functions in the body. RNAs and thus proteins are, therefore, essential mediators of what is
written in our instruction manual DNA. Which parts of the DNA are transcribed into RNA
and finally translated into proteins vary between the different cell types, depending on the
cell’s differentiation status. Thus, for example, a brain cell (neuron) shows a different gene
expression pattern than a liver cell (hepatocyte) (the gene expression pattern is thereby also
the reason to be a neuron and hepatocyte, respectively). Which genes are expressed in cells
is highly regulated by multiple complex molecular mechanisms affecting either the DNA,
RNA, or protein level [6, 7]. The different possible sequencing structures, their origin, and
NGS applications are depicted in Fig. 1.4.
1.2.1 DNA
DNA stands for Deoxyribonucleic acid and is a macromolecule (composed of smaller
molecules). The backbone of the DNA consists of alternating molecules: deoxyribose and
phosphate, complemented by the important nucleobases A (Adenine), C (Cytosine), G
(Guanine), and T (Thymine) bound to the deoxyribose. Thus, the genetic code is written by
those four letters. The DNA molecule is double-stranded, orientated antiparallel, and
3-dimensionally organized as a helix.
The nucleotides are held together by intermolecular hydrogen bonds between the two
strands, whereby A only pairs with T and G only pairs with C (complementary base
pairing). Consequently, if you know the sequence of one strand, you automatically know
the sequence of the other one (Fig. 1.1). The directionality of the DNA is determined by the
polarity of the molecules and is given in 5’ to 3’ direction (Fig. 1.1). Thus, a DNA sequence
TGCCA may need to be considered:
• in reverse, ACCGT
• as a complement, ACGGT
• as a reverse complement, TGGCA
The two strands are labeled arbitrary:
• positive/negative; +/À
• positive/negative
5´
A
C
T
G
A
C
C
G
A
A
3´
|
|
|
|
|
|
|
|
|
|
3´
T
G
A
C
T
G
G
C
T
T
5´
Fig. 1.1 Schematic illustration of DNA
1 Next Generation Sequencing (NGS): What Can Be Sequenced?
3
written in our instruction manual DNA. Which parts of the DNA are transcribed into RNA
and finally translated into proteins vary between the different cell types, depending on the
cell’s differentiation status. Thus, for example, a brain cell (neuron) shows a different gene
expression pattern than a liver cell (hepatocyte) (the gene expression pattern is thereby also
the reason to be a neuron and hepatocyte, respectively). Which genes are expressed in cells
is highly regulated by multiple complex molecular mechanisms affecting either the DNA,
RNA, or protein level [6, 7]. The different possible sequencing structures, their origin, and
NGS applications are depicted in Fig. 1.4.
1.2.1 DNA
DNA stands for Deoxyribonucleic acid and is a macromolecule (composed of smaller
molecules). The backbone of the DNA consists of alternating molecules: deoxyribose and
phosphate, complemented by the important nucleobases A (Adenine), C (Cytosine), G
(Guanine), and T (Thymine) bound to the deoxyribose. Thus, the genetic code is written by
those four letters. The DNA molecule is double-stranded, orientated antiparallel, and
3-dimensionally organized as a helix.
The nucleotides are held together by intermolecular hydrogen bonds between the two
strands, whereby A only pairs with T and G only pairs with C (complementary base
pairing). Consequently, if you know the sequence of one strand, you automatically know
the sequence of the other one (Fig. 1.1). The directionality of the DNA is determined by the
polarity of the molecules and is given in 5’ to 3’ direction (Fig. 1.1). Thus, a DNA sequence
TGCCA may need to be considered:
• in reverse, ACCGT
• as a complement, ACGGT
• as a reverse complement, TGGCA
The two strands are labeled arbitrary:
• positive/negative; +/À
• positive/negative
5´
A
C
T
G
A
C
C
G
A
A
3´
|
|
|
|
|
|
|
|
|
|
3´
T
G
A
C
T
G
G
C
T
T
5´
Fig. 1.1 Schematic illustration of DNA
1 Next Generation Sequencing (NGS): What Can Be Sequenced?
3