(unitii)chapter&6:the&structure&of& dna -...

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(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 –  Allows the proper structures to form at the

appropriate ;me –  Allows appropriate growth at the

appropriate ;me

•  Contains the informa;on for proper cellular func;on –  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 –  Cellular reproduc;on (asexual) –  Organismal reproduc;on (sexual or asexual)

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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 –  Carbon –  Phosphorous –  Nitrogen –  Hydrogen –  Oxygen

•  When Watson and Crick (1952) discovered that the 3-‐Dimensional structure of DNA –  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

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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

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•  There are four common nitrogenous bases found in DNA –  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


•  In nature, each nitrogenous base can take one of two conforma;ons

•  For the nitrogenous bases, there are two conforma;ons –  Conven;onal form –  Tautomeric state

•  Defini;on of Tautomers: –  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 –  Conven;onal –  Tautomeric

•  For all of the nitrogenous bases, the equilibrium strongly favors the conven;onal form

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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 –  Phosphate group is polar –  Phosphate group has a slight nega;ve charge

•  Ester bonds link the phosphate to the rest of the nucleo;de –  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 –  Allows for polymeriza;on of nucleo;des –  Allows for synthesis of DNA (or RNA) chains

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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 –  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

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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 –  A phosphodiester bond is formed between the two

nucleo;des –  A byproduct of the reac;on is one molecule of water

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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 –  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


•  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

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•  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)


•  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

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•  Each strand of a DNA molecule has complementary sequence –  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

•  There are important conven;ons that need to be followed when wri;ng the sequence of a DNA strand –  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 –  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 –  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 –  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

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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 –  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

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DNA Secondary Structure: Important Physical Features of the Double Helix •  The shape of base pairs results in two

extremely important physical features –  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 –  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 –  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

•  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) –  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 –  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)

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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 –  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


•  By the second decade of life, other secondary symptoms arise due to the extremely high cholesterol levels –  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

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•  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 –  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 –  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 –  Some of these conforma;ons are physiologically

relevant –  Some of these conforma;ons are not physiologically

relevant

•  The three conforma;ons DNA forms are as follows –  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) –  Salt Concentra;on –  Water Content (humidity)

•  Each conforma;on will have its own structural proper;es

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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 –  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 –  The bases are ;lted with respect to the axis –  There are 11 bases per turn

•  The grooves of A-‐DNA have the following geometry –  The major groove is deep and narrow –  The minor groove is shallow and broad

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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 –  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 –  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)

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Strand Denatura;on and DNA Renatura;on: Introduc;on

•  This ability of DNA to denature and renature is important for two biological processes –  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 –  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)


•  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

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•  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 –  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

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•  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 –  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 –  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


•  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)

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RNA Structure: Introduc;on •  RNA is chemically similar to DNA with a couple of

major differences –  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 –  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 –  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: –  Each is synthesized from the monomer

building block-‐nucleo;des –  Nucleo;des are polymerized in exactly

the same way

•  Below are the differences: –  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

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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): –  G:C base pair (3 H bonds) –  A:U base pair (2 H bonds)

•  In order for a single strand of RNA to base pair with itself, non-‐canonical base pairing is also cri;cal –  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 –  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)

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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 –  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 –  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

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•  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


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RNA Structure: Overview of Ter;ary Structure

•  Beyond secondary structure, RNA can form higher order ter;ary structure –  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 –  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 –  Pseudoknot Mo;fs –  A-‐Minor Mo;f –  Tetra-‐loop Mo;f –  Ribose Zipper Mo;f –  Kink-‐turn mo;f

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