This document discusses the structure of nucleic acids like DNA and RNA. It explains that DNA can take on different conformations and its structure varies with sequence, contrary to the original Watson-Crick model which assumed a single structure. The key consequences of the Watson-Crick model are that DNA is double-stranded with complementary bases, allowing for redundancy and easier replication. The document also discusses different forms DNA can take on (A, B, Z forms), G-quadruplex structures, DNA supercoiling, the structure of transfer RNA including its acceptor stem, CCA tail, and anticodon arm, and common modifications to bases in tRNA.

1. STRUCTURE OF NUCLEIC
ACIDS
Abu sayeed
DEPARTMENT OF CHEMISTRY
ALIAH UNIVERSITY

2. DNA is a highly flexible molecule that can undergo a series of
transformations leading to many conformations with different
biological functions.
The structure of DNA as originally proposed by Watson and Crick
depended on one major assumption, that the structure of DNA
was independent of its sequence
We now know from X-ray crystal structure analysis of DNA
segments, that the structure of DNA varies dramatically with
sequence.

3. The first important consequence of the
Watson-Crick model of DNA was that
the molecule was double helical and
that the two strands contained
complementary base sequences. This
meant that the genetic information is
redundant. This redundancy allows
repair of damaged DNA and simplifies
replication of the DNA via strand
separation.
Another important consequence of
the Watson-Crick structure was the
anti-parallel nature of the DNA
chains. Anti-parallel chains cause
considerable difficulty for replication
and transcription.

11. In molecular biology, G-quadruplexes (also known as G-tetrads or G4-DNA) are
nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded
structure. Four guanine bases can associate
through Hoogsteen hydrogen bonding to form a square planar structure called a
guanine tetrad, and two or more guanine tetrads can stack on top of each other to
form a G-quadruplex. The quadruplex structure is further stabilized by the
presence of a cataion especially potassium, which sits in a central channel
between each pair of tetrads. They can be formed of DNA, RNA, LNA, and PNA,
and may be Intramolecular bimolecular, or tetramolecular Depending on the
direction of the strands or parts of a strand that form the tetrads, structures may be
described as parallel or antiparallel

12. Why helix : sugar pucker
The sugar pucker determines the shape of the a-helix, whether the helix
will exist in the A-form or in the B-form. The five membered ring is for
steric reasons not planar (Pitzer –transannular– tension, because all
bond would be ecliptic). One atom or two are turned out of the plane by
50 pm. In the ribofuranose, the plane C1’-O4’-C4’ is fixed. Endo-pucker
means that C2’ or C3’ are turned out of this plane into the direction of O5’.
Exo-pucker describes a shift in the opposite direction. C2’- endo and C3’-
endo are in equilibrium. In RNA we find predominantly the
C3’- endo conformation. DNA may adjust and is able to take on both
conformations. For an exact nomenclature of sugar puckers see below.

15. A B Z
Helix sense Right
handed
Right-handed
Left handed
Repeating unit 1 bp 1bp 2 bp
Rotation/bp 33.6° 35.9° 60°/2
Mean bp/turn 10.7 10.0 12
Inclination of bp to
+19° -1.2° -9°
axis
Rise/bp along axis 2.3Å 3.32Å 3.8Å
Pitch/turn of helix 24.6Å 33.2Å 45.6Å
Mean propeller twist +18° +16° 0°
Glycosyl angle anti anti C: anti, G: syn
Sugar pucker C3'-endo C2'-endo C: C2'-endo, G: C2'-
exo
Diameter 26Å 20Å 18Å

18. DNA supercoiling
Extra helical twists are
positive and lead to positive
supercoiling, while
subtractive twisting causes
negative supercoiling.
Many topoisomerase enzymes
sense supercoiling and either
generate or dissipate it as
they change DNA topology.
DNA of most organisms is
negatively supercoiled.

19. RNA

20. Transfer RNA (t-RNA)

22. 1. The 5'-terminal phosphate group.
2. The acceptor stem is a 7-base pair (bp) stem made by the base pairing of
the 5'-terminal nucleotide with the 3'-terminal nucleotide (which contains
the CCA 3'-terminal group used to attach the amino acid). The acceptor
stem may contain non-Watson-Crick base pairs.
3. The CCA tail is a cytosine-cytosine-adenine sequence at the 3' end of the
tRNA molecule. This sequence is important for the recognition of tRNA by
enzymes and critical in translation. In prokaryotes, the CCA sequence is
transcribed in some tRNA sequences. In most prokaryotic tRNAs and
eukaryotic tRNAs, the CCA sequence is added during processing and
therefore does not appear in the tRNA gene.
4. The D arm is a 4 bp stem ending in a loop that often
contains dihydrouridin

23. 5. The anticodon arm is a 5-bp stem
whose loop contains the anticodon.
6. The T arm is a 5 bp stem containing
the sequence TΨC where Ψ is
a pseudouridine.
7. Bases that have been modified,
especially by methylation, occur in
several positions throughout the
tRNA. The first anticodon base, or
wobble-position, is sometimes
modified to inosine (derived from
adenine), pseudouridine (derived
from uracil) or lysidine (derived from
cytosine).