STRUCTURE OF NUCLEIC ACIDSAbu sayeed

DEPARTMENT OF CHEMISTRYALIAH UNIVERSITY

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.

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.

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

Why helix : sugar pucker

The sugar pucker determines the shape of the α-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.

  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 axis

+19° -1.2° -9°

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

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.

RNA

Transfer RNA (t-RNA)

http://en.wikipedia.org/wiki/File:TRNA-Phe_yeast_1ehz.png

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

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).