The Structure of DNA


Do you recognize this molecule? This is DNA, or
deoxyribonucleic acid. By the end of this
video, you will be able to identify the key
structural features of DNA, as well as describe
the importance of those features for function. During this video, we will look
at different representations of the DNA molecule to
better view certain details, but all views represent
this same structure. Inside the cell, you
will most commonly find double- stranded DNA, in
which two strands intertwine to form a double helix. The most common form of
the DNA double helix, which is what we
will discuss here, is also called B-form DNA. Now, let’s move to a more
simplified representation of DNA to discuss the details. We can unwind the
double helix like this so that we can see the
chemical structure inside. Each strand is a
polynucleotide, meaning the strand is made up of
many individual units called nucleotides. A nucleotide has three
components: the five-carbon sugar, a phosphate
group, and one of four possible
nitrogenous bases– adenine, guanine,
thymine, and cytosine. The nitrogenous base is
always attached at the 1′ carbon of the sugar. If we count from
there, we can see that there is a phosphate
between the 5′ carbon of one sugar and the 3′ carbon of the neighboring sugar. The sugar is called
deoxyribose because it is missing a hydroxyl group
at the 2′ carbon which is present in ribose. Because of this, nucleotides
in DNA, deoxyribonucleic acid, are called deoxynucleotides. Nucleotides attach to each
other in the DNA strand by phosphodiester bonds. The phosphate group
of one nucleotide binds to the 3′ oxygen
of the neighboring nucleotide. Thus, we can see that the sugars
and phosphate groups make up the DNA backbone. The carbon numbering
is key to describing the directionality of the DNA
strand, 5′ to 3′. Looking within the sugars, there
is an intrinsic orientation difference between
the two strands. On the top strand, you can
see that the 5′ carbon of each sugar is on the left
and the 3′ carbon is on the right. The opposite is true
for the bottom strand. Reading left to
right, that makes the top strand orientation
5′ to 3′ and the bottom strand
orientation 3′ to 5′. These strands are also sometimes
called Watson and Crick. Keep in mind that this
double-stranded DNA is still a double helix and we have
simplified the representation by flattening and unwinding
the helix here to better see the atomic structure. Although the nucleotides
come together through covalent
bonds in the backbone, the two DNA strands interact
through non-covalent hydrogen bonds between the bases. Each base forms
multiple hydrogen bonds with its complementary base
on the opposite strand. Bound together by
hydrogen bonds, each unit is called a base pair. The hydrogen bonding
contributes to the specificity of base pairing. Thymine preferentially
pairs with adenine through two hydrogen bonds and
cytosine preferentially pairs with guanine through
three hydrogen bonds. Thymine and cytosine are called
pyrimidines, characterized by their single ring structure,
and adenine and guanine are called purines,
which have double rings. The geometry of the AT or
TA and GC or CG base pairs is the same, allowing for
symmetry and base stacking in the helix. This mostly has to do with the
distance between the backbones and the angles to which the
bases attach to the backbone. Other base pairs,
like GT, for example, do not have the same geometry,
cannot form strong hydrogen bonds, and disturb the helix. The double helix structure
of DNA is highly regular. Each turn of the helix measures
approximately ten base pairs. In addition to the hydrogen
bonding between the bases, the stacking of the bases also
stabilizes the double helix structure. These pi-pi
interactions form when the aromatic rings
of the bases stack next to each other and share
electron probabilities. The regularity of
the helical structure forms two repeating
and alternating spaces, called the
major and minor grooves. These grooves act as
base pair recognition and binding sites for proteins. The major groove contains
base pair specific information while the minor groove is
largely base pair nonspecific. This is because of the patterns
of hydrogen bond acceptors and donors that proteins can
interact with in the grooves. In this way, the DNA
can be acted upon in either a sequence specific
or non-sequence specific manner, allowing proteins to
position themselves correctly in the genome to carry out
their designated tasks. This is the DNA double
helix, and you’ve now learned the structural features
that influence its function. We hope you’ve enjoyed exploring
this amazing molecule with us.