04 - Nucleic Acid Structure and Hybridization Nucleic Acid...

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Unformatted text preview: Nucleic Acid Structure and Hybridization 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. 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) 2.0 nm A-DNA 11 pairs/turn, turn every 2.8 nm (2.5 nm ?) right handed bases exhibit a tilt 20 with respect to the helix axis found in low water content (lower then normal) 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 2.8 nm (Watson et al., 2004) 2.6 nm 1.8 nm (Watson et al., 2004) 4.5 nm first found in d(CG) polymers 12 base pairs/turn turn every 4.5 nm, tilt 7 degrees, left handed found in test tubes when very high salt conc. role in: Regulation : proteins with Z-DNA binding domains; Z-DNA in promoter regions of some genes chromosomal breakages large-scale deletions/rearrangements (in mammals) 2008 Alzheimers disease Z-DNA Formed when purines make one strand and pyrimidines the other third strand can be accommodated In test tube, but also likely in vivo during DNA recombination or repair gene therapy possibilities Triple-helical DNA Triplex-forming oligonucleotides :principles and applications Karen M. Vasquez1 and Peter M. Glazer2,* Quarterly Reviews of Biophysics 35 , 1 (2002), pp. 89107. Cambridge University Press 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 normal to helix axis (degrees) +19-1.2 +/- 4.1-9 Rise/base pair along helix axis () 2.3 3.32 +/- 0.19 (3.4) 3.83....
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04 - Nucleic Acid Structure and Hybridization Nucleic Acid...

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