fall 09 lecture 04

fall 09 lecture 04 - Nucleic Acid Structure and...

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Nucleic Acid Structure and Hybridization DNA and RNA structure Learning Objectives: Explain the chemical forces determining DNA structure. Describe the conformational features of A, B, and Z DNA structures and when each structure occurs in vivo. Describe how base pairs can be identified in the major groove based on H-bond donors and acceptors.
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Different forms of DNA B-DNA Approximately 10 base pairs per turn Turn is every 3.4 nm Bases are perpendicular to the helix axes Right handed Represents most of the in vivo DNA 2 nm (Watson et al., 2004)
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- 11 pairs/turn, turn every 2.8 nm (2.5 some sources), right handed - bases exhibit a tilt with respect to the helix axis (20 degrees) - found in low water content (lower then normally found in the cell) - DNA-RNA and RNA-RNA helices in a test tube (but it might exist in vivo as well - locally and temporarily) - A-like DNA found in dormant spores of Bacillus A-DNA 2.6 nm (Watson et al., 2004)
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found in test tubes when very high salt conc. first found in d(CG) polymers 12 base pairs/turn turn every 4.5 nm, tilt 7 degrees, left handed role in regulation of gene expression: discovery of proteins with Z-DNA binding domains; new discovery: Z-DNA in promoter regions of some genes (including housekeeping) - regulation Implicated in chromosomal breakages and large- scale deletions/rearrangements (in mammals) 2008: implication in Alzheimer’s disease Z-DNA 1.8 nm Watson et al., 2004)
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Formed when purines make one strand and pyrimidines the other – then the third strand could be accommodated In test tube, but also likely in vivo during DNA recombination or repair gene therapy possibilities Triple-helical DNA Quarterly Reviews of Biophysics 35 , 1 (2002), pp. 89–107. " 2002 Cambridge University Press Triplex-forming oligonucleotides : principles and applications Karen M. Vasquez1 and Peter M. Glazer2,*
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Property A-Form B-Form Z-Form Helical sense Right-handed Right-handed Left-handed Rotation/base pair (degrees) 33.6 35.9 +/- 4.2 -60/2 Mean base pairs/turn 10.7 (11) 10.0 +/- 1.2 (10) 12 Inclination of base normals to helix axis (degrees) +19 -1.2 +/- 4.1 -9 Rise/base pair along
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This note was uploaded on 07/10/2010 for the course BIOL 308 taught by Professor Miskovic during the Fall '09 term at Waterloo.

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fall 09 lecture 04 - Nucleic Acid Structure and...

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