Nucleic acids.pdf

Unit 1: Nucleic acids Contents 1. DNA 2. RNA ✓ Watson – Crick model of DNA ✓ mRNA ✓ Prokaryotic DNA (C...

Unit 1: Nucleic acids Contents 1. DNA 2. RNA ✓ Watson – Crick model of DNA ✓ mRNA ✓ Prokaryotic DNA (Circular, Supercoiled, Palindromic) ✓ rRNA ✓ Plasmids ✓ Eukaryotic DNA (Repetitive sequences, split genes, ✓ tRNA nucleosomes) ✓ non-coding RNA ✓ Mitochondrial and chloroplast DNA ✓ micro RNA and Si RNA. ✓ Guanine quadruplex (G4) DNA  Nucleic acids Types of nucleic acids – DNA and RNA Nucleic acids are polymeric macromolecules made up of repeated units of monomeric 'nucleotides' Nucleotides: Sugar + phosphate + nitrogenous base. Nucleoside: Sugar + nitrogenous base.  Nucleotide Each nucleotide is made up of i. a sugar called deoxyribose ii. a phosphate group -PO4 iii. an organic base  Nitrogenous bases In 1950, Erwin Chargaff stated that, in DNA, the amount of T equals the amount of A and the amount of G equals the amount of C. A=T, G=C Thus, A+G=T+C  Major and minor grooves Major groove: nitrogen and oxygen atoms of the base pairs pointing inward toward the helical axis. Minor groove: nitrogen and oxygen atoms point outwards. The major groove is the site for protein recognition of specific DNA sequences or regions.  Sugar Puckering Sugar puckering is the process of twisting the sugar molecules in DNA. Essential for DNA's proper functioning. It makes the DNA double helix stable and strong. The sugar puckers in DNA/RNA structures are predominantly: i. C3′-endo in A-DNA or RNA ii. C2′-endo in B-DNA  Anti and Syn forms of nucleosides The N-glycosidic bond joins the 1'-carbon of the deoxyribose sugar to the heterocyclic base. Rotation about this bond gives rise to syn and anti conformations. anti conformation is more stable Peptide bond Watson – Crick model of DNA A- DNA  Watson – Crick model of DNA In 1953, Watson and Crick postulated a 3-dimensional model of DNA structure. According to their model, 2 helical DNA chains are wound around the same axis to form a right-handed double helix. The two chains are antiparallel (opposite polarity). The two strands are oriented in opposite directions, with one strand oriented in the 5’ to 3’ direction and the other strand oriented in 3’ to 5’ direction The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix and the purine and pyrimidine bases of both strands are stacked inside the double helix. The phosphate group bonded to the 5' carbon atom of one deoxyribose is covalently bonded to the 3' carbon of the next The DNA double helix, or duplex, is held together by 2 forces, hydrogen bonding between complementary base pairs (A=T and G≡C) and base-stacking interactions.  Watson – Crick model of DNA The base pairs are 0.34 nm apart in the DNA helix. A complete (360°) turn of the helix takes 3.4 nm. Therefore, there are 10 base pairs (bp) per turn. The external diameter of the helix is 2 nm. Because of the way the bases bond with each other, the two sugar-phosphate backbones of the double helix are not equally spaced from one another along the helical axis. This unequal spacing results in grooves of unequal size between the backbones; one groove is called the major (wider) groove, the otherthe minor (narrower) groove The complementarity between the DNA strands is due to the hydrogen bonding between base pairs. There is an average of 25 hydrogen bonds within each complete turn The phosphate groups in the backbone are ionized and negatively charged (at neutral pH), thus DNA is strongly acidic in nature. The helix can be virtually any length; when fully stretched, some DNA molecules are as much as 5 cm (2 inches) long.  