characterization of nucleic acids

Nucleases

the ones that degrade DNA molecules by breaking phosphodiester bonds in a DNA strand

Endonuclease

capable of hydrolyzing internal bonds within a polynucleotide chain

Exonuclease

removes nucleotides one at a time from the end of a DNA molecule

RNAse H

cleaved the RNA strand of a DNA-RNA hybrid

Methyl groups

this prevents degradative enzyme action on the bacterium’s DNA

By their mode of action

How are the three classes of restriction enzymes distinguished?

Type II restriction endonuclease

Most important class of restriction endonuclease in lab and clinical analysis

Inverse palindromic

it describes the mechanism of type II restriction endonucleases towards sites that allows reading the same forward and backward on complementary strands

Isoschizomer

it recognizes and cuts DNA at the same site

Neochizomer

it recognizes/bind at the same sequence but cleaves at different sites

Isocaudamers

it produces the same nucleotide extensions but has diffferent recognition site

Restriction-Modification System (R-M system)

collective term for endonuclease and methylase

Hemimethylation

half-methylation

Restriction digest

preliminary mapping done to locate the cutting site and examine the sizes of fragments

• Locate the cutting site

• Examine the sizes of fragments

How does Restriction digest function?

• DNA polymerase I

• Klenow fragment

• Taq DNA polymerase

• Transcription polymerase

Enumerate the 4 polymerases

DNA polymerization and DNA degradation

What is the dual activity done by DNA polymerase I?

3’-5’ exonuclease activity

the one that acts in DNA polymerization in proofreading newly synthesized strands

5’-3’ exonuclease activity

the one that plays a role in DNA degradation by degrading a strand ahead of the advancing polymerase