MBMB 451A Section One - Fall 2007

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Nucleic Acids

Chemical structure and base composition
	1. Numbering system of nucleic acids
		a.  phosphate (alpha, beta, gamma)
  		b.  base (1,2,3,...) figure 5-2a
  		c.  sugar (1', 2', 3', ...) figure 5-1a and b
		d.  shorthand notation  figure 5-2b
	2. Phosphate linkages - phosphoester bonds
		a. phosphomonoester bond figure
		b. phosphodiester bond figure
		c. phosphotriester bond
	3.  nucleotide 
		a. normal base composition table 5-1
		b. modified bases - figure a and b 	
		c. tautomers - figure 5-9 is an example    
	4.  sugar ring - 
		a. nucleotide vs. nucleoside
		b. deoxyribose vs. ribose  see figure 5-1
		c. base-catalyzed hydrolysis of RNA (not DNA)
			due to 2'-OH of RNA  figure 5-3 
		d.  ring pucker:  endo vs. exo and C-3' vs C-2'
			figure 29-9 a & b and figure 29-10 a & b

Double Helical Structures 
	1.  Watson Crick Structure:  B-DNA - figure 29-1 a & b
		a.  antiparallel orientation,  3' vs 5' ends 
		b.  base pairing interactions - figure 5-12
			i.  always a purine-pyrimidine (steric constraints)
			ii.  tautomeric forms of bases  figure 5-9
		c.  double helical parameters - table 29-1
			i.  helical sense: right vs left
			ii. major vs minor groove
			iii. base pairs per helical turn
			iv. helix rise per base pair or helical pitch:distance from one step to the next
			v.  helical twist: angle between two adjacent base pairs
				=360 deg/base pairs per turn
			vi.  base tilt: slant of the step, not completely planar
			vii. glycosidic conformation: anti vs syn -  figure 29-8
			viii.sugar ring pucker: 4 out of 5 ring atoms are nearly planar
				the 5th atom is usually the C-2 or C-3 atom
				endo vs exo
		d.  real DNA deviates from the ideal B-DNA form
			i.  local deviations are common
			ii.  some DNA is naturally bent
			iii.  deviations are sequence dependent
	2.  A-DNA figure 29-2 a & b
		a.  wider and flatter than B-DNA
			i.  very shallow minor groove
			ii.  deeper major groove
		b.  tilt is 20 deg (most tilted)
		c.  dried out DNA, 75% vs 92% humidity
		d.  flat ribbon wound around a 6 angstrom hole
		e.  found in spores because of close packaging and 
		    RNA-RNA/RNA-DNA hybrids assume an A-DNA like structure
	3.  Z-DNA  figure 29-3 a & b
		a.  Characteristics of
			i.  occurs in alternating purine-pyrimidine tracts
			ii.  favored in high salt;helps eliminate electrostatic repulsion
				of phosphate groups (8 vs 12 angstrom distance)
			iii.  methylation of deoxycytidine helps formation of Z-DNA
			iv.  phosphate backbone forms a zig-zag conformation
		b.  double helical parameters
			i.  syn vs. anti conformation
				purines flip to assume syn orientation figure 29-4
			ii.  helical sense is left handed 
			iii. deep minor groove, no major groove		
		c.  biological role of Z-DNA
			i.  unclear at this point
			ii.  anti Z-DNA antibody detection, artifactual
			ii.  methylation proved to be less artificial
  	4.  Unusual DNA structures
		a.  palindrome vs. mirror repeat
			i.  see example - figure key is placement of invert repeats
			ii.  hairpin - figure 
			iii.  cruciform - figure
		b.  Hoogsteen base pairing - figure 29-12
			i.  triplex formation - figure a and b
			ii.  G tetraplex - found at telomeres - figure a and b

Forces that help to form the DNA double helix
	1.  Rigid phosphate backbone
	2.  Stacking interactions - electronic interactions between planar bases
	3.  Hydrophobic interactions - highly negative phosphate backbone vs. nonpolar bases
	4.  Hydrogen bonding is not the most energtically signicant component
		note: maintenance of distance from the two phosphate backbone requires Pur-Pyr
	5.  Ionic interactions - salt stabilizes the duplex form of DNA
		shielding of phosphate backbone

Denaturation and Renaturation figure 5-14
	1.  Tm: (melting temperature) temperature at which half of the DNA is melted
		Marmur-Doty equation for Tm correlated to G+C percent and salt 
			Tm=41.1 XG+C + 16.6 log[Na+] + 81.5
		figure 5-16 and figure 5-17
	2.  Denaturation is a cooperative process -
		caused by: heat, change in pH, organic solvents (urea, formamide)
	3.  Hyperchromic shift - increase of absorbance of DNA when it goes from being double- to single- stranded
		40% increase in absorbance figure 5-15
	4.  Annealing:Hybridization

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Methods-Nucleic Acids: Part A and Part B  |  DNA Supercoiling  |  Nucleosome  | Transcription: Part A and Part B  | 
Higher Ordered Structure  |  Chromatin Transcription  |  Regulation of Transcription  |  Course Material

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Last updated on August 30, 2007 .