Forms of DNA Deviations from the Watson-Crick DNA structure were found in cellular DNA. Watson and Crick proposed the strand complementarity, antiparallel strands, and the requirement for A=T and G≡C base pairs in the B- DNA which is the most stable form of DNA under physiological conditions Two structural variants, A and Z forms have been well characterized in crystal structures. Whether A-DNA occurs in cells is uncertain, but short stretches (tracts) of Z-DNA is found in both prokaryotes and eukaryotes. (Difference can be learned from journal)  Conditions Favoring A, B and Z-form of DNA Whether a DNA sequence will be in the A-, B- or Z-DNA conformation depends on at least three conditions. i. The ionic or hydration environment, which can facilitate conversion between different helical forms. A-DNA is favored by low hydration, whereas Z-DNA can be favored by high salt. ii. The DNA sequence: A-DNA is favored by certain stretches of purines (or pyrimidines), whereas Z-DNA can be most readily formed by alternating purine-pyrimidine steps. iii. The presence of proteins can bind to DNA in one helical conformation and force the DNA to adopt a different conformation. In living cells, most of the DNA is in a mixture of A and B-DNA conformations, with a few small regions capable of forming Z-DNA.  Hoogsteen base pairing Thymine (T) can bind to a Watson–Crick base-pairing of T-A by forming a Hoogsteen hydrogen bond. Thymine hydrogen bonds with the adenosine (A) of the original double-stranded DNA to create a T-A*T base-triplet. Under acidic conditions, a protonated cytosine, represented as C+, can form a base-triplet with a C-G pair through Hoogsteen base-pairing, forming C-G*C+. The TA*T and CG*C+ base pairs are the most stabilized triplet- base pairs that can form, while a TA*G and CG*G are the most destabilized triplet-base pairs. In a Hoogsteen base pair, the N7 position of the purine base (as a hydrogen bond acceptor) and C6 amino group (as a donor), bind the Watson–Crick (N3–C4) face of the pyrimidine base Function: Triple-stranded DNA has been implicated in the regulation of several genes. Triplex DNA  Triplex DNA Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. A triplex is formed when a single DNA strand binds to the major-groove of a Watson–Crick duplex. The bases of the third strand form hydrogen-bonds to the duplex purine strand, forming Hoogsteen or reverse Hoogsteen pairs. Nucleotides participating in Watson-Crick base pair can form a number of additional hydrogen bonds; e.g., a cytidine residue (if protonated) can pair with the guanosine residue of a G≡C nucleotide pair, and a thymidine can pair with the adenosine of an A=T pair (called Hoogsteen pairing) This allows the formation of triplex DNAs.  Characteristics of Prokaryotes Comprise of eubacteria and archaebacteria. Cells lack a nucleus and other organelles. Most prokaryotes are small, single-celled organisms that have a relatively simple structure. The cells are surrounded by a plasma membrane, but they have no internal membrane-bound organelles within their cytoplasm.  Prokaryotic DNA / Nucleoid In prokaryotes genetic material is in the form of a single molecule or chromosome. The chromosomes of most bacteria are circular, double-stranded DNA, but some bacteria may have a linear chromosome. Prokaryotes lack a distinct nucleus, but have an irregularly shaped central area containing DNA and protein known as the nucleoid. It has a central protein core from which supercoiled loops of DNA radiate. Nucleoid proteins resemble the histone proteins found in eukaryotic chromosomes which help the folding of the DNA into its compact structure. Some bacteria, have more than one chromosome, eg. Vibrio cholerae and Borrelia burgdorferi (causative agents of cholera and Lyme disease, respectively).  Size and Shape of DNA Molecules The size of a DNA molecule is expressed as the number of nucleotide bases or base pairs per molecule. Thus, a DNA molecule with 1000 bases is 1 kilobase (kb) of DNA. If the DNA is a double helix, then kilobase pairs (kbp) is used. Thus, a double helix of 5000 base pairs in size would be 5 kbp. When dealing with large genomes, the term megabase pair (Mbp) for a million base pairs is used.  Chromosome of Escherichia coli Escherichia coli has about 4.64 Mbp of DNA in its chromosome. Each base pair is 0.34 nm in length along the double helix, and each turn of the helix contains approx. 10 base pairs. Therefore, 1 kbp of DNA is 0.34 μm long with 100 helical turns. (1000nm = 1 μm) The E. coli genome is thus 4640 X 0.34 μm = 1.58 mm long. Since cells of E. coli are about 2 μm long, the chromosome is several hundred times longer than the cell itself.  