From Christoph's Personal Wiki
ZHUNT (aka Z-Hunt or ZHunt) is an algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form. The original algorithm was written by Dr. P. Shing Ho in 1986 and was later developed by Tracy Camp, P. Christoph Champ, Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of Z-DNA (with P. Shing Ho as the principal investigator). ZHUNT is available for use Online at ZHunt Online.
- linking number
- change in helical twist
- change in writhe = ΔWr = ΔLkm – <ΔTw>
- overall energy associated with the transition from B-DNA to Z-DNA; ΔG° = K(ΔLkm – ΔTwm)2
- K = 1100RT/N, for N number of base pairs in the DNA plasmid (see:  for description)
- partition function
Note: The following table is a list of test sequences with their corresponding conformational assignments and Z-scores (now called "PZ" scores). This "Z-score" should not be confused with the statistical "Standard score". Here, it describes the propensity of a given sequence to adopt the left-handed form of DNA; it is simply a probability score.
Sequence/conf. assignments | Z-score ----------------------------|------------ CGCGCGCGCGCGCGCGCGCGCGCG | 2 x 10e+11 ASASASASASASASASASASASAS | | CGCGCGCGCGCG | 4 x 10e+07 ASASASASASAS | | CACACACACACACACACACACACA | 2 x 10e+05 ASASASASASASASASASASASAS | | CACACACACACA | 2 x 10e+04 ASASASASASAS | | CGCGCGCGCGCG GCGCGCGCGCGC | 2 x 10e+08 ASASASASASAS SASASASASASA | | CGCGCG GCGCGC CGCGCG GCGCGC | 7 x 10e+04 ASASAS SASASA ASASAS SASASA | | * * * * * * | CCCGCCCGCCCGCCCGCCCGCCCG | 8 x 10e+04 ASASASASASASASASASASASAS | | * * * * * * | CAGGCAGGCAGGCAGGCAGGCAGG | 1 x 10e+03 ASASASASASASASASASASASAS | | * * * * * * * * * * * * | CCCCCCCCCCCCCCCCCCCCCCCC | 52 ASASASASASASASASASASASAS | | ATATATATATATATATATATATAT | 38 SASASASASASASASASASASASA | | AAAAAAAAAAAAAAAAAAAAAAAA | 3 x 10e-07 ASASASASASASASASASASASAS |
|Various test sequences are shown with their corresponding Z-score as assigned by Z-hunt [version 1]. Z-scores are defined as the number of random base pairs that must be scanned, on average, to find a sequence with equal or better Z-forming capacity relative to the sequence in question. The conformation selected by Z-hunt for each nucleotide (A for anti and S for syn) are indicated below each sequence. Bases which deviate from perfect purine-pyrimidine alternation are designated by dots above that nucleotide. Discontinuities in the conformational phases produced by Z-Z junctions are represented by gaps separating the sequence.|
Keywords and abbreviations
- Keywords: Z-DNA; Nuclear factor I; Transcription regulation; Thermogenomics
- Abbreviations: ZDR, potential Z-DNA regions; NFI, nuclear factor I; CSF, colony stimulating factor
- wikipedia:DNA supercoil
- wikipedia:Gibbs free energy
- wikipedia:Linking number
- wikipedia:Möbius strip
- ↑ 1.0 1.1 Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
- ↑ 2.0 2.1 Champ PC, Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510.
- ↑ 3.0 3.1 Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". Methods, [Epub ahead of print]. PMID: 18848994. DOI:10.1016/j.ymeth.2008.09.007
- ↑ Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
- Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". Methods, [Epub ahead of print]. PMID: 18848994. DOI:10.1016/j.ymeth.2008.09.007
- Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA, 91(20):9549-9553.
- Schroth GP, Chou PJ, Ho PS (1992). Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J Biol Chem, 267(17):11846-55.