The document provides an overview of DNA and its binding proteins, detailing DNA's structure as a double helix and the different types of DNA (A-DNA, B-DNA, Z-DNA). It discusses the functions of DNA-binding proteins, including transcription factors and histones, and describes various motifs such as helix-turn-helix, zinc fingers, and leucine zippers that facilitate DNA binding. Additionally, the document highlights methods for identifying DNA-protein interactions, including electrophoretic mobility shift assays and chromatin immunoprecipitation.

1. DNA binding proteins

2. WHAT IS DNA :-
 DNA is a group of molecules that is responsible
for carrying and transmitting the hereditary
materials or the genetic instructions from parents
to offsprings.”
 Apart from being responsible for the inheritance of
genetic information in all living beings, DNA also
plays a crucial role in the production of proteins.
Nuclear DNA is the DNA contained within the
nucleus of every cell in a eukaryotic organism. It
codes for the majority of the organism’s genomes
while the mitochondrial DNA and plastid DNA
handles the rest.

3. DNA Structure :-
 The DNA structure can be thought of like a twisted
ladder. This structure is described as a double-helix, as
illustrated in the figure above. It is a nucleic acid, and
all nucleic acids are made up of nucleotides. The DNA
molecule is composed of units called nucleotides, and
each nucleotide is composed of three different
components, such as sugar, phosphate groups and
nitrogen bases.
 The basic building blocks of DNA are nucleotides,
which are composed of a sugar group, a phosphate
group, and a nitrogen base. The sugar and phosphate
groups link the nucleotides together to form each
strand of DNA. Adenine (A), Thymine (T), Guanine
(G) and Cytosine (C) are four types of nitrogen bases.

4. DNA Structure :-

5. TYPES OF DNA :-
There are three different DNA types :-
 A-DNA: It is a right-handed double helix similar to the
B-DNA form. Dehydrated DNA takes an A form that
protects the DNA during extreme condition such as
desiccation. Protein binding also removes the solvent
from DNA and the DNA takes an A form.
 B-DNA: This is the most common DNA conformation
and is a right-handed helix. Majority of DNA has a B
type conformation under normal physiological
conditions.
 Z-DNA: Z-DNA is a left-handed DNA where the double
helix winds to the left in a zig-zag pattern. It was
discovered by Andres Wang and Alexander Rich. It is
found ahead of the start site of a gene and hence, is
believed to play some role in gene regulation.

6. DNA BINDING DOMAINS :-
 The transcription factor that interacts with an upstream or response
element.
 It has two basic domains a dna-binding domain specifically recognizes
the target sequenc -an activation domain contacts a basal transcription
factor.
 DNA-Binding proteins serve two principal functions :-
# To organize and compact the chromosomal DNA.
# To regulate and effect the processes of transcription, DNA
replication, and DNA recombination.
 DNA-binding proteins have the specific or general affinity for single or
double stranded dna by help of DNA-binding domain(DBD).
 A DBD can recognize a specific dna sequence or have a general affinity
to DNA.
 Sequence specific DNA binding proteins generally interact with major
groove of B-DNA because it exposes more functional groups that identify
a base pair.

7. CONTI…….
 The transcription factors which modulate process of
transcription, various polymerases, nucleases which cleave
DNA molecules involving in chromosome packaging.
 DNA binding proteins are :-
 Non-Histone
 Histone
 There are several motifs present which are involved in DNA
binding that facilitate binding to nucleic acid such as :-
 Helix turn helix
 Zinc fingers
 Leucine zippers
 Helix loop helix

8. Histone :-
 Histones are a special group of proteins found in the
nuclei of eukaryotic cells responsible for DNA folding
and chromatin formation.
 Are Basic Proteins.
 Molecular weights between 11,000 Da and 21,000 Da.
 Histones are positively charged.
 Due to abundance of positive amino-acids, arginine
and lysine.
 Histones have five major classes : H1, H2A, H2B, H3
and H4 .
 Histones are characterized :-
 Central nonpolar domain, forms a globular structure.
 N-terminal and C-terminal regions that contain most of
the basic amino acids.

9. Histone structure :-

10. Helix turn helix :-
 In, proteins helix turn helix is a major structural motif capable
of binding DNA
 Helix-turn-helix are typically found in prokaryotic DNA binding
proteins
 Helix turn helix proteins consist of two short helices of 7 to 9
amino acids long but separated or linked by non helical
segment of 3 to 4 amino acids, which are actually responsible
for turning the protein
 There are variations among HtH proteins such as- Di HTH, Tri
Helical HTH, Tetra helical HtH and Winged HtH.

11. Helix turn helix Structure :-
 The structure consists of two a helices joined by a
short strand of amino acid
 The recognition and binding to DNA by helix turn helix
proteins is done by the two a helices one occupying
the N-terminal end of the motif the other at c terminal.
 C terminal binds to major groove, N-terminal helps to
position the complex.

