Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1996-08-07
2003-06-10
Slobodyansky, Elizabeth (Department: 1652)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S069100, C435S091100, C435S091200, C536S023500
Reexamination Certificate
active
06576418
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to a method for isolating and Identifying the nucleotide sequence of the human gene for the type IV collagen a5(IV) chain. The present invention is directed to the determination of the nucleotide sequence of the gene for the a5(IV) collagen chain in individuals by any method known to the art e.g. cloning from genomic DNA libraries or amplifying gene regions with the polymerase chain reaction (PCR) and studying their physical properties or nucleotide sequences. In addition, the invention is directed to the use of the nucleotide sequences of the a5(IV) gene to amplify or identify the nucleotide sequences of the a5(IV) gene.
BACKGROUND OF THE INVENTION
Basement membranes (BM) are special extracellular, sheet-like structures that separate cells of organs from the underlying connective tissues. They form flexible boundaries that provide physical support and biological signals required for maintainance of morphology and orderly development of distinct tissue patterns. The BM protein components can have different subunits and molecular compositions that possess the necessary functional elements for the tissues concerned. This has become more apparent as new chains with restricted tissue distributions have been found e.g. for type IV collagen and laminin. The basement membranes have also an Important role in the correct regeneration of tissues following injuries such as during post-wound reformation of skin and nerves. Basement membranes also function as macromolecular filters e.g. in kidneys where the glomerular basement membrane is the sole filtration barrier between the capillary lumen and the urinary space, hindering the blood to urine leakage of macromolecules and blood cells.
Basement membranes are composed of several specific components that include type IV collagen, laminin, entactin (nidogen) and proteoglycans. Type IV collagen is the major structural component of basement membranes and it forms the framework of these extracellular structures. In addition, basement membranes contain SPARK (BM-40), fibronectin and type VII collagen that are also present in other extracellular structures. The exact molecular compositions of basement membranes in different tissues Is not well known but there Is growing evidence that even the ubiquitous basement membrane components as type IV collagen and laminin have different chain compositions in different tissues. Additionally, there are some proteins such as pemphigoid antigen that are present only In the basement membranes of skin.
Type IV collagen is the major structural component of basement membranes and It can provide up to 60 % of the structure. As all collagens, the type IV collagen molecule is formed by three a chains coiled around each other to form the collagen triple helix with the repeated Gly-X-Y-triplet amino acid sequence containing regions. The molecule has a triple-helical 400 nm-long collagenous part and a C-terminal globule with a diameter of about 15 nm. The collagenous domain sequence has several interruptions in the otherwise continuous collagenous Gly-X-Y repeat sequence that give flexibility to the type IV collagen molecules as opposed to the rigid rod-like molecules of fibrillar collagens with uninterrupted helices. The triple-helical type IV collagen molecules can form dimers by the attachment of two NC domains and tetramers by the 30 nm overlapping cross-linking of four molecules of their amino terminal ends (Timpl, Eur. J. Biochem. 180: 487-502, 1989).
The major form of the molecules consists of two &agr;1(IV) and one &agr;2(IV) chain. The applicants have determined the entire amino acid sequence of these two chains from man by cloning and sequencing cDNA clones covering the coding region (Soininen et al., FEBS. Lett., 225: 188-194, 1987; Hostikka and Tryggvason, J. Biol. Chem., 263: 19488-19493, 1988). The results showed that the &agr;1(IV) chain is synthesized as a 1969 amino acid residue polypeptide as compared to 1712 residues in the &agr;2(IV) chain. The carboxyl terminal NC domains of the two chains are very similar with 63 % identical amino acid residues. The sequence identity of the two chains is much less conserved in the triple-helical region with only 49 % identity; where only 22 % of the X and Y residues in the collagenous Gly-X-Y-repeat sequence are conserved. Two other distinct type IV collagen &agr; chains, referred to as &agr;3(IV) and &agr;4(IV), have been described (Butkowski et al., J. Biol. Chem., 262: 7874-7877, 1987; Saus et al. J. Biol. Chem. 263: 13374-13380, 1988; Gunwar et al., J. Biol. Chem., 265: 5466-5469, 1990).
