8/29/11 (Unit II) Chapter 6: The Structure of DNA Introduc;on to DNA Structure: The Importance of DNA Structure • 
DNA, since it carries all the informa;on for a given organism, must be a molecule that contains an incredible amount of informa;on • 
Contains informa;on for proper development of an organism – 
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Contains the informa;on for proper cellular func;on – 
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Allows the proper structures to form at the appropriate ;me Allows appropriate growth at the appropriate ;me DNA encodes the informa;on to produce proteins involved in respira;on DNA encodes the informa;on to produce proteins that are important in sending and receiving signals between cells All the appropriate informa;on is also passed on to subsequent genera;ons – 
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Cellular reproduc;on (asexual) Organismal reproduc;on (sexual or asexual) 1 8/29/11 Introduc;on to DNA Structure: How It Holds The Informa;on of Heredity • 
The ability of DNA to hold all of this informa;on lies in both its chemistry and 3-­‐
Dimensional structure • 
DNA contains only five different types of atoms – 
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When Watson and Crick (1952) discovered that the 3-­‐Dimensional structure of DNA – 
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Carbon Phosphorous Nitrogen Hydrogen Oxygen Found that the molecule takes the shape double helix More importantly understood how the different atoms found in DNA are covalently linked together and how these linkages are viewed in 3-­‐dimensions Watson and Crick saw that DNA was a polymer made of repea;ng building blocks known as nucleo;des Building the DNA Molecule: The Chemical Structure of Deoxyribonucleic Acid • 
Each nucleo;de consists of three basic components –  Phosphate group –  A five carbon sugar (deoxyribose) –  A nitrogenous base • 
The phosphate group and the deoxyribose are part of the DNA backbone, whereas the nitrogenous bases are located towards the interior of the DNA molecule • 
More specifically, it is the sequence and number of these nitrogenous bases (which are part of nucleo;des) that give each gene its own iden;ty –  Genes differ in the number of bases –  Genes differ in the sequence of bases 2 8/29/11 Building the DNA Molecule: Nucleo;de Structure and The Pentose Sugars •  To start, each nucleo;de will contain a central pentose (5 carbon) sugar •  The sugar that is used in DNA is deoxyribose •  Within the ring, there are four carbon atoms (labeled 1’, 2’, 3’ etc) joined by an oxygen atom •  The fi[h carbon (the 5’ carbon) projects upward from the ring •  To build the nucleo;de, we are going to a\ach other chemically reac;ve groups to specific carbons in the pentose sugar Building the DNA Molecule: The Nitrogenous Base Component •  The presence of the nitrogenous bases in nucleic acids was discovered by Friedrich Miecher a[er he started to determine the chemistry of his nuclein •  They are called nitrogenous bases due to the fact that they are have a high nitrogen content •  They are considered a base due to the fact that they have the proper;es of a base (proton acceptors) •  By and large, the structure of DNA the nitrogenous bases are non-­‐polar, which is important for DNA structure –  The bases are hydrophobic –  The bases are located towards the interior of a molecule of DNA 3 8/29/11 Building the DNA Molecule: The Nitrogenous Base Component • 
There are four common nitrogenous bases found in DNA – 
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Adenine Guanine Cytosine Thymine • 
Adenine and Guanine are known as purines and have a double ring • 
Cytosine, Thymine are known as pyrimidines and have a single ring Building the DNA Molecule: The Nitrogenous Base Component • 
In nature, each nitrogenous base can take one of two conforma;ons • 
For the nitrogenous bases, there are two conforma;ons – 
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Defini;on of Tautomers: – 
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Tautomers are isomers that readily interconvert at equilibrium Tautomeriza;on results in the migra;on of a proton and a resul;ng shi[ from single to double bond, or vice versa The two states in equilibrium with each other – 
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Conven;onal form Tautomeric state Conven;onal Tautomeric For all of the nitrogenous bases, the equilibrium strongly favors the conven;onal form 4 8/29/11 Building the DNA Molecule: Nucleo;de Structure and The Phosphate Group • 
