The Cell - Challenges in Delivery of Therapeutic Genomics and Proteomics - page 8

bonds between base pairs and consequent strand separation. This separation may be
partial or complete, and leads to an increase in the ultraviolet (UV) absorption prop-
erties called hyperchromicity. The DNA reverts back to double helical structure or
anneals when temperature or pH is favorable. Complete separation requires a longer
time to anneal compared to partial separation. First, a small region anneals by colli-
sions, and then the whole strand zippers together very fast. DNA double-helix for-
mation can therefore be confirmed from its hypochromic effect on UV absorption.
The meltdown temperature is species specific and determined by base composition
of DNA in that species. Species having higher G-C content show higher meltdown
temperature on account of tighter bonding between G-C compared to weaker bond-
ing between the A-T base pair. RNA duplexes and RNA-DNA hybrids can also be
denatured in a similar way. If DNA from two species are denatured together in a
solution and allowed to anneal, some hybrid duplexes also form, indicating common
evolution. Hybridization is an important biotechnological tool for detecting a specific
RNA or DNA.
Mutations are the permanent alterations in the DNA sequence structure and affect
the genetic message and thus its expression. There are several reasons for the muta-
tive changes such as oxidative damage, presence of alkylating agents, exposure to
near UV radiations, spontaneous deamination of bases, and so on. All such reasons
bring about permanent and inheritable changes in the genome, resulting in faulty
expression of the genetic message [1-16] .
1.2.1 DNA Supercoiling
There are several stages in the life of a cell, and the structure of chromosomes also
varies with the stage. During interphase, they exist as a network of long, entangled,
thin strands of DNA, and as the cell approaches the division stage, they become con-
densed and compacted.
The long-stranded DNA molecules are condensed into the chromosome to allow
packaging into the eukaryotic chromosome and also to aid in their allocation into
daughter cells during cell division. A number of proteins help the DNA to coil and
wind, organizing into loops, rosettes, and so forth, with an increasing complexity
that enables it to condense into manageable size without entanglement ( Fig. 1. ).
However, this organization is so perfectly managed that essential activities like repli-
cation, repair, transcription, and so on, are not hindered. Each chromosome is a long
linear molecule that links with several proteins to form a compacted structure. This
DNA and protein network is called a chromatin. Each somatic cell contains pairs of
similar chromosomes called homologous chromosomes.
The proteins that bind to the DNA are known as histone proteins and nonhistone
proteins. The first level of compaction is a nucleosome, which is a “beads-on-a-
string” structure where the core is a group of eight histones, (two of each H2A, H2B,
H, and H) and the DNA is the string. They are further condensed into a 0-nm
chromatin fiber with the aid of the fifth histone, H1. The nucleosomes become
organized into regular repeating arrays providing around 100-fold condensations.
Further compaction is less understood but involves attachment of a 0-nm fiber to