make-na

Automation of making nucleic acid helices by NAB.

New make-na server!

News

5/15/09: Fixed improper terminals when hydrogens are created. Removed terminal 5' phosphates from underhanging strands to be consistent with blunt and overhanging strands.

Instructions

Using the make-na server should be intuitive. ASCII-art is used to depict duplexes and the server tries its best to infer what is meant by the depiction.

I have tried to put some flexibility in duplex creation. The server will create A-, B, and SB-DNA as well as A- and B-RNA. Z-DNA and Z-RNA are not supported yet. If someone wants it, I'll try to add it. Mismatches are supported as well as uneven over-hangs and under-hangs. For example, these would all be valid ASCII-art duplexes:

  ATACCGATACGATAGAC
    TGGCTATGCTATCTGTA

      CGATACGATAGAC
    uGGCuAuGCuAuCuGuA

      ACTATAGGATACCAT
       GATAggCTATGGTA

Moreover, the program does its best to ignore comments and other mark-up, so the following will work just fine (the alignment of the two strands will be interpreted correctly):

     #   This is my favorite DNA.
     5' -    ATACCGATACGATAGAC    -3'
     3' -      TGGCTATGCTATCTGTA  -5'

Comments start with a "#" (preceeded by optional whitespace) and all non-alphabetic information is ignored on sequence lines, except for calculating alignment of the strands. Blank and whitespace only lines are ignored.

It is currently necessary to specifiy both strands, even if a blunt-ended canonical Watson-Crick helix is intended. This may change if I get enough requests.

Disclaimer

I've been picked on just a little for these models. To discourage additional criticism, I include the following disclaimer:

These models may deviate from ideality (whatever ideality really is). I built this server to facilitate the making of models for downstream use in crystallography, NMR, and perhaps molecular dynamics. The pure A-, B-, and SB- forms with canonical WC pairing are unmodified from the NAB fiber-diffraction forms as created by the fd_helix function. See the NAB manual for details. I may apply some limited regularization by molecular dynamics to non-standard models or unusal helix types like Z-DNA. In all cases, take these models with a grain of salt. You will want to apply your own molecular dynamics or constraints from experimental data before you make conclusions from these models. I am not responsible for any misfortune that may befall you if you use these models. Use these models at your own risk.

Having solved several structures containing DNA, I can say with some authority that much variation in nucleic acid structure exists. Considering this variability, please realize that these models are actually very conservative.

References

A- and B-RNA and DNA parameters and SB-DNA parameters (the "SB" option) come from fiber diffraction data as described in the NAB manual. Here are the references for these types, ripped straight from the manul:

• Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations. X-ray diffraction analyses of the molecule conformations of (polyadenylic acid) and (polyinosinic acid).(polycytidylic acid). Arnott, S.; Hukins, D.W.L.; Dover, S.D.; Fuller, W.; Hodgson, A.R. J.Mol. Biol. (1973), 81(2), 107-22.
• Left-handed DNA helices. Arnott, S; Chandrasekaran, R; Birdsall, D.L.; Leslie, A.G.W.; Ratliff, R.L. Nature (1980), 283(5749), 743-5.
• Stereochemistry of nucleic acids and polynucleotides. Lakshimanarayanan, A.V.; Sasisekha- ran, V.Biochim. Biophys. Acta 204, 49-53.
• Fuller, W., Wilkins, M.H.F., Wilson, H.R., Hamilton, L.D. and Arnott, S. (1965). J. Mol. Biol. 12, 60.
• Arnott, S.; Campbell Smith, P.J.; Chandraseharan, R. in Handbook of Biochemistry and Molecular Biology, 3rd Edition. Nucleic Acids--Volume II, Fasman, G.P., ed. (Cleveland: CRC Press, 1976), pp. 411-422.

If you have any suggestions or comments, please use my contact page.

© 2006 James Stroud. All rights reserved.
Revised May 17, 2009.