Nucleic Acids Flashcards
DNA
deoxy-ribonucleic acid
nucleotide and examples
pentose sugar + nitrogenous base + phosphate
CTU (pyramidines) AG (purines)
what type of bond does the ribose sugar - nitrogenous base make
B-glycosidic bond
nucleoside
pentose sugar + nitrogenous base
what direction is DNA synthesized in
5’P ———– 3’OH
what direction do DNA strands run in
antiparallel
DNA DIMENSIONS
diameter =
each turn of the helix =
distance between each bp =
minor groove =
major groove =
sugar pucker of deoxyribose =
- 20 Å = 2 nm
- 34 Å = 3.4 nm
- 3.4 Å = 0.34 nm
- 6 Å = 0.6 nm
- 12 Å = 1.2 nm
- C2 endo sugar pucker
are bases placed in a anti or syn conformation with the sugar
anti = limits steric hindrance between base and sugar
chargaffs rule and why it is so important
[A] = [T] [C]=[G]
- arrangement maintains complementarity and uniform structure of DNA double helix
watson and crick bond stability
A/T = 2 H bonds
C/G = 3 H bonds
what 2 things lead to the stability of DNA double helix
-base stacking interactions between adjacent bases
- H bonding interactions between sugar-base
what conformation leads to the B form DNA sugar pucker
C2 endo (C2 is above the plane)
C2 endo sugar pucker refers to what form of nucleic acid
B form DNA
what conformation leads to the A form DNA sugar pucker
C3 endo (C3 is above the plane)
syn base conformation =
anti base conformation =
= base is directly above the sugar = not favoured
= base is beside the sugar = favoured
structure of a tetraplex
- 4 guanine residues aligned in a square through h bonding
- hoogsteen edge + watson&crick edge interacts
- stabilized by K+ ions in between each tetraplex
3 conformations of dsDNA
A form = shorter, wider, right handed twists
B form = regular DNA, right handed twists
Z form = zigzag arrangement, left handed twists
how can dna have a triple helix
through Hoogsteen base pairing of a third helix that binds to the double helix
Hoogsteen base pairing
syn A / anti T syn G / anti C
A/T + T G/C + C
what is the hoogsteen edge
the edge that H bonds from both pyramidine + imazidole rings
what is the watson&crick edge
the edge that H honds from only the pyramidine ring
Key differences between RNA and DNA
RNA = single stranded DNA = double stranded
RNA = uses a U instead of a T
RNA = OH on C2 of ribose DNA = H on C2
RNA = G/U and A/U base pairing
RNA STRUCTURE
primary =
secondary =
tertiary =
quaternary =
primary = original sequence of nts
secondary = intramolecular base pairing of nts
tertiary = intramolecular folding of structure
quaternary = intermolecular interactions
examples of RNA seconday structures
bulges, internal loops, stems/hairpins, junctions
examples of RNA tertiary structures
psuedoknots = discontinuous base pairing among the rna strand
kissing hairpins = 2 hairpin loops base pairing
stabilizing forces of RNA
- hydrophobic stacking interactions, van ders wals interactions, pi-pi interactions between aromatic bases
- hydrogen bonding
- electrostatic interactions between phosphate (-) and metals (Mg2+, Na+, K+)
what is the function of metals such as Mg2+ in RNA
they stabilize the RNA A form helix by fitting really well and are involved in catalytic activities ex. hammerhead ribozyme
GNRA tetraloop (hairpin loops secondary structure)
4-base hairpin loops
G = guanine
N = any base
R = A/G (purine)
A = adenine
h bonding between G/A (2 bonds)
UNCG tetraloop (hairpin looks secondary structure)
4-base hairpin loops
U = urucil
N = any base
C = cytosine
G = guanine
h bonding between U/G
what type of metals stabilize the bends in bulges (secondary structure)
Mg2+ stabilizes the bends in bulges and Ca2+ can stabilize the overall structure
Hammerhead Ribozyme (tertiary structure)
function =
structure of ribozyme =
Ions involved =
ph dependant =
function = catalyzes the cleavage of phosphodiester bonds in RNA
structure = made of 3 stem loops, stems 1&3 have base pairing at the cleavage site
2 Mg2+ ions aid in the attack of the 2’OH attacking the 3’P for cleavage
ph between 5-8
