Secondary Structure of Nucleic Acids Flashcards
ssDNA folds back on itself to create
+ Single-stranded loop
+ Base-paired stem
Hairpin structures
+ Loop: size varies
+ Stem: homologous bases paired
Cruciform structures
Form if inverted repeats base pair with the complementary sequence on strand
Inverted repeats cause
Stem
Base separating inverted repeats cause
Loop
T or F: Cruciform DNA probably does not form in vivo.
False
Holiday structures
+ Junction of 4 loops
+ Permit crossing over during meiosis
Lacks free ends
Closed DNA
Circular genomes
Closed DNA
Bacteria form nucleoids
Closed DNA
Where are circular genomes found?
+ Viruses
+ Chloroplast
+ Mitochondria
Twist in DNA duplex along axis in space
Supercoiled DNA
DNA placed under tension
Supercoiled DNA
Only occurs in closed molecule
Supercoiled DNA
Single nick releases tension and supercoiling
Supercoiled DNA
1 twist
1 superhelical turn
No supercoils
Relaxed DNA
Applies to open or closed DNA
Relaxed DNA
Twist DNA opposite to the duplex
Negative supercoils
Relieves torsional stress by unwinding helix
Negative supercoils
If sufficient stress, strand separation occurs
Negative supercoils
Twist DNA in same direction as duplex
Positive supercoils
Winds duplex tighter
Positive supercoils
Never occurs in vivo
Positive supercoils
Superhelical density =
Number of superhelical turns of helix per 10 bp
Linking number =
Number of times that the duplex crosses itself (deltaW =deltaT)
W =
writhe (turning of double helix in space)
T =
twist (rotation of strands around each other)
Writhe is increased
Twist unchanged
Negative supercoil
Twist decreased
Writhe unchanged
Underwound
Higher L means
Higher negative supercoiling or unwinding
Lower L means
Lower negative supercoiling or overwinding
Toposiomers
A topologically distinct isomer
Topoisomerases (Topo)
+ Change L
+ Break 1 or both strands
Helicases
+ Separate strands
+ Do not change L
DNA gyrase
Facilitates supercoiling
