Purine and Pyrimadine bases that make up the nitrogen bases of DNA, RNA and nucleotides. Exist as tautomers (see fig from textbook)

Transcription

1 Nucleic Acids DNA & RNA Basics DNA Right handed helix made of opposite oriented strands of nucleotides RNA single strands of nucleotides, often forming helix within the same strand and bound to proteins (diverse set of molecules) Bases Purine and Pyrimadine bases that make up the nitrogen bases of DNA, RNA and nucleotides Exist as tautomers (see fig from textbook) Nucleic acids - components 1

2 Sugar (ribose) backbone Chemical Structure of Nucleotides (Use figure above for notation) COUNT the atoms on base and ribose. Gives rise to 5 and 3 orientation 1) In a DNA duplex, strands are anti-parallel. 2) Individual strands are synthesized from the 5 OH of the ribose to the free 3 OH at the terminus of the strand. Thus, DNA sequences have directionality going from 5 to 3. 3) The anti-parallel strands are said to be complimentary due to the hydrogen bonding occurring between heterocyclic bases across strands of duplex. 4) DNA sequences are written 5 to 3 5) When a complimentary strand is given for the 5 to 3 strand, this is the reverse complement as it is the 3 strand sequence rewritten from 5 to 3 2

3 1) In a DNA duplex, strands are anti-parallel. 2) Individual strands are synthesized from the 5 OH of the ribose to the free 3 OH at the terminus of the strand. Thus, DNA sequences have directionality going from 5 to 3. 3) The anti-parallel strands are said to be complimentary due to the hydrogen bonding occurring between heterocyclic bases across strands of duplex. 4) DNA sequences are written 5 to 3 5) When a complimentary strand is given for the 5 to 3 strand, this is the reverse complement as it is the 3 strand sequence rewritten from 5 to 3 3

4 Chapter 24 Structure DNA Structure - Antiparallel -Right or left handed around common axis -Sugar-phosphate backbone exposed to solvent -Bases occupy core of center -Minor and Major grooves (where protein aa side chains will bind Base pairing constrained by duplex diameter & H- bond pattern Sterically Allowed Base Orientations Anti or Syn 4

5 The only other purine- pyrimidine pairings would be AC and GT and UA (in RNA). A C G T A U Pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond Forces That Stabilize Structure H bonding is required for specificity of base paring but contributes little to stability of DNA structure what does that mean? H bonding between bp are replaced by H boinds with bases and water when denatured so something else has to add to DNA structure stability Stacking!!!! Think of the purine and pyrimidine structure and the delocalized P orbitals stacked one over the other. The stacking interactions of the atoms also form van der Walls interactions The sequence influences the strength. Look at CG and AT! (see table from textbook for examples!!!) 5

6 DNA Forms B Form DNA Right handed, major form, hydrated Major Groove wide and deep, Minor Groove narrow and deep Bases are perpendicular to axis Anti for both purine and pyrimidine 11.6 bp/turn C2 endopucker A Form DNA Right handed, minor form, dehydrated Found in RNA-DNA interaction sites Wider and flatter helix than B DNA Major Groove narrow and deep, Minor Groove wide and shallow Bases are tilted 20o to axis Anti for both purines and pyrimadines C3 endopucker This is the double helical form of double stranded RNA Z Form DNA Left handed, minor form, dehydrated Evidence for Z DNA is binding proteins Found near start of genes may alter protein binding to proteins for transcription Found with high alternating purine-pyrimidine sequences (dgc), during negative supercoiling and high salt or select cation binding (reducing electrostatic repulsion from phos groups. Not a stable helix Flat or missing major grouve, narrow and deep minor groove Bases are nearly flat Alt anti syn Endopucker C2 Pyrimidines C3 Purines 6

7 DNA has limited flexibility DNA forms transition from one form to another based on conditions (water, ions or binding proteins) There are changes within each form (pitch of base pairs) depending on sequence 6 (plus base) torsional angles have restricted rotational freedom Alpha and zeta are restricted due to interactions between ribose and P groups. Already mentioned x syn and anti conformation Most are in anti except Z DNA Rotation within the ribose is limited to accommodate phosphate repulsion and substituents of ribose atoms The ring can not remain planar due to crowding and either C2 or C3 will be out of plane (with C5) 7

8 DNA can be Supercoiled Consider a closed, circular double stranded DNA. -twisting one strand (over or under) will cause kinks leading to a supercoil - The number of coils cannot be altered without first cleaving at least one or both of the strands Topology Writhe & Twist L = T + W L = linking number. The number of times one DNA strand winds around the other. Can not be changed without breaking a strand. T = twist. Number of helical winding of DNA strands around each other W = writhing. Number of turns (coils) the duplex makes around the superhelix (superhelicity). Right hand (+) left hand (-). Linking Number L describes the topological property and determines the degree of supercoiling L = T + W - circular DNA of 4200 bp linking number of B DNA (10 bp per turn) is 4200/10 = 420. A and Z have a different bp per turn value! If no supercoiling then W = 0 and T = 420. Positive and Negative SC L is constant and for every new double helical twist (caused by intercalation or protein winding) there must be an equal and opposite superhelical twist. Positive Supercoiling Negative Supercoiling From G Koudelka Molc Visualization SUNY Buffalo 8