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Inverted Repeats and Cruciform Extrusion in DNA

Student-Run Research Seminar

Speaker: Eva Strawbridge, UC Davis
Location: 693 Kerr
Start time: Wed, Nov 2 2005, 12:10PM

DNA has a number of characteristics, not yet completely understood, which could potentially regulate its activities and the activities of products directly derived from DNA's primary sequence, such as RNA and proteins. The effect of DNA supercoiling on characteristics, such as inverted repeats can result in dramatic changes in secondary structure. During transcription, the two strands of the DNA duplex are forced apart winding the DNA coil 'tighter' in one direction (positive supercoiling) and 'uncoiling' the duplex in the other (negative supercoiling). Under stress from negative supercoiling, inverted repeats in DNA may extrude to form either perfect or imperfect cruciform structures in order to 'absorb' the energy of supercoiling. These cruciforms can have both important regulatory functions as well as cause dangerous mutations. Extruded cruciform structures are generally undesirable in DNA because of the potential for mutation. Consequently, one would expect inverted repeats to be distributed in such a way as to minimize the danger of mutation while still maintaining DNA's transcriptional functions. The purpose of this research is to examine the distributions of inverted repeats as well as equilibrium energetics associated with cruciform formation.