Supercoiling The DNA molecule is extremely long relative to the dimensions of a cell and has to be organized and packed into the cell genome by supercoiling. Enzymes called Topoisomerases introduce additional turns into the double helix that causes the DNA strand to wind up on itself and adopt a more compact form. Positive supercoiling: The topoisomerases break the DNA polynucleotide and rotate the two ends relative to each other. The enzyme then rejoins the ends and the polynucleotide reacts by winding up on itself. Negative supercoiling: Topoisomerases can also remove coiling in a process called negative supercoiling by creating a turn in the opposite direction.  Palindromic DNA A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule wherein reading in a certain direction (e.g. 5' to 3') on one strand matches the sequence reading in the same direction (e.g. 5' to 3') on the complementary strand. There are two types: 1. Palindromes that occur on opposite strands of the same section of DNA helix. 5' GGCC 3’ 3' CCGG 5‘ 2. Inverted Repeats: In this case, two different segments of the double helix read the same but in opposite directions. 5' AGAACAnnnTGTTCT 3' 3' TCTTGTnnnACAAGA 5'  Plasmids Plasmids are small, double-stranded, autonomously replicating extrachromosomal DNA molecules Exist both as circular and linear plasmids, but most known plasmids are circular. Have few genes, generally less than 30. Genetic information contained in plasmids is not essential to the bacterium, and cells that lack them usually function normally. But, many plasmids carry genes that confer a selective advantage to the bacterium in certain environments. Plasmids size ranges from 1kb upto 250 kb in length. Types, based on copy number: i. Stringent plasmids: Plasmids having a low copy number with just one or two copies present. ii. Relaxed plasmids: Plasmids having a high copy number with 10 or more plasmid molecules present  Plasmids Some small plasmids use the cells enzymes to replicate while the larger plasmids may carry genes that encode their own replicative enzymes. Some plasmids integrate into the host genome. This integrated form of plasmid is called an Episome and replicates as part of the chromosome. Plasmids are inherited stably during cell division, but they are not always equally apportioned into daughter cells and sometimes are lost. The loss of a plasmid is called curing. It can occur spontaneously or be induced by treatments that inhibit plasmid replication but not host cell reproduction. Some commonly used curing treatments are acridine mutagens, ultraviolet and ionizing radiation, thymine starvation, antibiotics, and growth above optimal temperatures.  Types of Plasmids Many different types of plasmids are found in bacteria. They are classified according to the genes they carry and the characteristics they confer on the host cells. Major types of plasmids identified are: 1. Resistance (R) plasmids 2. Fertility (F) plasmids 3. Col plasmids 4. Degradative plasmids 5. Virulence plasmids  Types of Plasmids Resistance (R) plasmids Fertility (F) plasmids Col plasmids Degradative plasmid Virulence plasmids Cryptic Plasmids Carry genes that make plasmids allow genes to contain genes that Helps the host plasmids confer the Do not have any bacteria resistant to be transferred between make bacteriocins (also bacterium digest ability to cause disease apparent effect on the antibiotics such as bacterial cells through known as colicins), compounds that are to the bacterium phenotype of the cell ampicillin and conjugation which are proteins that not commonly found in harboring them. chloramphenicol kill other bacteria and nature, such as thus defend the host camphor, xylene, bacterium toluene, and salicylic acid. Carry one or more F plasmid contains These plasmids contain Eg. Ti plasmid in They code for enzymes antibiotic resistance genes that direct the genes for special Agrobacterium required for their genes transfer of the F enzymes that break tumefaciens that causes replication and plasmid from one down specific Crown Gall disease in maintenance in the bacterial cell to another compounds. plants. host cell. via sex pilus. frequently The F plasmid may carry Salmonella enterica accompanied by the additional genes which contains virulence genes encoding