JCAOligoTutorialDNA

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(New page: ==What is this DNA stuff?== If you've never heard of DNA, first read http://en.wikipedia.org/wiki/Dna and maybe pick up a textbook for the basics. The critical things you should understan...)
(What is this DNA stuff?)
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If you've never heard of DNA, first read http://en.wikipedia.org/wiki/Dna and maybe pick up a textbook for the basics.
If you've never heard of DNA, first read http://en.wikipedia.org/wiki/Dna and maybe pick up a textbook for the basics.
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The critical things you should understand:
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The critical things you should understand before trying to do this tutorial:
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*DNA is made of 4 bases in a specific sequence (A, T, C, and G) controlled by covalent bonds
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*DNA is a chemical entity, but we represent its sequence in the computer
 +
*DNA is made of 4 deoxyribonucleotides, A, T, C, and G (casually called bases) in a specific sequence determined by covalent bonds
*DNA molecules have directionality, one end is the 5' terminus, the other end is the 3' terminus
*DNA molecules have directionality, one end is the 5' terminus, the other end is the 3' terminus
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*By convention, DNA sequences are always written out in the 5' to 3' direction unless stated explicitly with "5'-" and "3'-" or alternatively drawing the sequence as a line with a barb at one end.  The barb refers to the 3' end.
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*By convention, DNA sequences are always written out in the 5' to 3' direction unless stated explicitly with "5'-" and "3'-" Alternatively, DNAs can be represented in cartoon form as a line with a barb at one end.  The barb refers to the 3' end.
*DNA can be circular or linear
*DNA can be circular or linear
*DNA can be single stranded or double standed
*DNA can be single stranded or double standed
*Double standed DNAs anneal to each other by Watson-Crick base pairing
*Double standed DNAs anneal to each other by Watson-Crick base pairing
*The sequence of the complementary strand of a double standed DNA is the "reverse-complement" of the other strand
*The sequence of the complementary strand of a double standed DNA is the "reverse-complement" of the other strand
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*The "reverse" and "complement" operations on a DNA sequence do not result in biochemically-meaningful molecules.  You must always do both to get the sequence of the complementary strand
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*The "reverse" and "complement" operations on a DNA sequence do not result in biochemically-meaningful sequences.  You must always do both (reverse-complement) to get the sequence of the complementary strand
*With some exceptions, bacterially replicating DNAs are double stranded circular molecules regardless of whether they are genomic DNAs or plasmid DNAs.
*With some exceptions, bacterially replicating DNAs are double stranded circular molecules regardless of whether they are genomic DNAs or plasmid DNAs.
*Even when DNAs are circular double stranded molecules, we represent them as linear single-stranded sequences using our software tools like ApE
*Even when DNAs are circular double stranded molecules, we represent them as linear single-stranded sequences using our software tools like ApE

Revision as of 01:48, 15 April 2008

What is this DNA stuff?

If you've never heard of DNA, first read http://en.wikipedia.org/wiki/Dna and maybe pick up a textbook for the basics.

The critical things you should understand before trying to do this tutorial:

  • DNA is a chemical entity, but we represent its sequence in the computer
  • DNA is made of 4 deoxyribonucleotides, A, T, C, and G (casually called bases) in a specific sequence determined by covalent bonds
  • DNA molecules have directionality, one end is the 5' terminus, the other end is the 3' terminus
  • By convention, DNA sequences are always written out in the 5' to 3' direction unless stated explicitly with "5'-" and "3'-" Alternatively, DNAs can be represented in cartoon form as a line with a barb at one end. The barb refers to the 3' end.
  • DNA can be circular or linear
  • DNA can be single stranded or double standed
  • Double standed DNAs anneal to each other by Watson-Crick base pairing
  • The sequence of the complementary strand of a double standed DNA is the "reverse-complement" of the other strand
  • The "reverse" and "complement" operations on a DNA sequence do not result in biochemically-meaningful sequences. You must always do both (reverse-complement) to get the sequence of the complementary strand
  • With some exceptions, bacterially replicating DNAs are double stranded circular molecules regardless of whether they are genomic DNAs or plasmid DNAs.
  • Even when DNAs are circular double stranded molecules, we represent them as linear single-stranded sequences using our software tools like ApE
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