The chemistry of the phosphate group is important in allowing DNA to be a polymer (i.e. the phosphate group is important in linking nucleo;des together) • 
The phosphate group consists of a phosphorus and four oxygen atoms • 
The phosphorous is located centrally in the phosphate group, and each of the four oxygen atoms are bound to the phosphorous • 
The bonds between the phosphorous and each oxygen atom is unequal –  They share electrons unequally –  Oxygen atoms are slightly nega;ve –  Phosphate is slightly posi;ve Building the DNA Molecule: Nucleo;de Structure and The Phosphate Group • 
At physiological pH, the phosphate group is a proton donor – 
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Phosphate group is polar Phosphate group has a slight nega;ve charge Ester bonds link the phosphate to the rest of the nucleo;de – 
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They have the property of being extremely stable These bonds are easily broken by enzyma;c hydrolysis (by adding water) • 
The chemistry of the phosphate group also allows for linking of nucleo;des together • 
Phosphate bonds are stable, yet easily broken – 
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Allows for polymeriza;on of nucleo;des Allows for synthesis of DNA (or RNA) chains 5 8/29/11 Building the DNA Molecule: Construc;ng a Nucleo;de-­‐The Basic Building Block of DNA • 
To build a nucleo;de one must start with a nucleoside • 
A nucleoside consists of only a pentose sugar and a nitrogenous base • 
The nitrogenous base is bound to the 1’ carbon through an N-­‐glycosidic linkage, which is formed through a condensa;on reac;on • 
There are proper naming conven;ons for each type of nucleoside – 
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Deoxyguanosine (if containing guanine and dexoyribose) Deoxycy;dine (if containing cytosine and deoxyribose) Deoxyadenosine (if containing adenine and deoxyribose) Deoxythymidine (if containing thymine and deoxyribose) Building the DNA Molecule: Construc;ng a Nucleo;de-­‐The Basic Building Block of DNA • 
In a nucleo;de the phosphate group is bound to the 5’ carbon • 
Like the nitrogenous base and the phosphate group are added to the pentose via condensa;on reac;ons with water as the byproduct • 
A nucleo;de can have one, two or three phosphates bound to the 5’ carbon –  The phosphate that is bound to the 5’ carbon is known as the α phosphate –  The second phosphate from the 5’ carbon is the β phosphate –  The third phosphate from the 5’ carbon is the γ phosphate 6 8/29/11 Building the DNA Molecule: Naming the Nucleo;des •  The name of a nucleo;de comes uses as a root the name of the nucleoside followed by the number of phosphates the nucleo;de contains –  A nucleo;de containing deoxyribose, adenosine and one phosphate is deoxyadenosine monophosphate –  A nucleo;de containing deoxyribose guanosine and two phosphates is deoxyguanosine diphosphate –  A nucleo;de containing deoxyribose, thymidine and three phosphates is deoxythymidine triphosphates Building a DNA Molecule: A Strand of DNA Is Composed of Chains of Polynucleo;des • 
A single polymer of DNA is considered a strand, with each strand having specific polarity (the two ends have different free func;onal groups) • 
To create a DNA strand, a polymer must be formed of repea;ng nucleo;des • 
A strand of DNA is only formed in the 5’  3’ direc;on and never in the 3’  5’ direc;on • 
In forming a strand of DNA, the nucleo;des will only be added onto the 3’ end of a growing DNA strand • 
In order to join two nucleo;des together, a condensa;on reac;on must occur between the free 3’OH group of the final nucleo;de in a growing strand and the 5’ PO4 group in the nucleo;de to be added – 
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A phosphodiester bond is formed between the two nucleo;des A byproduct of the reac;on is one molecule of water 7 8/29/11 Building the DNA Molecule: DNA Base Pairing • 
DNA is a double stranded molecule and therefore, two strands must be able to interact with each other • 
The results of two very important experiments were important for showing how the two strands of a DNA molecule interact – 
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Erwin Chargaff’s biochemical experiments (first) Watson and Crick’s X-­‐ray diffrac;on studies (second) • 
Chargaff wanted to determine the rela;ve concentra;on of each nitrogenous base within a molecule of DNA • 
