Microsoft PowerPoint - Nucleic acid structure [Compatibility Mode]

The Structures of DNA and RNA DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides linked in a chain through phosphodiester bonds..

DNA Structure The building blocks of DNA are nucleotides, composed 3 components: –a 5-carbon sugar called deoxyribose –a phosphate group (PO4) –a nitrogenous base • adenine, thymine, cytosine, guanine, uracil.

DNA vs RNA If the sugar in a nucleotide is deoxyribose, the nucleotide is called a deoxynucleotide; if the sugar is ribose, the term ribonucleotide is used.

Nucleosides – RNA: adenosine, guanosine, cytidine, uridine – DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, (deoxy)thymidine DNA nucleoside RNA nucleoside The combination of a base and sugar is called a nucleoside.

Nucleotides The nucleotide structure consists of –the nitrogenous base attached to the 1’ carbon of deoxyribose –the phosphate group attached to the 5’ carbon of deoxyribose –a free hydroxyl group (-OH) at the 3’ carbon of deoxyribose.

Sugars O HOCH2 5’ 1’ 4’ 3’ 2’ O HOCH2 OH OH OH O HOCH2 OH H OH Ribose Deoxyribose Generic Structure Carbons are given numberings as a prime.

Conformation of ribose opposite side of the plane relative to the C-5’ atom same side of the plane relative to the C-5’ atom.

Bases - Purines N N N N 1 2 3 4 5 6 7 8 9 Adenine Guanine A G N N N N H NH2 N N N N H O H NH2.

Bases - Pyrimidines N N 5 6 1 2 3 4 Thymine Cytosine NH N O T O H H3C C N N NH2 O H Thymine is found ONLY in DNA. In RNA, thymine is replaced by uracil. Uracil and Thymine are structurally similar NH N O U O H Uracil Which are “keto” and which are “amino” pyrimidine bases?.

Each base has its preferred tautomeric form cytosine Guanine.

Common forms o Proton shift Thymine Guanine Cytosine Adenine Rare forms.

Phosphate Groups Phosphate groups are what makes a nucleoside a nucleotide Phosphate groups are essential for nucleotide polymerization P O O O O X Basic structure:.

Phosphate Groups Number of phosphate groups determines nomenclature P O O O O CH2 P O O O P O O O O CH2 Monophosphate e.g. AMP Diphosphate e.g. ADP Free = inorganic phosphate (Pi) Free = Pyro- phosphate (PPi).

Triphosphate e.g. ATP P O O O P O O O O P O O O CH2 Phosphate Groups No Free form exists.

DNA Structure Nucleotides are connected to each other to form a long chain phosphodiester bond: bond between adjacent nucleotides –formed between the 3’ –OH of one nucleotide and the phosphate group of the next nucleotide The chain of nucleotides has a 5’ to 3’ orientation. Nucleic acids are synthesized in a 5' to 3' direction..

CH2 Phosphodiester bond Base Base OH.

Nucleic Acid Structure Polymerization Nucleotide Sugar Phosphate “backbone”.

Double stranded Nucleic acids and Base pairing Most DNA exists in the famous form of a double helix, in which two linear strands of DNA are wound around one another. The major force promoting formation of this helix is complementary base pairing: A's form hydrogen bonds with T's (or U's in RNA), and G's form hydrogen bonds with C's..

DNA Structure The double helix consists of: – 2 sugar-phosphate backbones – nitrogenous bases toward the interior of the molecule – bases form hydrogen bonds with complementary bases on the opposite sugar-phosphate backbone • Adenine pairs with Thymine (2 H bonds) • Cytosine pairs with Guanine (3 H Bonds) Chargaff's Rules – Erwin Chargaff determined that • amount of adenine = amount of thymine • amount of cytosine = amount of guanine Chargaff's rule state that DNA from any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases.

Consequence of this disparity - Takes more energy (e.g. higher temperature) to disrupt GC-rich DNA than AT-rich DNA..

DNA Structure The two strands of nucleotides are antiparallel to each other –one is oriented 5’ to 3’, the other 3’ to 5’ The two strands wrap around each other to create the helical shape of the molecule..

McGraw-YW requred revo&.rctkm dap-lay_ 5' 3' Minor groove Major groove 3.4 nm 0.34 nm Major groove Minor groove 5' 3' 2 nm 3' 5'.

DNA is usually a right-handed double helix DNA is usually a right-handed double helix You can watch https://www.youtube.com/watch?v=nsvBg19YHXQ.

Does base-pairing have any relevance to biotechnology per se? yes! This simple chemistry is at the heart of •nucleic acid hybridization •polymerase chain reaction •antisense technology •mutagenesis and many other techniques commonly applied in biotechnology labs..

Forces involved in DNA Helix • Hydrogen bonds between complementary base pairs inside the helix (H bonds are not covalent and can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature) • Van der Waals base-stacking interaction.

Hydrogen Bonding determines the Specificity of Base Pairing, while stacking interaction determines the stability a helix. Hydrogen Bonding determines the Specificity of Base Pairing, while stacking interaction determines the stability a helix. H bonds contribute to thermodynamic stability and specificity of base pairing When polynucleotide strands are separate water molecules are lined up on the bases When bases come together in the double helix, the water molecules are displaced from the bases creating disorder and increase in entropy stabilizing the double helix.

Second contribution that stabilizes the double helix Stacking interactions between bases Bases are flat, relatively water insoluble molecules, stack on each other roughly perpendicular to the direction of the helical axis. Electron cloud interactions (π-π) between bases in the helical stacks contribute to the stability of double helix.

