Nov. 5, 2004. MBB 407/511 Lecture 17: Structures of DNA and RNA (Part II). 6Å. 3.4Å. 34Å. DNA is:1) double stranded 2) a right-handed helix. Helix vs Spiral. Merriam Webster’s Collegiate Dictionary. Helix ( n )—a. “Something spiral in form.”
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Structures of DNA and RNA
DNA is:1) double stranded
2) a right-handed helix
Helix vs Spiral
Merriam Webster’s Collegiate Dictionary
Helix (n)—a. “Something spiral in form.”
b. “A coil formed by winding wire around a uniform tube.”
c. “A curve traced on a cylinder…”
What are hydrogen bonds?
A-T bp have 2 H bonds
G-C bp have 3 H bonds G-C bp are more stable
Helix has constant diameter
1) Purines always pair with pyrimidines
2) The H bonding distance between
the A-T and G-C bp is the same
1. Strands must run anti-parallel
in order to get H bonding
Phosphodiester bonds link
Unequal offsetting of the two strands
Base pair spacing = 3.4Å/bp
10.5 bp/helix repeat
Helix diameter ~ 20Å
Nucleic acids absorb UV light Why?
Determine [nucleic acid]
For dsDNA: 1 A260 unit = 50 mg/ml of DNA
UV light absorbance increases as DNA goes from double-stranded to single-stranded
Melting temperature (Tm)
What is the basis of hyperchromic shift? Stacked bases absorb less UV light
Melting temperature Tm increases with G:C content
(0.3M NaOAc, 0.5M NH4OAc, 0.4 M LiCl)
Monovalent cations neutralize the repulsive
effects of the phosphate groups
(70% Ethanol or 50% isopropanol)
To concentrate DNA/RNA by exluding H20
Alkali hydrolyzes RNA
Alkali denatures dsDNA
The 2’OH groups are susceptible
to nucleophilic attack
At high pH, deprotonation of bases
disrupts hydrogen bonding
RNA is single stranded and is most stable when it
Engages in intrastrand base pairing
Messenger RNAs (mRNAs)
Transfer RNAs (tRNAs)
Ribosomal RNAs (rRNAs)
Small nuclear RNAs (snRNAs)
Catalytic RNAs (“Ribozymes”)
— self-splicing (e.g., group I and group II introns)
— cleavage of other RNAs (e.g., RNA component of RNaseP cleaves tRNAs)
— “hammerhead RNAs” (
Group II intron
of tRNA 5’ ends
1. Cleavage reactions
2. Transesterification reactions
They are single-stranded
—can adopt complex
They have 2’ OH groups
Newest ribozymes: the snRNAs in the spliceosme
& the 23S rRNA in ribosomes
What are the implications?
—5’3’ exo and 3’ 5’ exo
DNA is very stable: it stores the genetic information
There aren’t many DNases in the cell.
DNA is protected.
RNA is very unstable: its turnover is important
for regulating gene expression
Lots of RNases in the cell. RNAs generally not protected.
Some RNAs more stable than others:
rRNAs and tRNA aka “stable RNAs
mRNAs have half-lives from minutes to hours
“Why is thymine found only in DNA, uracil only in RNA?”
Deamination of cytosine in DNA is very common in the cell,
but can lead to mutations after DNA replication.
There is a repair system that looks for uracil attached to deoxyribose sugars and excises the base then replaces the uracil with a cytosine.
If uracil was a normal base in DNA, the cell might not detect the U:G bps
and there would be too many C:G to U:T mutations.