In 1940, Chargaff developed a paper chromatography method to analyze the amount of each nitrogenous base present in a molecule of DNA • 
Chargaff observed several important rela;onships among the molar concentra;ons of the different bases • 
In 1940 Chargaff proposed three important rules with regards to the nitrogenous base composi;on of DNA, which became known as Chargaff’s rules Building the DNA Molecule: DNA Base Pairing • 
Chargaff rules are as follows –  [A] = [T] –  [G] = [C] –  [A] + [G] = [T] + [C] or the concentra;on of purines is equal to the concentra;on of pyrimidines • 
Chargaff also found that the base composi;on, as defined by the percentage of G and C (G+C content) for DNA is the basically the same for organisms of the same species, and different for organisms of different species • 
The G + C content can vary from 22 – 73% depending on the organism 8 8/29/11 Building the DNA Molecule: DNA Base Pairing • 
Watson and Crick built off Chargaff’s work • 
Watson and Crick isolated and crystallized DNA then subjected it to X-­‐ray diffrac;on analysis to determine the structure of the DNA • 
Their results show that the secondary structure of DNA was a double helix • 
In the double helix, the two DNA strands interacted through base pairing (showing a physical reason for Chargaff’s observa;ons –  Adenine pairs with thymine (2 H bonds) –  Guanine pairs with cytosine (3 H bonds) Building the DNA Molecule: DNA Base Pairing • 
The two strands in a DNA molecule lie in an an;parallel configura;on –  Opposite orienta;on = an;-­‐parallel –  Allows the nitrogenous bases to align properly for efficient base pairing –  The free 5’ ends of each strand are on opposite sides of the molecule –  The free 3’ ends of each strand are also on opposite sides from each other • 
Base pairing is advantageous to the DNA chemistry –  Excludes water from the interior of the DNA molecule –  Creates entropy which allows for stabiliza;on of the double helix 9 8/29/11 Building the DNA Molecule: DNA Base Pairing • 
Each strand of a DNA molecule has complementary sequence – 
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There are important conven;ons that need to be followed when wri;ng the sequence of a DNA strand – 
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Due base pairing between the two strands Where there is an Adenine in one strand, there will be a Thymine opposite etc. The two strands do not have the same sequence The sequence of each strand is wri\en separately Only the sequence of the nitrogenous bases is wri\en out The sequence of each strand is ALWAYS wri\en in the 5’  3’ direc;on A 5’ is wri\en before the 5’ most nitrogenous base and a 3’ is wri\en a[er the 3’ most nitrogenous base For the DNA molecule on the right the sequence of the two strands are as follows – 
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For the strand 5’  3’ bo\om to top (le[ strand) the sequence is 5’ CAGT 3’ For the strand 5’  3’ top to bo\om (right strand) the sequence is 5’ ACTG 3’ DNA Secondary Structure: The Structure Confers Stability and Allows The Molecule To Hold Vast Amounts of Informa;on • 
If DNA is to be the primary molecule responsible for holding gene;c informa;on, then it must have three important characteris;cs – 
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It must hold vast amounts of informa;on The molecule must be extremely stable Must be easily replicated • 
DNA is able to hold vast amounts informa;on in its sequence of nitrogenous bases • 
Although there are only four nitrogenous bases each gene can s;ll has its own iden;ty – 
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The number of bases varies for each gene Sequence of bases varies for each gene The reason why we say “bases” is that a gene is only defined by the base sequence for only one of the strands 10 8/29/11 DNA Secondary Structure: The Structure Confers Stability and Allows The Molecule To Hold Vast Amounts of Informa;on • 
The stability of the double stranded DNA molecule comes from two important forces – 
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Hydrogen bonding between the base pairs Base stacking interac;ons • 
In actuality, the base pairs lie flat upon one another and so instead of looking like “rungs on a ladder” they look like a stack of coins • 
The bases in DNA stack together, which results in increased stability by elimina;ng water from the interior of the DNA molecule • 