it acquires from the plasmids. virulence determinants, chromosome and these specific enzymes or are transferred to the resistance to toxic recipient cell during heavy metals conjugation. Eg. RP4 plasmid in Eg. F factor Eg. ColE1 of E.coli Pseudomonas and other bacteria Types of Plasmids  Applications of Plasmids As a vector, plasmids have many applications. Softwares enable us to record DNA sequences of plasmids and know their significance. Applications of plasmids are : i. In Genetic engineering: Plasmids help amplify, or produce many copies of certain genes and code for proteins in cells. Eg. Production of insulin in E.coli cells. ii. In Gene therapy: Plasmids can be used to transfer genes into human cells. If a patient has a hereditary disorder involving a gene mutation and his cells lack a specific protein, inserting a plasmid into his DNA would allow cells to express the protein that they are lacking.  Eukaryotic DNA Eukaryotic genome is compacted into several linear chromosomes by histone proteins to form a nucleosome. The nucleosomes are then folded into chromatin fibers. The degree of DNA packing changes throughout the cell cycle. Two forms of chromatin are: i. Euchromatin: The chromosomes or regions of chromosomes that show normal cycle of chromosome condensation and decondensation in the cell cycle. ii. Heterochromatin: The chromosomes or chromosomal regions that usually remain condensed— more darkly staining than euchromatin— throughout the cell cycle, even in interphase. Contains a telomere and a centromere region. Telomere: A specific set of sequences at the end of a linear chromosome, stabilizes the chromosome and is required for replication. Each chromosome has two ends and, therefore, two telomeres. Centromere: The region of a chromosome containing DNA sequences to which mitotic and meiotic spindle fibres attach.  Eukaryotic DNA (Repetitive sequences, split genes, nucleosomes) DNA sequences appear many times within a genome. DNA sequences may be categorized as:- i. Single copy DNA sequences/unique-sequences DNA - Present in one to a few copies in the genome. It makes up approx. 55–60% of the genome. ii. Moderately repetitive DNA sequences - Present in 10 - 105 copies in the genome. Found throughout the euchromatin. Average 300bp in size. involved in regulation of gene expression. May be classed as:- a) Microsatellites / Minisatellites (VNTR, DNA 'fingerprints). b) Dispersed-repetitive DNA, mainly transposable elements (LINES/SINES). iii. Highly repetitive DNA sequences (satellite DNA) - Present in about 105 to 107 copies in the genome.  Eukaryotic DNA Unique DNA repetitive DNA sequences Moderately repetitive DNA Highly repetitive DNA sequences sequences dispersed repeated DNA/interspersed tandemly repeated DNA repeated DNA long interspersed elements (LINEs) Minisatellites short interspersed elements (SINEs) Microsatellites Repetitive sequences can be arranged within the genome in one of two ways: i. Distributed at irregular intervals, known as dispersed repeated DNA or interspersed repeated DNA. ii. Repeats clustered together so that the sequence repeats many times in a row is known as tandemly repeated DNA.  Repetitive DNA sequences Dispersed repeated DNA sequences Tandemly Repeated DNA sequences Consists of a family of repeated sequences interspersed Arranged one after another in the genome in through the genome with unique sequences of DNA. head to tail organization. Small numbers of families have very high copy numbers Common in eukaryotic genomes. and makeup most of the dispersed repeated sequences in the genome. Short sequences 1-10 bp long or associated with Much of moderately-repeated DNA consists of genes and much longer sequences. transposable elements. The greatest amount of tandemly repeated DNA Both types of elements are considered to be retrotransposable (i.e. can replicate via an RNA copy is in centromeres and telomeres. reinserted as DNA by reverse transcription). At each centromeres there are 100-1000 copies They have significant roles in genomic function and of simple, short tandemly repeated sequences evolution. (highly repetitive sequences). The majority of inserted elements are truncated and often rearranged relative to full-length elements. Types of Dispersed repeated DNA sequences {Transposable elements (mobile genetic elements)}  Long interspersed elements (LINEs) Short interspersed elements (SINEs) 1. LINEs (long interspersed nuclear elements) 1. SINEs (short interspersed nuclear elements) are a type of are longer non-LTR retrotransposons. much shorter non-LTR retrotransposons. 