Properties:

 

DNA & RNA: a Comparative Account:

 

·         DNA is the genetic material in most of the organisms including many viruses, while RNA acts as the genetic material in some viruses but not in all.

·         The total concentration of DNA of a cell in a given species is constant and characteristic, but the concentration of RNA varies from one cell type to the other; active cells contain more RNA than resting cells.

·         More than 90% of the cellular DNA is located in the Nucleus, whereas more than 90% of the total cellular RNA is found in cytoplasm and so also in the nucleolus as rRNA and in the rest of karyolymph as pre-mRNA and tRNA and few more Sc and Sn RNAs.

·         A small percentage DNA is also found in cytosolic mitochondria and plastids The amount of DNA of a gamete mother cell is exactly twice the amount of its gamete or the amount of DNA of a gamete is exactly half of the amount found in gamete mother cell.

·         The DNA is a macromolecule of very high order ranging from ~ 4000 bp to few billion bp largest genome ever to be recorded for plants is Paris japonica with 53.2pg X 978 X 10^6, while RNA molecules, also macromolecules but they are not as big as DNA.

·         They are polymers of nucleotides, where phosphodiester bonds covalently link nucleotides to each other.  

·         Both DNA and RNA polynucleotides have 5’ ppp or 5’p at their 5’ends and 3’OH; both have 5’ >> 3’ polarity.

·         The DNA molecules are very stable; their life span is same as that of the life span of cells, when compared to RNA whose half-life varies from few minutes to few days (rRNA 120 days).

·         DNA synthesis is restricted to certain stage of cell’s life cycle, but RNA synthesis is not, it takes place all the time and as long as cell exists.

·         When both DNA and RNA exist in the cell, DNA acts as the genetic material and RNA plays a secondary but very important role but not as the genetic material. The RNA in viruses acts as the genetic material.

·         DNA undergoes replication at a specific stage of the cell cycle, but cellular RNAs are incapable of replication.

·         DNA in cellular organism is grouped into DNA-Protein structures called chromosomes, while RNAs are free except rRNA organized into ribosomes.

·         Only viral RNAs are endowed with replication ability, so also viral DNAs, but none of the other cellular RNAs have the ability to replicate.  Rarely the reverse transcribed into cDNAs; during evolution some of them transported into the nucleus and integrated into chromosomal DNA, but non functional; you can say they are ‘molecular Fossils”

·         DNA molecules are very stable, but RNA molecules subjected to rapid turnover.

·         Chemically DNA gives characteristic purplish color with D-amino picolinic acid (DAP) reagent; Feulgan regent, acetocarmine and acetoorcien  stains chromosomal DNA purple to reddish color while RNA gives a little greenish color reaction with Resorcinol reagent.

·         DNA can exist as single stranded molecule in many viruses; it can be linear or circular depending upon the viruses.  Most of the eukaryotic organisms contain DNA as ds structure and most of them organized into chromosomes and this ds DNA is linear with protected telomeric ends.

·         RNA exists in the form of genetic RNA in viruses, but eukaryotic cells it plays a subsidiary role to DNA.  And it is found in variety of forms such as tRNA, rRNA, mRNA, si/miRN, snoRNA scRNA snRNA, Tasi RNA, Rasi RNA, xist RNA another 30-40 different RNAs;  Only mRNAs and tRNA have coded information in form codons and anticodons.

 

Chemistry of Nucleic Acids:

·         DNA and RNA are composed of Phosphoric acid, nitrogenous base, and a pentose sugar. 

·         Pentose sugar is Deoxy ribose in DNA and Ribose in RNA. The deoxyribose is lacking OH moiety at 2C’ of the sugar but contain H, and the ribose possess OH group at 2C’ position.

 

·         The OH group at C-1 position is in beta configuration. 

·         Phosphate is phosphoric acid H2PO4^-2, depends upon the ambient pH of the solution or the environment. It is phosphate group that gives DNA and RNA acidic nature.

·         Nitrogenous bases are of two types, one Purines and the other type is Pyrimidines.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

www.chemwiki.ucdavis.edu

 

 

 

 

 

 

 

 

 

 

 

 

www.commons.wikimedia.org

 

A nucleotide

 

 

 

Purines, namely Adenine (A) and Guanine (G), each contain two heterocyclic rings with double bonds, and the bases are covalently linked to Ribose sugars at 1C’ by a glycosidic bond (between 9N’ of purine and 1C’ of pentose sugar), the resultant compound is called Nucleoside, which when added with a phosphate group to 5C’ of the sugar (i.e. CH2OH of the sugar), it forms an ester bond, and such a structure is called nucleotide.

 

Pyrimidines namely Cytosine(C), Thymine (T) and Uracil (U), each contain one heterocyclic ring with at least one double bond and they are linked to sugars through 1’N of pyrimidine with 1C’ of pentose sugar, which when added with a phosphate to 5’ it becomes pyrimidine nucleotide.