In order to have the base pairs lie flat on one another, each base pair must be slightly twisted with respect to previous base pair DNA Secondary Structure: The Structure Confers Stability and Allows The Molecule To Hold Vast Amounts of Informa;on 11 8/29/11 DNA Secondary Structure: Important Physical Features of the Double Helix • 
The shape of base pairs results in two extremely important physical features – 
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Major Groove Minor Groove • 
The grooves are present because the two bonds that a\ach a base pair to its deoxyribose sugar rings are not directly opposite (not a true 180 degrees) • 
The major and minor groove form as a result of the angle at which the two sugars protrude from the base pairs – 
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120 degrees for the narrow angle (minor groove forma;on) 240 degrees for the wide angle (major groove forma;on • 
The major groove is about twice as wide (22 A) as the minor groove (12 A) • 
The grooves allow for proteins to bind to the DNA DNA Secondary Structure: Important Physical Features of the Double Helix • 
Proteins that bind the DNA in a sequence specific manner bind the major groove – 
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Below are the pa\erns of donors and acceptors for each of the four possible base pairs (A= acceptor D = Donor H=non-­‐polar hydrogen M=methyl group) – 
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The wide geometry of the major groove allows proteins to gain access to the sequence informa;on Each base pair has its own unique combina;on of hydrogen bond acceptors and donors which line the edge of the major groove A-­‐T (ADAM) T-­‐A (MADA) G-­‐C (AADH) C-­‐G (HDAA) Proteins that bind the DNA in a sequence non-­‐specific manner o[en bind the minor groove – 
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Pa\erns of hydrogen bond acceptors and donors lining the minor groove are incredibly similar For A-­‐T or T-­‐A base pairs (ADA) For G-­‐C or C-­‐G base pairs (AHA) 12 8/29/11 DNA Secondary Structure: Important Physical Features of the Double Helix and Disease • 
Many diseases result from a changes in DNA sequence that abrogate (block) DNA binding – 
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The changes in DNA sequence result in a change in the pa\ern of hydrogen bond acceptors and donors in the major groove The protein that is supposed to bind the DNA in a sequence specific manner can no longer do so because the pa\ern has changed • 
Familial Hypercholersterolemia (FH) is a gene;c disorder caused by changes in DNA sequence in the LDLR gene (Low-­‐Density Lipoprotein Receptor) • 
The LDLR gene encodes a protein that is expressed in the liver and adrenal cortex • 
This protein encoded by the LDLR gene is responsible for removing 66-­‐80% of all LDL from the blood • 
Pa;ents with FH exhibit disease symptoms at birth star;ng with a cholesterol level above the 95 percen;le DNA Secondary Structure: Important Physical Features of the Double Helix and Disease • 
By the second decade of life, other secondary symptoms arise due to the extremely high cholesterol levels – 
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Arcus Cornae Tendon Xanthomas Recurrent nonprogressive polyarthri;s Tenosynovi;s Artheroschlerosis • 
Without aggressive treatment, pa;ents can die of secondary symptoms by age 30 • 
There is no cure for FH, pa;ents require aggressive normaliza;on of LDL levels –  Dietary management –  Drug therapy to reduce the amount of free LDL in the blood 13 8/29/11 DNA Secondary Structure: Important Physical Features of the Double Helix and Disease • 
There are two iden;fied changes in the sequence of the LDL gene that can result in loss of a specific protein called from Sp1 from specifically binding the DNA encoding LDLR gene – 
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One is a change from a C-­‐G base pair  G-­‐C base pair at a specific posi;on (-­‐139) The other is a change from a C-­‐G base pair  T-­‐A base pair at another specific posi;on (-­‐60) • 
A pa;ent needs only one of these changes to lose Sp1 binding, which will lead to FH development • 
Each of these base changes in DNA sequence will change the pa\ern of hydrogen bond acceptors and donors in the the major groove – 
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For the C-­‐G  G-­‐C change, (HDAA  AADH) For the C-­‐G T-­‐A change (HDAA  MADA) DNA Secondary Structure: DNA Can Form Mul;ple Types of Double Helices • 
