DNA structure - ANSWER-- nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
- sugars (ribose, deoxyribose)
- sugars linked by phosphate groups (sugar-phosphate backbone)
*form antiparallel strands
In mammilian DNA, which base has various forms - ANSWER-cytosine
Chargaff's rule - ANSWER-A...
BCH5413 Exam Questions| Already
Answered| GRADED A+
DNA structure - ANSWER-- nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
- sugars (ribose, deoxyribose)
- sugars linked by phosphate groups (sugar-phosphate backbone)
*form antiparallel strands
In mammilian DNA, which base has various forms - ANSWER-cytosine
Chargaff's rule - ANSWER-A=T and C=G
Is DNA conservative or semi-conservative? - ANSWER-semi-conservative
- parental sequence and daughter strand bind together
Alternative Double stranded DNA conformation
- A and Z DNA - ANSWER-A DNA
- dehydrated form
- right handed helix
- 11 bp per helical
- bp tilted 19 degrees
- major groove narrow and deep
- found with dsRNA and RNA-DNA duplex
z-DNA
- >1% of cellular DNA
- favored by G-C repeats and alternating purines-pyrimidines
,- left handed helix
- 12 bp per turn
- bp tilted 9 degrees
- major groove flattened, nearly gone
- bound by poxvirus E3L virulence factor and down regulates apoptosis genes
Non-duplex DNA structures
- cruciform DNA - ANSWER-- inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA
Alternative modes of base pairing - ANSWER-Watson Crick:
A--T and C---G
- adenine is at anti-conformation
Hoogsteen:
- adenine or guanine can be flipped to sin-conformation (different H-bonding)
Hoogsteen base pairing
- when can it occur - ANSWER-- in triplex and quadruplex DNA structures
Triplex DNA - ANSWER-- pyrimidine rich strand
- negative supercoiling
Chair DNA - ANSWER-- two G-rich strands
- down regulation of c-myc transcription
Intrinsic Bends in DNA - ANSWER-- distortion of the ideal B-DNA conformation resulting from base
stacking in the nucleotide sequence
,Eg. Adenine-tract DNA results in 20 degree bends
- also can be found in duplex-oligonucleotide model DNA
- causes 23 degree bend and mis-stacking of one GC
- DNA is not a uniform structure
Does B-DNA have a perfect structure? - ANSWER-No
- sequence specific local variation in twist between paired bases, sugat conformation, tilt of base pairs,
rise distance, etc.
Supercoiled DNA
- negative v. positive - ANSWER-- left handed under-twisted DNA is in a negative supercoil
- right handed over-twisted DNA is in a positive supercoil
*most is negatively supercoiled (topoisomerase releaves supercoiling)
Denaturation/Melting of DNA - ANSWER-- separation of DNA strands
- can happen due to temp, salt concentration, G---C content, and length of DNA (Hyperchromicity effect)
- as temp increases, absorption of light increases due to bases becoming less shielded when they melt
apart
The (greater/lower) the G+C content and the (higher/lower) the salt, the more stable the DNA duplex -
ANSWER-greater G+C and higher salt
What are higher stringency conditions - ANSWER-high heat and low salt
What else can melt DNA? - ANSWER-pH
, DNA renaturing and hybridization - ANSWER-- add complementary RNA and re-anneal by gradually
lowering temp.
Where are chemical groups present in the DNA - ANSWER-major and minor groove
How do sequence specific DNA binding proteins bind in a sequence specific manner - ANSWER-the
amino acids of sequence specific DNA binding proteins recognize the pattern of chemical groups in the
major/minor groove
- may interact through different bonding to permit sequence specific recognition
Zinc finger binding proteins - ANSWER-- custom designed DNA binding proteins
- two beta sheets attached to an alpha helix coordinate by a zinc molecule
- triple zinc finger can bind in the major groove of DNA
Zinc finger custom design - ANSWER-swapping the alpha helix domain and beta-hairpin segments allows
for different sequence specificity
- a single zinc finger protein can recognize 3bp of DNA
Zinc finger and DNA binding specifics - ANSWER-- AA of zinc finger at position 6 recognizes first
nucleotide of DNA
- AA of zinc finger at position 3 recognizes second nucleotide of DNA
- AA of zinc finger at position -1 recognizes third nucleotide of DNA
Zinc finger table - ANSWER-helps determine what amino acid sequence of the zinc finger will match up
to what specific triplet sequence of DNA
What is the use of custom designed DNA-binding proteins - ANSWER-potential for designing a DNA-
binding protein to bind to a single site (DNA sequence) in the genome
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