2. Each LINE is around 1000- 7000 base pairs 2. They are about 100 to 700 base pairs in length. long. 3. SINEs are also DNA elements that amplify themselves 3. They are widespread in the genomes of throughout eukaryotic genomes through RNA eukaryotes. intermediates. SINEs make up about 13% of the 4. They make up 21.1% of the mammalian mammalian genome. genome. 4. The internal regions of SINEs originate from tRNA. 5. LINEs can transcribe into mRNA and 5. It remains highly conserved. translate into a protein that can function as 6. The copy number variation and mutations in the SINEs can a reverse transcriptase enzyme. be incorporated to construct the phylogeny-based This reverse transcriptase produces DNA classification of species. copies of the LINEs RNA. 7. SINEs can be grouped into three main types: CORE-SINEs, 6. These DNA copies can be integrated into V-SINEs, and AmnSINEs. the genome at a new site. 8. Alu element is the most common SINE in primates. 9. When SINEs insert within or near exons, they can cause improper splicing or change the reading frame. This leads to disease phenotypes such breast cancer, colon cancer, leukaemia, haemophilia, cystic fibrosis, colon cancer, Dent’s disease, neurofibromatosis, etc.  Tandemly Repeated DNA sequences alpha-satellite DNA is an example of tandemly repeated sequence This is a highly repetitive sequence, each centromere contains a tandem array of alpha-satellite repeats that extend for millions of base pairs and are arranged in a hierarchy of higher order repeats. These vary between 100-5000 on different chromosomes (0.2-10 Mb). Some contain 17bp binding sites for the centromere-specific DNA binding protein CENP-B. They have been recently cloned and used to construct artificial human chromosomes.  VNTR Minisatellites and microsatellites, together are classified as VNTR (variable number of tandem repeats) DNA occur at more than 1,000 locations in the human genome repeated 5-50 times. repeated 5-50 times.  Split Genes Gene is a continuous, uninterrupted sequence of nucleotides which codes for a single polypeptide chain. Sequences of some eukaryotic genes are interrupted by nucleotides that are not represented within the amino acid sequence of the protein. Genes are first transcribed into hnRNA (heterogeneous RNA), and then excised (spliced) and the interrupting sequence is removed, and not included in the mature mRNA - translated into protein. These interruptions are - introns, inserts, intervening sequences or ‘silent’ DNA. Sequences which are included in the mRNA and translated are called exons. Although the coding regions are interrupted, they are present in the same order in the genome as in the mRNA. Therefore are called split genes. No split genes are reported yet in prokaryotes.  Split Genes Two types of split gene sequences Normal sequence (exons) Interrupted sequence (introns) Sequence of nucleotides that is included in interrupted sequences are not included into the mRNA and is translated. mRNA which is transcribed from DNA of split genes. sequences code for a particular polypeptides These sequences do not code for any chain peptide chain.  Split Genes - Characteristics Each interrupted gene begins with an exon and ends with an exon. The exons occur in the same precise order in the mRNA in which they occur in the gene. The same interrupted gene organisation is consistently presented in all the tissues of organisms. Most introns are blocked in all reading frames. i.e. termination codons occur frequently in their three reading frames. Therefore, most introns don’t have coding functions. In some cases, different exons of a gene code for different active regions of the protein molecule. E.g. antibodies. Thus, introns are relics of evolutionary processes that bring together different ancestral genes to form new larger genes. Introns may provide increased recombination rates between exons of a gene and may be of significance in genetic variation. Introns are known to code for enzymes involved in the processing of hn RNA.  