unusual dna structures
m-dna (metal dna), ring expanded bases, non standard bases (nanotech)
what is M-dna
metal- dna
- dna + divalent metal ions (Co2+, Ni2+, Zn2+) placed in the middle of dna
- widens dna helix
what are ring expanded bases
bases are expanded through the addition of a benzene ring
expanded base1 + reg base 2 = hydrogen bonding
ex. expanded A + T = 2 h bonds
ex. expanded G + C = 3 h bonds
- widens the dna helix and makes it more stable than normal dna helix
what are non standard bases and why are they used
-artificial nucleobases that are inserted within the a-helix in between the standard bases through the use of metal ion coordination
- used to increase the information storage of DNA by addition of artifical nucleobases that can carry more genetic contents (info) and can be used for nanotech
dna origami
matching multiple ssDNA through base pairing in order to make a defined dsDNA structure
types of drugs x DNA interactions
- intercalating agents (EtBr)
- groove binders (Netropsin)
- alkylating agents (Mechloroethamine)
- chain cutters (Bleomycin (BLM))
- chain terminators
INTERCALATING AGENTS
function and example =
structure =
binding forces
function = EtBr, fits in between bps in the dna helix and therefore disrupts the dna structure hence, distrupting transcriptional processes
structure = flat planar aromatic structure
binding = by Van der Wals base stacking as well as electrostatic interactions ((+) on the ends of EtBr/ (-) P)
GROOVE BINDERS
function and example =
structure =
binding forces =
function = Netropsin/DAPI, non-covalently bind to the major/minor grooves of dna minor groove binders are more common
structure = cresent shaped molecules
binding = by H bonding as well as electrostatic interactions ((+) on the ends of Netropsin/ (-) P)
ALKYLATING AGENTS
function and example =
structure =
binding forces =
function = Mechloroethamine (Nitrogen Musturd), agents that introduce alkyl groups to dna therefore disrupt the structure by making DNA stand cuts and prevent replication from happening, used for anticancer drug theraphy
structure = highly electrophilic compounds that form covalent bonds with DNA
CHAIN CUTTERS
function and example =
Site of cleavage =
function= BLM, intercalating agents that cut the DNA chain of cancer cells through free radical mediated scission by using Fe2+ as a cofactor. The indroduced radical then reacts with O2 to mediate the scission, used for anticancer drug theraphy
site of cleavage = cleaves 4’H or 5’H
intermolecular interactions between
Protiens-DNA
- stacking interactions - dna bases + aromatic protien side chains (rare)
- water mediated H bonding
- electrostatic interactions - Lys/Arg + P
dna binding proteins bind to specific bps in a _________ _________ manner through the ______ groove usually
sequence specific
major
what and where are the 3 aa-base interactions that only involve 2 H bonds
- Arg - GC (major groove)
- Gln - AT (major groove)
- Asn - GC (minor groove)
PROTEIN-DNA COMPLEXES (MAJOR GROOVE)
Lambda Repressor
motifs =
aa-base interaction =
binding forces =
motifs = HTH motif between helix 2 and helix 3, helix 3 is found in the major groove
aa-base interaction = Gln-AT in the major groove
binding forces = H bonding from 5 P’s + aa’s throughout the protein , electrostatic interactions from P - 2Lys
PROTEIN-DNA COMPLEXES (MINOR GROOVE)
Mu Repressor
motifs =
binding site =
motifs = winged HTH motif
binding site = unstructured domain/tail binds to the minor groove of DNA
3 protein-RNA recognition features
- proteins recognize the shape of RNA and not the sequence
- protiens bind to the single stranded regions of RNA such as loops and bulges
- Adaptive binding is common as binding changes the structure of the entire protein-RNA complex
RNA BINDING PROTEINS
BIV TAR TAT (Arg rich)
structure =
binding forces =
structure = forms B-hairpin loop stucture that binds to the major groove of RNA and widens it
binding forces = electrostatic interactions between Lys/Arg + RNA
