PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 3839689

Graphical coding of nucleic acid sequences.

E Mizraji·J Ninio
View original source ↗Export metadata ↓

Abstract

When, in a nucleic acid sequence, the four letters C, G, A, T (or U) are replaced by suitable graphical symbols, some patterns become immediately apparent. Two sets of symbols, constructed for the analysis of either purine/pyrimidine alternations, or of regions of complementarity within a sequence are shown. In addition, another mode of coding is presented, in which the four letters are represented by vectors. The sequence is thus transformed into a planar trajectory. We show, in the case of the gene for human beta hemoglobin, that such a coding enables an easy discrimination between introns and exons.

Explore related subjects

Base SequenceComputersHemoglobinsHumansSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

E Mizraji, J Ninio. 1985. Graphical coding of nucleic acid sequences.. https://doi.org/10.1016/s0300-9084(85)80262-5

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2016

miR-503-3p promotes epithelial-mesenchymal transition in breast cancer by directly targeting SMAD2 and E-cadherin.

Although progress in clinical and basic research has significantly increased our understanding of breast cancer, little is known about the molecular mechanism underlying breast cancer metastasis. Identification of effective therapeutic targets to prevent breast cancer metastasis is urgently needed. The function of miR-503-3p has been investigated in other cancers, but its role in breast cancer remains undefined. Here, we found that miR-503-3p was overexpressed in breast cancer tissue and plasma compared with adjacent normal breast tissue and with plasma from healthy individuals. Moreover, we identified miR-503-3p to be an oncogene of breast cancer cell proliferation, migration and invasion. Upregulation of miR-503-3p in breast cancer cells inhibited expression of epithelial-mesenchymal transition (EMT)-related protein SMAD2 and the epithelial marker protein E-cadherin by directly binding to their mRNA 3' untranslated region, whereas increased expression of mesenchymal marker proteins, including vimentin and N-cadherin. Taken together, our findings support a critical role for miR-503-3p in induction of breast cancer EMT and suggest that plasma miR-503-3p may be a useful diagnostic biomarker for breast cancer.

Base Sequence↗
PubMed2003

Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors.

Through exhaustive two-hybrid screens using a budding yeast genomic library, and starting with the splicing factor and DEAH-box RNA helicase Prp22p as bait, we identified yeast Prp45p and Prp46p. We show that as well as interacting in two-hybrid screens, Prp45p and Prp46p interact with each other in vitro. We demonstrate that Prp45p and Prp46p are spliceosome associated throughout the splicing process and both are essential for pre-mRNA splicing. Under nonsplicing conditions they also associate in coprecipitation assays with low levels of the U2, U5, and U6 snRNAs that may indicate their presence in endogenous activated spliceosomes or in a postsplicing snRNP complex.

Base Sequence↗
PubMed1997

Studies on formation and stability of the d[G(AG)5]* d[G(AG)5]. d[C(TC)5] and d[G(TG)5]* d[G(AG)5]. d[C(TC)5] triple helices.

We have targeted the d[G(AG)5]. d[C(TC)5] duplex for triplex formation at neutral pH with either d[G(AG)5] or d[G(TG)5]. Using a combination of gel electrophoresis, uv and CD spectra, mixing and melting curves, along with DNase I digestion studies, we have investigated the stability of the 2:1 pur*pur.pyr triplex, d[G(AG)5]*d[G(AG)5].d[C(TC)5], in the presence of MgCl2. This triplex melts in a monophasic fashion at the same temperature as the underlying duplex. Although the uv spectrum changes little upon binding of the second purine strand, the CD spectrum shows significant changes in the wavelength range 200-230 nm and about a 7 nm shift in the positive band near 270 nm. In contrast, the 1:1:1 pur/pyr*pur.pyr triplex, d[G(TG)5]*d[G(AG)5].d[C(TC)5], is considerably less stable thermally, melting at a much lower temperature than the underlying duplex, and possesses a CD spectrum that is entirely negative from 200 to 300 nm. Ethidium bromide undergoes a strong fluorescence enhancement upon binding to each of these triplexes, and significantly stabilizes the pur/pyr*pur.pyr triplex. The uv melting and differential scanning calorimetry analysis of the alternating sequence duplex and pur*pur.pyr triplex shows that they are lower in thermodynamic stability than the corresponding 10-mer d(G3A4G3). d(C3T4C3) duplex and its pur*pur.pyr triplex under identical solution conditions.

Base Sequence↗