DNA Structure, Synthesis and Sequencing Flashcards
What bases are pyrimidines?
Cytosine and Thymine
What bases are purines?
Adenine and Guanine
Describe the structure of pyrimidines?
One ring structure
What carbon does DNA attach to on a ribose sugar?
1’ carbon
Synthesis of DNA requires the addition of what to the growing chain?
A nucleotide triphosphate (NTP)
What releases energy in the synthesis of DNA?
Release of the diphosphate from the NTP
What do the bases bond via and where?
They bond via a phosphodiester bond between the 3’ carbon of one nucleotide and the 5’ carbon of the next
What is the chemical energy that holds DNA strands together made up of?
Hydrogen bonding between base pairs and the base stacking energy between adjacent bases
What is DNA hybridisation?
The balance between the bonding energy and the heat energy or entropy which is a measure of how much energy it takes to keep a molecule in a particular conformation
What happens to DNA if the change in Gibbs Free Energy is negative?
The DNA will anneal and be double stranded
What happens to DNA if the change in Gibbs Free Energy is positive?
DNA will melt ad become single stranded
What will an increase in temperature do to DNA?
It will increase the magnitude of the entropy and drive the DNA towards melting
What happens when there is no hydroxyl on the 3’ position?
You cannot attach the next nucleotide
Does single stranded DNA have a higher absorbance in UV than double stranded DNA?
Yes (0.027 Au vs 0.020 AU at 1ug/ml)
What is Tm?
Melting temperature
What affect does longer DNA strands have on the Tm?
It increases the Tm
If there are mismatches between two strands, what happens to the enthalpy change?
The enthalpy change will be less (weaker binding)
Oligos only anneal with what?
Exact/extremely close to exact sequences
Are oligonucleotides single or double stranded?
Single stranded
What is an oligonucleotide?
a polynucleotide whose molecules contain a relatively small number of nucleotides
What does the ‘reverse’ in reverse transcriptase refer to?
It refers to the reversal of synthesis from generating RNA from a DNA template to generating DNA from an RNA template.
What happens if a dideoxy base is mixed with a normal deoxy NTP base?
It creates at random termination of the chain at the dideoxy base
