DNA Structure Search

The DNA Structure Search engine searches a gene sequence for repeat tracts with the propensity to form H-DNA or Z-DNA. Users provide search criteria in an online form and results are returned in a web page listing the repeat sequences found along with descriptive information about them, including length, percent G, position on the chromosome, and gene region in which they were found. Results from searches in the human and mouse genomes are enriched with links to NCBI Entrez Gene and GenBank. Additionally, users may choose to download their search results to a file, and the search engine allows users upload a sequence to be searched.

If you would like to use the DNA Structure Search engine please contact Dr. Guliang Wang, for login credentials.


Sequences with the Propensity to Form H-DNA

Sequences with the propensity to form H-DNA are mirrored purine runs separated by a relatively short spacer. The search engine allows the user to specify the minimum length for the mirrored arms, the minimum and maximum allowable spacer length, the minimum percent G of the arms, and whether or not a mismatch in the arms is allowed. The user may also choose to omit from the search results mirror repeat elements where the arms are comprised of a simple A repeat or where the entire mirror repeat element is a GA repeat. By default the search engine omits mirror repeat elements consisting solely of poly A or poly G tracts or poly A tracts with a G at the extremities (e.g. GAAAAAAAAAAAAAAAG).

The search results include all possible variations of a tract with the propensity to form H-DNA. The variations are grouped into families, with each family originating from a single purine run that includes an interruption of one or more contiguous pyrimidines. Tracts of the same family number differ by the position of the spacer along the originating purine run. Tracts that arise from adjacent pyrimidine-interrupted purine runs are assigned different family numbers, yet may share an arm.


Sequences with the Propensity to Form Z-DNA

Sequences with the propensity to form Z-DNA are alternating purine/pyrimidine tracts (APPTs), with a preference for GC repeats. The engine scores the APPTs, giving each GC dinucleotide a score of 25 and each GT dinucleotide a score of 3. A user-defined minimum score determines which APPTs are included in the search results.


Triplex-Forming Oligonucleotide Target Sequence Search

The Triplex-forming Oligonucleotide Target Sequence Search engine was developed to facilitate the use of TFOs in gene-specific manipulation of human and mouse DNA. A web form gathers search criteria from the user, including the gene and species to be searched, the minimum percent G and maximum number of pyrimidine interruptions allowed in the TFO target sequence, the minimum target sequence length, and the length of promoter region to be searched. The user is also given the option choose whether to search a raw genomic sequence, a repeat-masked genomic sequence, or an uploaded sequence. The engine searches both strands of the gene sequence for purine runs, allowing non-contiguous pyrimidine interruptions. Search results are returned in a web page listing the found TFO target sequences along with descriptive information about them, including length, percent G, position on the chromosome, gene region in which they were found, matches to known repeat sequences, and PubMed identifiers for articles reporting validated TFO target sequences. The search results are enriched with links to NCBI resources: Entrez Gene, GenBank, BLAST, and PubMed.

The Triplex-Forming Oligonucleotide Search is freely available to all. If you use it in your work please cite Oligonuc7leotides 16:196-201 (2006).