D. [Conformations of DNA]

is polymorphic and dynamic

DNA

3 forms of DNA

B-DNA

A-DNA

Z-DNA

Helix Handedness:

B-DNA:

A-DNA:

Z-DNA:

right

right

left

Base Pairs (bp) per helical turn

B-DNA:

A-DNA:

Z-DNA:

10.5

~11

~12

Vertical rise per bp

B-DNA:

A-DNA:

Z-DNA:

3.4

2.56

3.7

Rotation per bp

B-DNA:

A-DNA:

Z-DNA:

+36

+33

-30

Helical Diameter

B-DNA:

A-DNA:

Z-DNA:

20

23

18

Major Groove

B-DNA:

A-DNA:

Z-DNA:

wide, deep

narrow, deep

flat

Minor Groove

B-DNA:

A-DNA:

Z-DNA:

narrow, deep

wide, shallow

narrow, deep

the canonical right-handed DNA helix that is the most common form of DNA. It is the standard form being considered the conformation adopted by nearly all sequences within a genome.

B-DNA

It is a double helix made of two antiparallel strands that are held together via hydrogen bonding in the A•T and G•C base pairs. The two strands of the duplex are antiparallel and plectonemically coiled.

B-DNA

has a smooth backbone

B-DNA

B-DNA conformation is actually highly variable and malleable. It can adopt

multiple conformations in response to the environment which can affect?

protein recognition

right-handed antiparallel helical duplex

A-DNA

underwound structure that is more compact along the helix axis and broader overall across the helix relative to B-DNA.

A-DNA

The base pairs of A-DNA are tilted to about ___° with respect to the helical axis

20

has been observed under conditions of reduced water content, such as in DNA fibers at 75% relative humidity or in solutions containing organic solvents or high salt concentrations.

A-DNA

biological relevance of A- DNA: under winding for replication fidelity

▪ by inducing the A-form, the polymerase exploits the structural features of the highly accessible _____ to ensure that the correct base has been added relative to the template sequence.

minor-groove

an ___-like DNA conformation may either form upon binding of certain proteins to DNA, or be an important intermediate step in forming the strongly distorted DNA conformation observed within at least some complexes with proteins.

A-DNA

left-handed, the most underwound form of the double-helix, has been mostly found in alternating purine-pyrimidine sequences (CG)n and (TG)n.

Z-DNA

the repeating unit of Z-DNA is __ bp

2 bp

the major groove in Z-DNA is not so much a groove but more a ____ outer surface, while the minor groove becomes a deep, narrow and largely inaccessible crevice.

convex

the backbone follows a zigzag path (some phosphate groups are closer and electrostatic repulsion between them is greater than in B-DNA)

Z-DNA

Z-DNA is stabilized by _____ _____ __________ or polyvalent cations that shield interphosphate repulsion better than monovalent cations.

high salt concentration

_________ is a major driving force for Z-DNA formation.

DNA supercoiling

usually in locations near the site of transcription initiation.

Z-DNA

As Z-DNA being the most underwound form of the double-helix, it consequently serves as a sink for the __________ (superhelical tension) in negatively supercoiled DNA. This expands the range of cellular situations that could support the formation, at least transiently, of Z- DNA.

torsional tension

Z-DNA helps to maintain the gene (close to it) in its activated, _________ state (nucleosomes do not bind to the very rigid Z- DNA form) - regulation of gene expression

nucleosome-free

Z-forming sequences accumulate near the ______ start site of genes in humans and other eukaryotes (~80% of the genes in human chromosome 22 have at least one Z-DNA sequence in the vicinity of their transcription start sites)

transcription

suggested additional functions of Z-DNA: (2)

RNA editing

gene transactivation

has several potential functions may be either beneficial or deleterious to the cell.

Z-DNA

Why do different forms of DNA exist?

not enough room

What are the 3-stranded and 4-stranded DNA structures?

H-DNA

Holliday Junction

G-Quadruplex

i-Motif

formed when a single DNA strand invades the major groove of a DNA duplex (but in order for the duplex to accommodate this third strand, it must unwind to broaden the major groove)

H-DNA

meaning of H in H-DNA

Hoogsteen

H-DNA: triple-stranded helices are favored in _____ supercoiled DNA (The invading third strand can be intermolecular or intramolecular.)

negatively

In H-DNA, the interaction between strands involves the ________of the Watson- Crick base pairs of the duplex to form base triplets which explains its name.

Hoogsteen edge

Its presence in large numbers suggests that naturally occurring DNA sequences can cause increased _______ when they assume the non-standard DNA structure formation

mutagenesis

How many strand in H-DNA

3

H-DNA is formed primarily in what sequences (sequences that have dyad symmetry within a strand, as in ...AGAGGGnnnGGGAGA. (If you read it backward, the sequence of bases is the same as when you read it forward.)

mirror repeat

Mirror-repeats occur more frequently in what genomes and have been documented to have effects on gene expression of several disease related genes.

eukaryotic

As with Z-DNA, the repeating sequence motif of H-DNA appears to be a source of _______ ________ resulting from double-strand breaks.

genetic instability

The HJ form is composed of how many DNA strands.

4

A DNA structure that is essential to several cellular processes

Holliday Junction

The Cellular processes of HJ includes? (4)

➢ _________-dependent DNA lesion repair

➢ ______ _________
➢ __________ of stalled replication forks, and

➢ proper _________ of homologous chromosomes during meiosis

1. recombination

2. viral integration

3. restarting

   1. segregation

essential intermediates in double-strand break repair

Holliday Junction

The G in G-quadruplexes refers to?

guanine

G-quadruplex is composed of how many DNA strands.

4

The four-stranded structures assembled from guanine-rich sequences

G-quadruplexes

G-quadruplexes is found primarily in?

telometric DNA repeats

central regions of genome

The strands og G-quadruplexes are held together by pairing the Watson-Crick edge of each guanine with the Hoogsteen edge of an adjacent guanine, creating a _______ of four guanines into G-tetrads.

cyclic arrangement

These tetrads of G-quadruplexes are stacked with a right-handed helical twist, and are stabilized by _____ cations (Na+ or K+) coordinated to the O2 oxygens of the guanines, and sandwiched between the base stacks.

monovalent

the I in I-motifs refer to?

intercalated

How many strands are in I-motif?

4

I-motifs is also known as?

I-form DNA

a transitory conformation that can form in sequences rich in cytosine.

I-motif

I-motif is stabilized by what condition?

acidic

they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine–cytosine base pairs.

I-motif

The I-motif is fashioned from two parallel C-strands ______ in a head-to-tail fashion. The two duplexes of poly(dC) are stabilized by base pairing the Watson-Crick edges of two cytosines to form hemi-protonated C- C+ pairs.

intercalated