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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Nov. 5, 2004
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…”
Examples of helices
Hydrogen Bonds Hold the Two DNA Strands Together
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
DNA Strands are Antiparallel
1. Strands must run anti-parallel
in order to get H bonding
Phosphodiester bonds link
The Double Helix Has Alternating Major and Minor Grooves
Unequal offsetting of the two strands
How is DNA Synthesized?
DNA can exist in 3 different 3-dimensional forms
Base pair spacing = 3.4Å/bp
10.5 bp/helix repeat
Helix diameter ~ 20Å
How to Detect DNA and RNA
Nucleic acids absorb UV light Why?
Determine [nucleic acid]
For dsDNA: 1 A260 unit = 50 mg/ml of DNA
Double stranded DNA denatures at high temperature
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
Cot Curve Analysis of DNA Samples
Visualizing DNA by Ethidium Bromide Staining
Nucleic Acids Can Be Precipitated
(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
The Effects of Alkali on DNA and RNA
Alkali hydrolyzes RNA
Alkali denatures dsDNA
The 2’OH groups are susceptible
to nucleophilic attack
At high pH, deprotonation of bases
disrupts hydrogen bonding
Q: Does RNA have a secondary structure?
RNA is single stranded and is most stable when it
Engages in intrastrand base pairing
How about the 3-D structure of RNAs?
Roles of DNAs and RNAs
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” (
Examples of catalytic RNAs
Group II intron
of tRNA 5’ ends
1. Cleavage reactions
2. Transesterification reactions
How come only RNAs be catalytic?
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?
DNA and RNA are Degraded by Nucleases
—5’3’ exo and 3’ 5’ exo
DNAs are more stable than RNAs
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
Answer to last lecture’s question:
“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.