Lecture 7: Nucleic Acid Structure I Flashcards
Primary DNA structure
single strand of bases
Secondary DNA structure
-helix
-stem loop
-pseudoknot
Tertiary DNA structure
-A, B, Z forms
-stem loop and psuedoknot
Quaternary DNA structure
-DNA around a histone
-RNA with monomers
purine bases
-adenine
-guanine
pyrimidine bases
-cytosine
-thymine
-uracil
Non B-form DNA structures
-form transiently during replication, recombination, or transcription
-ex: triplex DNA/H-DNA
-can cause DNA polymerase to stall = nicks, breaks, possible malfunction
triplex DNA/H-DNA
-G-quadruplex structures in guanine-rich regions of DNA
-i-motif in cytosine-rich region of DNA
-expanded triplex sequences
Expanded triplex sequences
can cause certain hereditary neurological diseases
G-quadruplex and i-motif structures
-essential roles in regulating transcription and genome stability
-disruption can lead to cancer and aging
Topoisomerases
-maintain DNA supercoiling
-target of anticancer drugs
B-DNA structure
-base pairing
-base stacking
-most stable under physiological conditions
-elongated and narrower than A
-larger degree of twist
A-DNA structure
-observed under dehydrating conditions and high salt
-compatible with RNA
-compressed and wider
B-DNA major binding groove
-wider and shallower than A
-highly accessible for proteins to bind
Major and minor grooves
SLIDE 8 adn SLIDE 9
Double stranded DNA
-conformationally flexible
Helix features A vs B
SLIDE 10
A-form DNA
-less solvent exposure
-under dehydrating conditions
-protects it under desiccating conditions
-often occurs in formation of DNA-RNA hybrid helix
SIRV2 virus protein
-certain protein that dehydrates DNA upon binding = A-form
-infects hyperthermophilic acidophile sulfolobus islandicus
DNA deformability
-structure can deviate locally (around a few bps) when bound to small molecules while still maintaining base pairing
-intercalators
-groove binders
Intercalators
-hydrophobic
-heterocyclic
-insert between bases through ring stacking
-Ex: TOTO
TOTO
-intercalator
-fluorescent label used to detect dsDNA in gels
Minor-groove binders
-outnumber major-groove binders
-ex: Netropsin
-some groove binders change twist
Netropsin
-antibiotic and antiviral
-interacts with sugars and an edge of the bases giving sequence-specific binding
DNA intercalating agents
-interfere with DNA replication, transcription and repair
-distortions to DNA structure also lead to mutations = mutagens
-Actinomycin D
Actinomycin D
-chemotherapeutic agent
-treats Wilms’ tumor
-pediatric kidney tumors
Superhelical (supercoiling)
-created by underwinding (negative) or overwinding (positive) DNA to lowest energy helical state (thermo favored B-form)
-circularized DNA after loss of bp
-compacts DNA
-tend to disrupt H bonding that may lead to repair and replication
DNA activity in replication and transcription
-topologically supercoiled form has greater activity than relaxed B-form
-supercoiling disrupts H bonding which may lead to repair and replication
Negative supercoiling
-underwinding
-form right-handed superhelix
-easier to unwind
- = repair, replication, recombination
Positive Supercoiling
-overwinding
-form left handed superhelix
-hard to unwind
-stabilizes DNA under extreme conditions
Supercoiling equation
Lk = Tw + Wr
-sum of Tw and Wr constant = one to one change
Lk
-linking number
-does not change once both ends are fixed (anchored to protein or circular DNA)
Tw
-twist
-turns in DNA chain
-one every ~10 bp for relaxed DNA
Wr
-writhe
-superhelical coild
SLIDE 19 MELTED DNA
SLIDE 19
For double stranded DNA with 110 base pairs, what is the relative length of the helical structure in A-form and B-form
B-form is longer than A-form
Linear DNA in eukaryotes
-supercoiled
-anchoring by nuclear proteins created topological domains
Linear DNA supercoiling
-induced by transcription and replication
-number of twists is constant while bps is decreased
Supercoiled DNA vs relaxed DNA
-more compact
-chromatin for packaging in nucleus
DNA of most organisms
negatively supercoiled
DNA replication and transcription winding
-overwound ahead of replication fork (positive)