When Watson and Crick determined the secondary structure of DNA, it was thought to be fairly simple without significant structural varia;on between DNA molecules • 
As it turns out that is not quite true as DNA can adopt mul;ple conforma;ons – 
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The three conforma;ons DNA forms are as follows – 
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B-­‐DNA A-­‐DNA Z-­‐DNA The DNA conforma;on present is generally determined by condi;ons of the solu;on in which the DNA is present in (or experimentally, the condi;ons in which crystallized) – 
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Some of these conforma;ons are physiologically relevant Some of these conforma;ons are not physiologically relevant Salt Concentra;on Water Content (humidity) Each conforma;on will have its own structural proper;es 14 8/29/11 DNA Secondary Structure: DNA Can Adopt A B-­‐Type Double Helix (B-­‐DNA) • 
The B-­‐DNA form is considered the Watson and Crick conforma;on and is the most predominant conforma;on in vivo • 
The B-­‐form of DNA is seen when the DNA is present in condi;ons of high humidity (> 95%) and rela;vely low salt • 
The B-­‐DNA forms a right handed double helix (has a right handed twist) • 
The grooves present in B-­‐DNA have the following characteris;cs – 
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In B-­‐DNA, the major groove is wide and of moderate depth In B-­‐DNA the minor groove is also of moderate depth, but is narrower • 
The distance between base pairs is about 0.34 nm • 
For each turn of the helix there will be 10.5 bp/
turn at a distance of approximately 3.4 nm DNA Secondary Structure: DNA Can Adopt an A-­‐Type Double Helix (A-­‐DNA) • 
The A-­‐DNA form can be observed if the water content is decreased and the salt concentra;on is increased during crystalliza;on • 
The A-­‐form has only been observed in vitro and is thus thought to not be physiologically relevant • 
The A-­‐DNA form takes the shape of a right-­‐
handed double helix • 
The A-­‐DNA form is more compact and slightly ;lted – 
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The bases are ;lted with respect to the axis There are 11 bases per turn The grooves of A-­‐DNA have the following geometry – 
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The major groove is deep and narrow The minor groove is shallow and broad 15 8/29/11 DNA Secondary Structure: DNA Can Adopt an Z-­‐
Type Double Helix (Z-­‐DNA) • 
The Z-­‐form of DNA was discovered by the Alexander Rich Lab in 1979 (MIT) • 
Z-­‐DNA was visualized in the laboratory when the DNA was crystallized under one of two condi;ons – 
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DNA crystallized under high-­‐salt condi;ons DNA crystallized in the presence of alcohol • 
The Z-­‐form of DNA can be present under physiological condi;ons when the DNA has long stretches of alterna;ng guanine and cytosine • 
The Z-­‐DNA is a le[ handed double helix, and turns in a counter-­‐clockwise fashion when viewed down its axis • 
The le[-­‐handedness of the helix occurs due to alterna;ng syn and an; conforma;ons of the n-­‐
glycosidic bond in consecu;ve G-­‐C nucleo;des • 
The backbone of the Z-­‐DNA has a zig-­‐zag appearance • 
The Z-­‐DNA grooves have the following characteris;cs – 
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The major groove is shallow, almost to the point of being non-­‐existent The minor groove is deep and narrow DNA Secondary Structure: DNA Can Adopt an Z-­‐Type Double Helix (Z-­‐DNA) 16 8/29/11 Strand Denatura;on and DNA Renatura;on: Introduc;on • 
This ability of DNA to denature and renature is important for two biological processes – 
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Replica;on (in vivo) Gene expression-­‐transcrip;on (in vivo) • 
Nucleic acid denatura;on is important for a number of experimental techniques in Molecular Biology • 
The two strands are held together by hydrogen bonds – 
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Hydrogen bonds are considered weak non-­‐
covalent forces Allows for the two strands to come apart really easily • 
If the DNA is heated just above physiologic temperature (near 100 C) or subjected to high pH, the DNA denatures (the two strands separate) • 
If the solu;on containing the DNA is slowly cooled, the DNA can renature (The two complementary strands can re-­‐form regular double helices) Strand Denatura;on and DNA Renatura;on: Introduc;on •  In the lab if DNA is heated just above physiologic temperature: –  The DNA denatures (the two strands separate) –  If the solu;on is slow cooled, the two complementary strands renature (form regular double helices) •  If the pH of the solu;on is increased: –  The DNA denatures because most other bases form hydrogen bonds more readily than nitrogenous bases –  If the solu;on is slowly re-­‐