Each nucleotide is composed of:

  1. A Sugar:
  2. One of these four nitrogen bases:
    1. Purines - have a double ring of carbon and nitrogen atoms.
      • Adenine
      • Guanine
    2. Pyrimidines - have a single ring of carbon and nitrogen atoms.
      • Thymine
        • Thymine is replaced by uracil in RNA.
      • Cytosine
  1. A phosphate group - PO4
  2. Base pairing:  The base pairing is always complementary between Guanine and Cytosine, and adenine and thymidine. This is called as Watson-Crick base pairing rule.  There are deviations from this rule.  But there are variations in base pairing; they are called Hoogsteen base pairing and reverse Hoogsteen and reverse Watson-Crick base pairing.
  3. What is exclusive of this specific base pairing? This rule stems from the fact that Guanine exists in ketonic form and cytosine in amino form in native state; similarly adenine in amino form and thymidine in ketonic form.  This ionic form drive exclusive base pairing between G and C and A and T.  Otherwise any base could have base paired with any base.  Dr. Donahue provided this ionic state information to J.D Watson.

 

·         Characteristically, nucleotides exhibit specific conformation, which is very important in the 3D structural organization, stability and functions of DNA or RNA.  In general, where the distribution of nucleotides in the chain is random, the sugar moiety shows a configuration of C2’ endo (puckered inwards to the plane of the ring) and C3’ exo (puckered out ward of the plane of the ring), hence the 5’CH-O-phosphate group and the 1’C of the base are on the opposite sides of the sugar plane, so it is called anti-conformation, (because of sugar puckering) which is the most prevalent conformations in most of the ds DNAs. 

 

 

 

Nucleic Acid Architecture: Tomado de:

http://www.chembio.uoguelph.ca/educmat/chm730/h730.htm

 

“anti- extends the base and pentose rings in opposite directions. For pyrimidines, this means that O-2 faces away from the pentose.

syn- orients the base and the pentose in the same direction”.

Ribose ring pucker arises because a flat pentagon puts all ring C atoms into eclipsed conformations, despite the fact that the pentagon angle of 108o is very close to the C tetrahedral angle of 109.5o. Puckering relieves the steric conflict due to eclipsed groups, at the expense of a slight deviation from tetrahedral bond angle. The pucker is described in terms of the pentose ring atom that is displaced furthest out of plane. When an adjacent atom is slightly displaced to the opposite side, this gives the 'S' or 'N' pattern twists, according to the orientation of the zigzag.


twofold symmetry = antiparallel

 The X distribution of the diffraction pattern indicates 2-fold symmetry; hence an antiparallel pair of strands was used in the model.
The X-ray diffraction pattern provided by Miss. R. Franklin and Dr. Williams showed antipolarity of the helical strands and ionic phosphate groups are excluded from the center of the helix and found at the periphery of the helix. Did Watson and Crick give credit to Franklins’ work?  In a race to Nobel laureate title Linus Pauling and Franklin missed (Miss Franklin’s demise early robbed her credit to the discovery to intelligent ds DNA model).

 

 

 

 

Common base pair geometry

 

 

 

This general rule, however doesn’t apply under certain situation where the nucleotide sequence is 5’CG CG CG CG 3’ and its repeats.  In such cases, if the sequence is repeated and extends to 6 and more than six base pairs in a stretch, the purines especially Guanines take C2’exo, and C3’endo, this leads to cis configuration, that is both 5’CH2O-P group and the base at1’C are towards the same side of the plane of the sugar, because of one purine and one pyrimidine alternating to each other in a stretch of six or more base pairs force the sugar to such puckering, which renders the sugar in to stressed state.   On the contrary the pyrimidines configuration remains ‘anti’ conformation.  Such sequences (CG) n or (GC) n are localized in certain segments of the DNA; their position and the size varies from one species to the other.  Methylation of C s in CG repeats produces certain ‘syn’ configuration of G. 

 

All single stranded DNA and RNA molecules have nucleotides with anti configuration with respect to their sugar puckering conformation.  Nucleotides, because of their heterocyclic rings and double bonds, strongly absorb light at UV region I.E 250-280 nm.  As they possess heterocyclic rings with double bonds they show hydrophobic features.

 

 

 

 

Parameters of Major DNA Helices

Parameters

A Form

B Form

Z-Form

Direction of helical rotation

Right

Right

Left

Residues per turn of helix

11

10

12 base pairs

Rotation of helix per residue (in degrees)

33

36

-30

Base tilt relative to helix axis (in degrees)

20

6

7

Major groove

narrow and deep

wide and deep

Flat

Minor groove

wide and shallow

narrow and deep

narrow and deep

Orientation of N-glycosidic bond

anti

anti

anti for Pyrimidines, syn for Purines

Comments

 

most prevalent within cells

occurs in stretches of alternating purine-pyrimidine base pairs