how do enzymes cut dna at a specific point?  and how do introns get
spliced out (are the coding segments already gone in the mRNA
sequences?)

I have a science background, but in physics, not biology, so I can
handle medium detail.  I sometimes read something saying that enzymes
are used to cut dna at a specific point, and wonder how it targets
such a point, and cuts it.

---

Clarification of Question by lusus-ga on 31 Oct 2002 09:40 PST

limbatus, you gave me the key to the intron question, thanks!  i'm
starting to read through these links.

by the first question, I mean, I sort of understand how DNA is
(metaphorically) "read" by a ribosome when making protiens, in that
free amino acids just match up with the nucleotides, so one thing
codes the other in a sort of assembly line fasion.. but how does an
enzyme "read" the nucleotide sequence to know where to cut?

---

Clarification of Question by lusus-ga on 04 Nov 2002 09:37 PST

Thanks for your comments, everyone.

I can't fully answer your question because I only know the basics
myself, but here's a good primer. It has no mention of introns though,
so *shrug* to that.

http://library.thinkquest.org/19037/therapy2.html

skermit-ga

Checkout New England Biolabs,
http://www.neb.com/neb/tech/tech_resource/restriction/re_frame.html
they have a good explanantion of restriction endonucleases, and a
brief description of intron endonucleases,
http://www.neb.com/neb/tech/tech_resource/restriction/intron_encoded/intron_frame.html

Introns get cut out of pre-mRNAs by a class of enzymes called
splieosomes. This splicing occurs before mRNAs are exported from the
nucleus.  You can see a simplistic video of a spliceosome working at
http://www.neuro.wustl.edu/neuromuscular/pathol/diagrams/splicefunct.html.
If you search for spliceosome on google you will get tons of hits.

You can read about restriction enzymes (which cut DNA at specific
locations; also called restriction endonucleases because they cut
bonds between nucleotides in the middle of a strand of DNA rather than
just the nucleotides at the end of a strand of DNA) at:
http://www.accessexcellence.org/AE/AEC/CC/restriction.html or
http://ghs.gresham.k12.or.us/science/ps/sci/ibbio/biotech/restriction.htm

okay here is a shot at explaining how restriction enzymes works at
cutting specific sites of your gene.

Your genes consist of a sequence of instructions made by arranging
molecules in a polymer strand.  The basic blocks used consist of a set
of sugar-based molecules called Deoxyribonucleic Acid (DNA).  DNA
consist of a sugar unit-a phospate unit-and a "base" unit.  There are
4 different kinds of "bases" in DNA: usually called Adenine (A),
Guanine (G), Cytosine (C) and Thymidine (T).  So your genes can be
seen to consist of sequences containing different combination of
AGCTGCTAGGCCTTAA.... and so on.

Restriction enzymes were discovered from nature that acts on specific
sequences i.e. this would mean specific points of your DNA/gene.  Most
of them will only cleave the gene/DNA where they encounter say a very
specific sequence for e.g. an enzyme called AAT II will only cut when
it sees the sequence 5"...GACGT^C...3" and cut at the point where the
^ sign is.  By the way, your DNA is organized as a matched pair. So in
reality there is an opposite set that mirrors the sequence, the 5" and
3" denotes the carbon positions of the sugar unit which forms the
backbone of the DNA polymer. So in reality try and visualize the
happening as follows:

Original strand of DNA= 5"...GACGTC...3"
                        3"...CTGCAG...5"
Add                     AAT II
you would get a cleave= 5"...GACGT3"   +     5"C...3"
                        3"...C5"         3"TGCAG...5"

hope this helps a bit

First, the accessibility of genetic info depends on the ability of
proteins to interact with DNA in a manner that allows it to be copied
as DNA (replication) or RNA (transcription).  You're asking about the
transcription process.  Now in prokaryotes, translation (protein
synthesis) can begin even before transcription is done.  Not so in
eukaryotes.  That first RNA that is transcribed is pre-mRNA and it
will get some more modifications.  Before it goes out to the cytosol
(because it's made in the nucleus) it will have to get the intervening
sequences (introns) cut out and the expressed sequences (exons) will
get joined or spliced together.  The introns have a high degree of
homology among all of us eukaryotes-ie they typically have a GU at the
5' end and an AG at the 3' end.  J. Steitz figured that one nucleic
acid is probably best recognized by another and she found the small
nuclear ribonucleproteins, snRNPs, or snurps.  They are 60-300nt RNAs
and their ends are partially complementary to the splice junction. 
Now the splicesome brings together the pre-mRNA and the snRNPs and a
variety of other proteins to make the mature mRNA.  The mechanism for
proper splicing is still a mystery and exons can get cut out so that
alternative splicing can give more than 1 protein product for a given
gene. Oh boy, this got really long but I hope that's what your after.

DNA is sectioned into small fragments by the use of enzymes.  Enzymes
are proteins that mediate reactions in a catalytic manner.  The enzyme
has an active site which binds to and reacts with specific nucleotide
segments of the DNA.

Specific enzymes react with, and bind to specific segments of DNA and
thus, because of this specificity, different sections of the DNA
molecule are hydrolyzed. The result is that the products of hydrolysis
are of a different chemical composition and structure and thus, when
assembled allow the total structure of the DNA molecule to re-created.