer technology in an effort to understand, predict and map the occurrence of biologically important DNA structures in genomes. Motivated by our previous research, we will focus on
non-canonical DNA structures (cruciforms, triplex, slippage- and Z-DNA). We will improve (and where necessary develop) tools for in silico prediction of these DNA structures. Predictions will be verified by carefully planned laboratory experiments, focusing on promoter regions of cancer-related genes (e.g. p53, MDM2, hsp90, EGFR) studied in the applicant's laboratory. Our ability to rapidly analyze full genomes will come from the use of special algorithms and applications built around FPGA hardware-acceleration cards. As a result, we will obtain annotations of genomes for predicted structures, occurence of such structures in oncogenes, as well as new methods and hardware for wider applications of accelerated sequence search.
Results
Publications
Total number of publications: 11
2013
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Preferential Binding of Hot Spot Mutant p53 Proteins to Supercoiled DNA In Vitro and in Cells
Plos One, year: 2013, volume: 8, edition: 3, DOI
2012
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Prediction of significant cruciform structures from sequence in topologically constrained DNA - a probabilistic modelling approach
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms., year: 2012
2011
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A dynamic programming algorithm for identification of triplex-forming sequences
Bioinformatics, year: 2011, volume: 27, edition: 18, DOI
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Architecture Model for Approximate Tandem Repeat Detection
22nd IEEE International Conference on Application-specific Systems, Architectures and Processors, year: 2011
2010
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Hardware Acceleration of Approximate Tandem Repeat Detection
18th IEEE Symposium on Field-Programmable Custom Computing Machines, year: 2010
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Identification of palindrome-forming sequences
Year: 2010
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Identification of triplex-forming sequences
Year: 2010
2009
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Architecture model for approximate palindrome detection
2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems, year: 2009
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Mutp53 non-B DNA structure binding to intronic sequences modulates gene expression in U251 cells
Year: 2009, type: Conference abstract
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Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins
Year: 2009, type: Conference abstract