Sequencing

Question 1

RNA has

Answer 1

2 OH group
A,G,C,U

Question 2

DNA has

Answer 2

1 OH group
A,G,C,T

Question 3

Di-deoxynucleotide (synthetic/artificial nucleotide) has

Answer 3

No OH group
A,G,C,T/U

Question 4

dNTP
ddNTP

Answer 4

dNTP: deoxynucleotide triphosphate (1 OH eksik)

ddNTP: dideoxynucleotide triphosphate (2 OH eksik)

Question 5

How does chain termination work

Answer 5

If the 3rd C of a nucleotide doesn’t have OH, phosphodiester bond cannot be formed
(between one’s OH and other’s P)

Question 6

Sanger Sequencing

Answer 6

“Chain termination method”
-Chain elongation stops when we get ddNTP during elongation
-Taq DNA polymerase cannot differentiate between dNTP and ddNTPs
-Terminators: ddNTPs
-Radiactively labelled primers/terminators are used (F & R)
-After termination, different length fragments are analyzed in Gel Electrophoresis under UV light

Question 7

Maxam-Gilbert procedure

Answer 7

Chemical method

Question 8

Sanger di-deoxy procedure

Answer 8

Enzymatic method

Question 9

Database (from mostly used to least used)

Answer 9

RDP (Ribosomal database procedure)
NCBI (National Center for Biotechnology Information)
ARB SILVA

Question 10

DNA Sequencing procedures

Answer 10

Maxam-Gilbert procedure
Sanger dideoxy procedure

Question 11

Maxam-Gilbert procedure

Answer 11

-chemical method
-not reliable
-depends on chemical degradation
-complex

Question 12

Sanger dideoxy procedure

Answer 12

-enzymatic method
-most reliable and used
-depends on enzymatic rxns
-simple

Question 13

What is SI

Answer 13

Similarity Index

Question 14

What % of SI we need

Answer 14

98-99%