acidified, the two complementary strands can re-­‐form regular double helices 17 8/29/11 Strand Denatura;on and DNA Renatura;on: Introduc;on •  The process of adding heat to denature the DNA only affects the hydrogen bonds (weak bonds) that allow base pairing to occur •  The phosphodiester bonds are covalent linkages which are much stronger than hydrogen bonds and are unaffected by temperature •  Enzyma;c ac;vity is needed to break phosphodiester linkages –  DNases –  Restric;on Endonucleases Strand Denatura;on and DNA Renatura;on: Denatura;on Kine;cs • 
Important insights into the proper;es of the double helix were obtained through classic experiments carried out in the 1950s on denatura;on kine;cs • 
In order to follow DNA denatura;on, ultraviolet light at a wavelength (λ) of 260 nm is used • 
DNA maximally absorbs light at a wavelength of 260 nm due to the nitrogenous bases • 
Single stranded DNA absorbs UV light at λ= 260 nm more efficiently than double stranded DNA – 
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Base stacking of double-­‐stranded DNA quenches the ability of the DNA to absorb UV light Na;ve double-­‐stranded DNA will absorb about 40% less UV light as compared to the same amount of single stranded DNA 18 8/29/11 Strand Denatura;on and DNA Renatura;on: Denatura;on Kine;cs • 
To study denaturata;on kine;cs, a solu;on of double stranded DNA is subjected to heat • 
Plot absorbance as a func;on of temperature – 
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Temperature is on the X-­‐axis Absorbance is on the Y-­‐axis As the solu;on is heated, the op;cal density (absorbance) at 260 nm markedly increases within a small range – 
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This phenomenon known as hyperchromicity Hyperchromicity: an increase in absorbance of light by a molecule at a given wavelength • 
The midpoint of the transi;on from double stranded to single stranded DNA is known as the mel;ng temperature or Tm • 
The mel;ng temperature denotes the point at which 50% of DNA in solu;on is single-­‐
stranded Strand Denatura;on and DNA Renatura;on: Denatura;on Kine;cs •  Mel;ng temperature is dependent on the composi;on of base pairs in a DNA molecule –  G:C base pairs contain 3 H bonds –  A-­‐T base pairs contain 2 H bonds •  The more G-­‐C base pairs, the higher the mel;ng temperature •  The less A-­‐T base pairs, the lower the mel;ng temperature •  Tm = 3(G-­‐C base pairs) + 2 (A-­‐T base pairs) 19 8/29/11 RNA Structure: Introduc;on • 
RNA is chemically similar to DNA with a couple of major differences – 
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Single stranded Can also base pair and form significant secondary structure • 
Instead of base pairing with a second strand, a single RNA strand can base pair with itself • 
“The structure of RNA is breathtakingly intricate and graceful” -­‐Harry Noller (2005) • 
There are many types of RNA that can adopt significant number of structures that are important for biological func;on – 
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tRNA (transla;on) rRNA (ribosomal RNA) snRNA (splicing) snoRNA (rRNA processing) Ribozymes (enzyma;c func;on) mRNA (gene regula;on) The significant secondary structural mo;fs are stabilized by base pairing – 
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Conven;onal base pairing (Watson-­‐Crick) Unconven;onal base pairing RNA Structure: DNA and RNA Structure Comparison • 
The structure of RNA and DNA are fundamentally quite similar, with and one significant chemical difference • 
Below are some similari;es: • 
Below are the differences: –  Each is synthesized from the monomer building block-­‐nucleo;des –  Nucleo;des are polymerized in exactly the same way –  RNA is generally found as a single stranded molecule: Has only 1 phosphodiester backbone (what makes RNA single stranded) –  The basic building blocks (nucleo;des) of RNA and DNA are slightly different (sugar and nitrogenous bases) –  RNA is more chemically reac;ve 20 8/29/11 RNA Structure: Ribonucleo;de Structure and The Pentose Sugars •  The Differences between Deoxyribose and Ribose: –  Differ in structure only by the presence or absence of a 2’ hydroxyl group –  For RNA, the 2’ carbon has a hydroxyl group bound to it –  For DNA, the 2’ carbon does not have a hydroxyl group (deoxy) bound, instead it has a hydrogen bound to it •  The presence of the 2’OH in ribose gives DNA and RNA different chemical proper;es –  Hydroxyl group is more reac;ve than the hydrogen –  RNA can fold into a greater array of structures –  Allows RNA to form a whole array of different types of base pairs –  DNA is more stable than RNA; RNA is more prone to degrada;on RNA Structure: Base Pairing Is Cri;cal For Allowing Secondary Structure To Form • 
