S1 nuclease mapping is a laboratory technique used to locate the 5' end of an RNA transcript within a mixture by using the S1 nuclease. The S1 nuclease is an endonuclease that degrades single-stranded DNA and RNA but does not degrade double-stranded DNA or RNA-DNA hybrids. In S1 mapping, a transcript is hybridized to a DNA template and treated with S1 nuclease, which degrades any unhybridized RNA. This allows mapping the 5' end of the transcript to the DNA template. S1 nuclease mapping can determine the exact locations of start and end points of transcription and any splice points within transcripts.

1. S1 Nuclease Mapping
Dr. Ema Sushan Minj
Department of Microbiology

2. S1 Nuclease mapping -
• Gene expression is the process by which information encoded in
a gene is used in the synthesis of a functional gene product
known as protein.
• In case of RNA transcript -
▫ The removal of introns
▫ The exact locations of start and end points of transcription
▫ The signals that determine the start and end of transcription

3. • Nuclease-S1 mapping is used to map the locations of the ends of
RNA molecules and of any splice points within them in relation to
specific sites (e.g., positions of restriction endonuclease cleavage)
within the template DNA.
• The S1 nuclease is purified from Aspergillus oryzae.
• S1 Nuclease is an endonuclease that degrades ssDNA and RNA,
but does not degrade dsDNA or RNA-DNA hybrids in native
conformation.

4. • Thus, its activity is similar to mung bean nuclease. The enzyme
will also cleave a strand opposite to a nick on the complementary
strand.
• The enzyme is used to remove overhang single-stranded termini
from dsDNA, for selective cleavage of ssDNA and for mapping
RNA transcripts.
• It is a laboratory method used to locate the 5’end of a
transcript in a mixture of RNA using nuclease S1.

5. Properties of S1 nuclease
• At high ionic strength, low pH (4-4.5) and in the presence of Zn
ions (cofactor), S1 nuclease digests ssDNA very efficiently.
• It is relatively stable against denaturing agents like urea, SDS
and formaldehyde.
• It removes single stranded regions from dsDNA. (Conversion of
cohesive ends to blunt ends)
• Cleaves hairpin loops generated during synthesis of DNA.

6. S1 mapping
• Technique developed by Berk and Sharp by the study of
adenovirus mRNAs.
• This technique is used for quantifying the amount of mRNA
transcript and it can therefore identify the level of
transcription of the gene in the cell at a given time.

8. DNA-mRNA hybridization

9. Thank you