DNA sequencing with [alpha-33P]-labeled ddNTP terminators: a new approach to DNA sequencing with Thermo Sequenase DNA polymerase

Dideoxy nucleoside triphosphate (ddNTP) analogues: Synthesis and polymerase substrate activities of pyrrolidinyl nucleoside triphosphates (prNTPs)

The dideoxynucleoside triphosphates (ddNTPs) terminate the bio-polymerization of DNA and become essential chemical component of DNA sequencing technology which is now basic tool for molecular biology research. In this method the radiolabeled or fluorescent dye labeled ddNTP analogues are being used for DNA sequencing by detection of the terminated DNA fragment after single labeled ddNTP incorporation into DNA under PCR conditions. This report describes the syntheses of rationally designed novel amino-functionalized ddNTP analogue such as Pyrrolidine nucleoside triphosphates (prNTPs), and their polymerase activities with DNA polymerase by LC-MS and Gel-electrophoretic techniques. The Mass and PAGE analyses strongly support the incorporation of prNTPs into DNA oligonucleotide with Therminator DNA polymerase as like control substrate ddNTP. As resultant the DNA oligonucleotide are functionalized as amine group by prNTP incorporation with polymerase. Hence prNTPs provide opportunities to prepare demandable conjugated DNA with other biomolecules/dyes/fluorescence molecule without modifying nucleobase structure.

Isolation and characterization of chondrolectin (Chodl), a novel C-type lectin predominantly expressed in muscle cells

In this study, we identified and characterized the mouse orthologue of the human chondrolectin gene, Chodl. Chodl is located at chromosome 16C3 and consists of six exons and five introns. The putative full-length mouse cDNA of Chodl consists of 2393 bp, with an open reading frame of 839 bp, 243 bp of 5' untranslated region and 1310 bp of 3' untranslated region. The predicted Chodl protein is a type I transmembrane protein containing one carbohydrate recognition domain (CRD) of C-type lectin in its extracellular portion and shares a significant similarity (45%) with layilin, a hyaluronan receptor. Reverse transcription-polymerase chain reaction and subsequent Southern blotting analysis revealed that in adult mice, Chodl is preferentially expressed in skeletal muscle, testis, brain, and lung. Analysis of the embryonic expression of Chodl showed that during gestation (embryonic day (E) 7-15) its expression is up-regulated. In situ hybridization on E15 mouse embryo revealed that Chodl is expressed in muscle cells of heterogeneous origin, including those from tongue, trunk, and tail. Furthermore, fluorescent immunostaining on limbs of newborn mice, localized the Chodl protein to striated muscle cells. Finally, Western blot analysis demonstrated expression of Chodl protein during the proliferation as well as differentiation phases of the myoblastic C2C12 cell line.

Specific methylation of the CpG-rich domains in the promoter of the human tissue transglutaminase gene

The activity of tissue transglutaminase is present in many cells and tissues but almost absent in leucocytes and lymphocytes. The present work describes the distribution of 5-methylcytosine along the bisulphite-converted promoter of the human tissue transglutaminase gene as being in an essentially repressed state. In this promoter, the chain-specific sequencing revealed the location of three CpG-rich domains whose methylation responds to an 'all or nothing' signal. While the CpGs of domain 1, at the 5'-end, and 2, in the mid-promoter, were fully methylated, those of domain 3, at the 3'-end, were fully unmethylated. Before the 5'-UTR sequence, from site+1 to site+67, also unmethylated, there was thus a striking contrast in the post-synthetic modification between the sequence, from -1594 to -436, containing domains 1 and 2, and the sequence, from -435 to -1, containing domain 3 with the core promoter.

Molecular cloning and functional expression of the gene for a cotton Delta-12 fatty acid desaturase (FAD2)

Two overlapping genomic clones spanning 16.5 kb of cotton DNA were found to encompass a Delta-12 fatty acid desaturase (FAD2-3) gene. A partial FAD2-3 cDNA clone was also analyzed. The FAD2-3 gene has one large intron of 2967 bp entirely within its 5'-untranslated region, only 12 bp upstream from the ATG initiation codon. Several potential promoter elements, including several light-responsive motifs, occur in the 5'-flanking region. The continuous FAD2-3 coding region is 1155 bp and would encode a protein of 384 amino acids. The polypeptide has four putative membrane-spanning helices, indicative of an integral membrane protein, and is most likely localized in the endoplasmic reticulum. Yeast cells transformed with a plasmid construct containing the cotton FAD2-3 coding region accumulate an appreciable amount of linoleic acid (18:2), not normally present in wild-type yeast cells, indicating that the gene encodes a functional FAD2 enzyme.

Molecular cloning and nucleotide sequence of a gene encoding a cotton palmitoyl-acyl carrier protein thioesterase

A cotton genomic clone containing a 17.4-kb DNA segment was found to encompass a palmitoyl-acyl carrier protein (ACP) thioesterase (Fat B1) gene. The gene spans 3.6 kb with six exons and five introns, and is apparently the first plant FatB acyl-ACP thioesterase gene to be completely sequenced. The six exons are identical in nucleotide sequence to the open reading frame of the corresponding cDNA, and would encode a preprotein of 413 amino acids. The preprotein can clearly be identified as a FatB acyl-ACP thioesterase from its similarity to the deduced amino acid sequences of other FatB thioesterase preproteins. A 5'-flanking region of 914 bp was sequenced, with the potential TATA basal promoter 324 bp upstream from the ATG initiation codon. The 5'-flanking sequence also has a putative CAAT box and two presumptive basic region helixloop-helix (bHLH) elements with the consensus motif CANNTG (termed an E box), implicated as being a positive regulatory element in seed-specific gene expression.

A rapid technique for the determination of unknown plasmid library insert DNA sequence directly from intact yeast cells

A polymerase chain reaction (PCR)-based technique is described which allows for the determination of library plasmid insert DNA sequence directly and rapidly from intact yeast cells. Yeast spheroplasts are used to template a PCR reaction to amplify the insert sequence. This PCR product is then purified and its sequence directly determined using thermal cycle sequencing. Readable sequence can reproducibly be obtained from multiple yeast colonies in just two days. Uses of this technique in yeast two-hybrid screening as well as other types of yeast library screens are discussed.