The conven;onal base pairs found in RNA are as follows (Watson-­‐Crick Base Pairs): – 
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In order for a single strand of RNA to base pair with itself, non-­‐canonical base pairing is also cri;cal – 
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G:C base pair (3 H bonds) A:U base pair (2 H bonds) More than 20 types of non-­‐canonical base pairs form with at least two H bonds The most common non-­‐canonical base pair is the G-­‐U base pair (will be present in almost all secondary structure) and base pairs through 2 H bonds In Non-­‐canonical base pairing one of the nitrogenous bases of the pair will be shi[ed sideways to allow for hydrogen bonds to form Other less common non-­‐canonical base pairs found in RNA secondary structure are as follows – 
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AU reverse Hoogstein (Adenine is shi[ed sideways in comparison to the canonical AU base pair) Sheared G-­‐A base pair(2 H bonds) G-­‐A imino (3 H bonds) – (note: 2 purines) 21 8/29/11 RNA Secondary Structure: Base-­‐Paired RNA Adopts an A-­‐type Helix • 
RNA readily forms secondary structure in the form of a helix • 
RNA adopts an A-­‐type helix configura;on – 
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DNA cannot adopt an A-­‐Type Helix under physiological condi;ons RNA can adopt an A-­‐Type double helix under physiological condi;ons • 
The RNA A-­‐Type Helix cannot adopt a B-­‐
conforma;on due to the 2’OH group • 
The A-­‐Type Helix RNA adopts is stabilized by the same forces as the DNA B-­‐Type Double Helix – 
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Hydrogen bonding between the base pairs Base stacking interac;ons RNA Secondary Structure: Base-­‐
Paired RNA Adopts an A-­‐Type Helix •  The RNA A-­‐Type Helix has 11 base pairs per turn and two grooves –  Major Groove –  Minor Groove •  The major groove is deep and narrow and is not well suited to protein-­‐RNA interac;ons •  The minor groove is shallow and wide and is much be\er suited to protein-­‐RNA interac;ons due to the presence of 2’ OH groups that extend out into the minor groove 22 8/29/11 RNA Secondary Structure: Base-­‐
Paired RNA Adopts an A-­‐Type Helix • 
OH groups in the minor groove, RNA binding proteins are unable to bind there in a sequence specific manner –  Many 2’ OH groups do not allow for iden;fica;on of specific base pairs –  RNA binding proteins instead iden;fy specific structures in the RNA • 
When two complementary stretches of sequence are near each other, a stem-­‐loop structure may form –  Not all sequences within the stretches are complementary (especially at the end) –  Intervening, non-­‐complementary sequence is looped out from the double-­‐helical segment as a hairpin, bulge or simple loop •  If mispairing occurs on one side of the helix •  If mispairing occurs on both sides –  Depending on the amount and loca;on of the non-­‐complementary sequence, there are many varia;ons on the stem-­‐
loop RNA Secondary Structure: Base-­‐
Paired RNA Adopts an A-­‐Type Helix 23 8/29/11 RNA Structure: Overview of Ter;ary Structure • 
Beyond secondary structure, RNA can form higher order ter;ary structure – 
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RNA binding proteins can recognize specific por;ons of an mRNA due to higher order 3-­‐dimensional structure The higher order 3D structure allows for proper func;ons of certain RNA (eg tRNA , rRNA, ribozymes) Ter;ary structures can arise from the interac;on of mul;ple secondary structures making use of significant non-­‐conven;onal base pairing – 
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tRNA rRNA snRNA • 
In some cases proteins are necessary to allow for the forma;on of higher order ter;ary structure • 
Below are several common examples of ter;ary structure – 
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Pseudoknot Mo;fs A-­‐Minor Mo;f Tetra-­‐loop Mo;f Ribose Zipper Mo;f Kink-­‐turn mo;f 24