Secondary structure of DNA Major and minor grooves The double helix DNA has two asymmetric grooves. The larger groove is called the major groove while the smaller one is called the minor groove Asymmetric spacing of the antiparallel helix backbones.

Why? Consequence of the geometry of the base pair The angle at which the two sugars protrude from the base pairs on one edge is ~120° (that generates a minor groove) and ~ 240° on the other edge (that generates a major groove)..

These grooves provide a topography and allow recognition by proteins  The structure of DNA is such that the bases are protected (backbone, complementary H- bonds, base-stacking), but also accessible. Diameter and periodicity are consistent 2.0 nm 10 bases/ turn 3.4 nm/ turn.

DNA-Protein Interaction Major grooves: Rich in chemical information Important for recognition and binding Characteristic pattern of hydrogen bonding in major groove that distinguishes A:T base pair from a G:C or even that matter from T:A Important as it allows proteins to unambiguously recognize DNA sequences without having to open and disrupt the double helix.

A: Hydrogen bond acceptors D: Hydrogen bond donors H: nonpolar hydrogens M: methyl groups Chemical groups exposed in the major and minor grooves.

A D A M in the major groove signifies an A:T base pair A A D H stands for a G:C base pair. Likewise M A D A stands for T:A base pair and H D A A is characteristic of a C:G base pair The base pairs cannot be easily distinguished in minor groove. An A:T base pair is A H A and so is T:A base pair. Characteristic pattern of hydrogen bonding between base pairs.

Types of DNA Structures • Three forms of DNA – A form: right handed helix – B form: the most likely biological conformation, right handed helix – Z form: form a left handed helix.

A- DNA B-DNA Z-DNA Helix Right-handed Right-handed Left-handed Width Widest Intermediate Narrowest Planes of bases planes of the base pairs inclined to the helix axis planes of the base pairs nearly perpendicular to the helix axis planes of the base pairs nearly perpendicular to the helix axis Central axis 6Å hole along helix axis tiny central axis no internal spaces Major groove Narrow and deep Wide and deep No major groove Minor groove Wide and shallow Narrow and deep Narrow and deep DNA conformations.

DNA conformations A- DNA These following features represented different characteristics of A-form DNA structure: 1. Most RNA and RNA-DNA duplex in this form 2. Shorter, wider helix than B. 3· Deep, narrow major groove not easily accessible to proteins 4· Wide, shallow minor groove accessible to proteins, but lower information content than major groove. 5· Favored conformation at low water concentrations 6· Base pairs tilted to helix axis and displaced from axis 7· Sugar pucker C3'-endo (in RNA 2'-OH inhibits C2'- endo conformation) 8· Right handed 9· Size is about 24 Å 10· Needs 11 base pairs per helical turn 11· Glycosyl bond conformation is Anti.

• Normal DNA is Right-handed helix • 20 Å wide • C-2' endo sugar pucker conformation • One complete turn approximately every 10 base pairs (= 34 Å per repeat / 3.4 Å per base) • planes of the base pairs nearly perpendicular to the helix axis • two principal grooves, a wide major groove and a narrow minor groove B-DNA DNA conformations.

 Z-DNA formation occurs during transcription of genes, at transcription start sites near promoters  Left-handed helix; Narrowest  18 Å and there are 12 base pairs per helical turn  For pyrimidines, the sugar pucker conformation is C-2' endo and for purines, it is a C-3' endo  no major groove; narrow + deep minor groove Z-DNA DNA conformations.

B Z A.

Non-B DNA DNA molecule moves, fidgets, does gymnastics, dances. Certain sequences adopt unusual structures and have functional roles; they may favour DNA breaks and further deletions, amplification, recombination, and mutations..

GCGATACTCATCGCA Hairpin.

Holliday junctions (formed during recombination) are cruciform structures.

DNA Supercoiling Biological role of supercoiling •DNA compaction •Helps the opening of the double helix during DNA replication and transcription •Site-specific recombination.

What is Supercoiling? Positively supercoiled (left handed supercoiling) DNA is overwound Relaxed DNA has no supercoils 10.4 bp In addition to the helical coiling of the strands to form a double helix, the double stranded DNA molecule can also twist upon itself. Supercoiling occurs in nearly all chromosomes (circular or linear) Negatively supercoiled DNA (right handed supercoiling) is underwound (favors unwinding of the helix); DNA isolated from cells is always negatively supercoiled.

DNA Supercoiling The DNA molecule on the left is a relaxed, closed circle and has the normal B conformation. Breaking the DNA helix and winding it by two turns before re- forming the circle produces two supercoils. The supercoils compensate for the overwinding and restore the normal B conformation. The molecule on the right has a locally unwound region of DNA. This conformation is topologically equivalent to negatively supercoiled DNA..

The tertiary structure is similar to DNA, but with several important differences: • Single stranded but usually forms intra-molecular base pairs • major and minor grooves are less pronounced • Uracil instead of thymine • Structural, adaptor and transfer roles of RNA are all involved in decoding the information carried by DNA RNA Structure.

Types of RNA in the human genome.

What about double stranded RNA? RNAs are usually single stranded, but many RNA molecules have secondary structure in which intramolecular loops are formed by complementary base pairing. Base pairing in RNA follows exactly the same principles as with DNA: the two regions involved in duplex formation are antiparallel to one another, and the base pairs that form are A-U and G-C..

Secondary structure of RNAs.

Double-helical DNA and RNA can be denatured Reversible denaturation and annealing (renaturation) of DNA.