Nucleosomes DNA is about 3 meters long and it has to be packed in a nucleus, which is only a few µm in diameter. In order to fit DNA into the nucleus, it must be packaged into a highly compacted structure known as chromatin. In the first step of the process, DNA is condensed through nucleosome assembly. Nucleosome is the fundamental repeating subunits of all eukaryotic chromatin. A nucleosome is about 11 nm in diameter and consists of a core of eight histone proteins two each of H2A, H2B, H3, and H4 around which a 147-bp segment of DNA is wound. It resembles "beads on a string of DNA" when observed with an electron microscope. Formation of nucleosomes: About 146 bp of DNA are wrapped 1.8 times in a left handed helix around the outside of an octamer of histones. It then Interacts with one molecule of histone H1 to form a particle containing ~166 bp of DNA called chromatosome. The chromatosome links with the linker DNA forming a nucleosome containing ~200 bp of DNA.  Chromosomal proteins Eukaryotic chromosomes are made up of DNA and proteins. 2 major types of proteins associated with DNA in the chromatin: 1. Histone proteins 2. Non Histones proteins 1. Histones Most abundant proteins associated with the chromosomes. They are very rich in basic proteins. At normal pH of the cell, the histones have net positive charge that facilitates their binding to the negatively charged DNA. This positive charge is found mainly on the amino group of the side chains of the basic amino acids lysine and arginine. Histones lack tryptophan. Histones are highly modified proteins, and the modifications include acetylation, methylation and phosphorylation.  Chromosomal proteins 1. Histones 5 major types of histones associated with eukaryotic DNA. Each class of histone consists of a: N – terminal, which is hydrophobic. C – terminal, which is hydrophilic. Central globular structure, which forms the central molecule. H2A, H2B, H3 and H4 together form an octamer while H1 links to the linker DNA outside the octamer. Functions of histones: 1. Depress the genetic activity: As the histones increase the compaction of the DNA , it depresses the genetic activity. 2. Structural role: They play a structural role in the packaging of DNA molecules and hence render them more compact.  Non histones They are all the proteins associated with the DNA apart from the histones. They are very different from histones. They are acidic proteins i.e. have a net negative charge and likely to bind the positively charged histones. Functions of non - histones i. Structural: They play a structural role in the shape of the chromosome. ii. Regulatory: They positively regulate the gene expression and stimulate genetic activity. They play an essential role in the transcriptional and translational activity. iii. Enzymatic: many enzymatic activities are associated with chromatin. Enzymes of chromosomal metabolism [ nucleic acid polymerases, nucleases] and enzymes of histone metabolism are all non – histone proteins.  Packaging DNA in Chromosomes various orders of packaging: i. First order of packaging : nucleosomes ii. Second order of packaging : solenoid fiber iii. Scaffold loop. iv. Chromatid. v. Chromosome.  Packaging DNA in Chromosomes Interaction between the DNA and histones takes place between negatively charged phosphates of DNA and positively charged groups of histone. The major electrostatic interaction of DNA phosphates are with the globular part of the core. The other interactions include hydrogen bonding between oxygen of phosphates of the DNA and histones. Thus this shows that DNA doesn’t appear to be buried into the core but contacts it at widely separated points. Solenoid model of nucleosomes: According to this model, the 10 nm fibre of nucleosomes gets coiled upon itself to form a 30 nm wide helix. This 30 nm structure is called as solenoid. It has 5 or 6 nucleosomes per helix. The histone N – terminal tails direct the DNA to wrap around the histone octamer disc. These N – terminals are thus required for the formation of 30 nm fibre as they interact with adjacent nucleosomes by making multiple H – bonds and thus stabilising the 30 nm fibre.  