12. Zinc finger :-
 The zinc-finger proteins are globular proteins, but
presents finger shaped motif to bind DNA, in
sequence specific manner, and it is referred to as
Zinc-Finger motif. There are innumerable examples
of such proteins, to quote few, eg. Sp1, TFIII-A and
ADR 1.
 A small group of amino acids co-ordinates a Zn+
ion to form a finger
 The finger contains ß-sheet and a-helical structure.
 In most proteins with the zinc fingers, the N
terminal region after cysteine has beta sheet and
the right side of the loop has alpha helical structure.
 In most proteins with the zinc fingers, the N
terminal region after cysteine has beta sheet and
the right side of the loop has alpha helical structure.

13. CONTI…..
 The name, Zinc finger protein, has derived from the
kind of loop it generates when a covalent bond
 Formation between a single zinc metal ion with 2
cytosine on one side and 2 Histidine on the other
side either side of the polypeptide.

14. Leucine zippers :-
 These proteins have a stretch of amino acids rich in
hydrophobic leucine and they are on one side of the
right-handed helix.
 The leucine zipper is a stretch of amino acids rich in
leucine residues that provide a dimerization motif.
 Dimer formation itself has emerged as a common
principle in the action of proteins that recognize
specific DNA sequences.
 The repeat of Leucine is for every 3.5 residues per
turn and this pattern repeats for every seven amino
acid residues.
 The leucines are located on one face of an a-helix
 Interactions between the leucines results in
dimerisation.

15. CONTI….
 If two such chains having the same type of helices and
hydrophobicity, they can easily interact with one another by
protein-protein interaction and form coiled coils.
 To illustrate this with an example, take a. B. C. D. E. F. G. H.
As a sequence of amino acids as one segment of the helix,
where a and are hydrophobic, then one finds hydrophobic
amino acids with hydrophobicity on the same side at every
3.5 amino acids, which is actually one turn of the helix.

16. Helix loop helix :-
 Helix-loop-helix proteins are a modification of the
continuous a helices of the leucine zipper
proteins in which the DNA-binding and
dimerization regions are separated by a loop,
resulting in a four-helix bundle
 The domain consist of two a-helices seperated
by a loop of aminoacids
 Transcription factors having HLH motif are
dimeric, each with one helix containing basic
aminoacid residues that facilitate DNA binding.

17. Helix loop helix structure :-
 The helix loop helix motif consists of two a-helices
seperated by a loop of aminoacids
 Two polypeptide chains with the motif join to form a
functional DNA-binding protein
 Transcription factor including this domain are in
dimeric form
 In general, one helix is smaller and due to the
flexibility of the loop allows dimerization by folding
and packing against another helix
 The larger helix typically contains the DNA-binding
regions.
 bHLH proteins typically bind to a consensus
sequence.

18. .
 Function :- BHLH transcription factors are often
important in development or cell activity.
 Regulation :- Since many BHLH transcription
factors are heterodimeric, their activity is often
highly regulated by the dimerization of subunits.
One subunit’s expression or availability is often
controlled whereas the other subunit is
constitutively expressed.

19. Proteins that specifically bindsingle-strandedDNA :-
A distinct group of DNA-binding proteins are the
DNA-binding proteins that specifically bind
single-stranded DNA. In humans, replication
protein A is the best-understood member of this
family and is used in processes where the
double helix is separated, including DNA
replication, recombination and DNA
repair. These binding proteins seem to stabilize
single-stranded DNA and protect it from
forming stem-loops or being degraded
by nucleases.

20. Sequence specific DNA binding :-
 Each transcription factor binds to one specific set
of DNA sequences and activates or inhibits the
transcription of genes near promoters.
 Firstly, they can bind the RNA polymerase
responsible for transcription, either directly or
through other mediator proteins; this locates the
polymerase at the promoter and allows it to begin
transcription.
 Alternatively, transcription factors can bind
enzymes that modify the histones at the promoter.
This alters the accessibility of the DNA template to
the polymerase
 Most of these base-interactions are made in the
major groove.

21. Sequence non specific DNA binding :-
 Structural proteins that bind DNA are well-understood examples of
non-specific DNA-protein interactions
 These proteins organize the DNA into a compact structure called
chromatin.
 In eukaryotes, this structure involves DNA binding to a complex of
small basic proteins called histones. In prokaryotes, multiple types of
proteins are involved.
 The histones form a disk-shaped complex called a nucleosome,
which contains two complete turns of double stranded DNA wrapped
around its surface.
 These non-specific interactions are formed through basic residues in
the histones making ionic bonds to the acidic sugar-phosphate
backbone of the DNA, and are therefore largely independent of the
base sequence.
 Other non-specific DNA-binding proteins in chromatin include the
high-mobility group (HMG) proteins, which bind to bent or distorted
DNA

22. Protein binding DNA identification :-
 There are many in vitro and in vivo techniques which
are useful in detecting DNA-Protein Interactions
 Electrophoretic mobility shift assay is a widespread
technique to identify protein-DNA interactions
 DNase footprinting assay can be used to identify the
specific site of binding of a protinteraction
 Chromatin immunoprecipitation is used to identify
the sequence of the DNA fragments which bind to a
known transcription factor.
 This technique when combined with high throughput
sequencing is known as ChIP-Seq and when
combined with microarrays it is known as ChIP-chip.

23. REFRENCE :-
 P.K. GUPTA

24. THANK YOU