Mitochondrial DNA Mitochondrial DNA (mtDNA) is the circular chromosome found inside the cellular organelle - mitochondria. Each mitochondrion contains several copies of DNA, and as each cell has many mitochondria, the number of mtDNA molecules per cell is very large. Most mtDNA molecules are circular, but in some species, such as the algae and the ciliate Paramecium aurelia are linear. In humans the mtDNA is 16,571 bp long and contain 37 genes. All the genes are essential for normal mitochondrial functioning. 13 of these genes encode enzymes involved in oxidative phosphorylation, 2 genes encode ribosomal RNAs, 22 genes encode transfer RNAs. Many of these macromolecules are encoded by mitochondrial genes, but some are encoded by nuclear genes and therefore are imported from the cytosol. Mitochondrial DNA molecules vary in size, from about 6 kb to 2500 kb.  Difference between mtDNA and nuclear DNA mtDNA nuclear DNA Shape Mitochondrial genome is circular nuclear genome is linear Size genome contains 16,569 DNA base pairs nuclear genome contains 3.3 billion DNA base pairs Genes. genome contains 37 genes that encode 13 proteins, 22 tRNAs, and Genome contains more than 30,000 genes 2 rRNAs Not able to independently produce all of the proteins needed for able to independently produce all of the proteins needed functionality and relies on imported nuclear gene products. for functionality Packaging genome is not enveloped, and is it not packaged into chromatin. genome is enveloped, and packaged into chromatin. inheritance mitochondrial mode of inheritance is strictly maternal. Therefore, nuclear genomes are inherited equally from both mitochondria-associated disease mutations are also always parents. inherited maternally. copy One mitochondrion contains dozens of copies of mtDNA and each only one copy of nuclear genome is present in a cell cell contains numerous mitochondria. Therefore, a cell contains several thousand copies of its mitochondrial genome. Non-coding genome contains few, noncoding DNA sequences. 3% of the Genome contains 93% of noncoding DNA sequences sequences genome is noncoding DNA Mitochondrial genes on both DNA strands are transcribed in a nuclear genes are usually transcribed one at a time polycistronic manner:  Chloroplast DNA Chloroplast DNA (cpDNA) is the DNA present in the organelle chloroplast. cpDNA is circular and range from 120 to 160 kb in size, with about 120 genes There are about 15 chloroplasts per cell, and each contains about 40 copies of the cpDNA. Each cpDNA includes genes for rRNAs, tRNAs, some ribosomal proteins, photosystem enzymes involved in capturing solar energy, catalytically active subunit of the enzyme RuBisCo (ribulose 1,5-bisphosphate carboxylase), and four subunits of a chloroplast-specific RNA polymerase. Functional chloroplasts depend on the coordinated activities of both nuclear and chloroplast gene products  Similarity between cpDNA and mtDNA Both cpDNA and mtDNA are extranuclear DNA. They are semi-autonomous, self-reproducing cytoplasmic structure, with their own genetic system. Both of them are maternally inherited and have endosymbiotic origins. cpDNA, though, are larger and more complex than mtDNA. cpDNA has about 120 genes whereas mtDNA has about 37 genes. Both of them encodes for proteins and RNAs vital to their functions. mtDNA encodes for proteins of electron transport chain involved in aerobic respiration (ATP synthesis). cpDNA, encodes for proteins essential to photosynthesis. Both cpDNA and mtDNA occur in multiple copies since there are several chloroplasts and mitochondria occurring inside a cell. A cell often contains thousands of copies of mtDNA and cpDNA. During mitosis and meiosis, mitochondria and chloroplasts randomly segregate.  Guanine quadruplex (G4) DNA In in vitro conditions Guanine bases have an unusual capacity to associate with one another Four Guanine can form a planar G-tetraplex The hydrogen bond of these 5 Guanine bases bond with each other Formation of this structure usually describes the G rich sequences in vitro