Of importance with respect to the present invention is our recent discovery of yet another novel human type IV collagen &agr;5(IV) chain by cDNA cloning (Hostikka et al., Proc. Natl. Acad. Sci. USA. 87: 1606-1610, 1990 and the parent U.S. patent application “Method for determining the nucleotide sequence of a novel &agr;5(IV) chain of human type IV collagen” Ser. No. 377,238, filed on Jul.7, 1989 now U.S. Pat. No. 5,114,840. Amino acid sequence comparison with the &agr;1(IV) and &agr;2(IV) chains and the data available of the &agr;3(IV) and &agr;4(IV) chains demonstrated that the &agr;5(IV) chain is a distinct gene product which is closely related to the &agr;1(IV) chain. In the NC domain the identity between the deduced amino acid sequences is 83 % with the &agr;1(IV) chain and with &agr;2(IV) chain 63 %; whereas in the collagenous domain the identities are 58 % and 46 %, respectively. Furthermore, all the interruptions in the collagenous Gly-X-Y-repeat sequence of the &agr;5(IV) chain coincide with those in the &agr;1(IV) chain but only partially with those In the &agr;2(IV) chain (Hostikka et al., Proc. Natl. Acad. Sci. USA. 87: 1606-1610, 1990 and the parent U.S. patent application “Method for determining the nucleotide sequence of a novel &agr;5(IV) chain of human type IV collagen” Ser. No. 377,238,filed on Jul. 7, 1989, now U.S. Pat. No. 5,144,840.
With &agr;5(IV)-specific peptide-antibodies, the chain was shown to be almost exclusively present in the GBM in the kidney (Hostikka et al., Proc. Natl. Acad. Sci. USA. 87: 1606-1610, 1990 and the parent U.S. patent application “Method for determining the nucleotide sequence of a novel &agr;5(IV) chain of human type IV collagen”Ser. No. 377,238, filed on Jul.7, 1989, now U.S. Pat. No. 5,144,840 and the continuation-in-part application “Immunological methods for the detection of the human type IV collagen &agr;5 chain”, filed Dec. 20, 1990, U.S. application Ser. No. 630,563 whereas the well characterized &agr;1(IV) and &agr;2(IV) chain are believed to be ubiquitous basement membrane (BM) components present in all BMs.
Using cDNA probes and both somatic cell-hybrids and in situ hybridization, the gene for the human type IV collagen &agr;5 chain COL4A5 was localized to the q22 region on the long arm of chromosome X (Hostikka et al., Proc. Natl. Acad. Sci. USA. 87: 1606-1610, 1990 and the parent U.S. patent application “A Method for determining the nucleotide sequence of a novel &agr;5(IV) chain of human type IV collagen” serial number 377,238, filed on Jul. 7, 1989, U.S. Pat. No. 5,144,840. This is different from the human genes COL4A1 and COL4A2 coding for the &agr;1(IV) and &agr;2(IV) chains that both are located on the terminal end of the long arm of the chromosome 13 (Boyd et al., Hum. Genet., 74: 121-125, 1986; Griffin et al., Proc. NatI. Acad. Sci. USA., 84: 512-516, 1987). The &agr;1(IV) and &agr;2(IV) chains are transcribed by different DNA strands from a common bidirectional promoter in opposite directions, so that the transcription initiation sites are separated by only 42-127 bp (Pöschl et al., EMBO J., 7: 2687-2695, 1988; Soininen et al., J. Biol. Chem., 263: 17217-17220, 1988).
The applicants have determined the complete structure of the human &agr;1(IV) gene (Soininen et al., J. Biol. Chem.,264: 13565-13571, 1989) and the partial structure for the human &agr;2(IV) gene (Hostikka and Tryggvason, FEBS Lett., 224: 297-305). The &agr;1(IV) gene contains 52 exons spre
Hostikka Sirkka L.
Tryggvason Karl
Zhou Jing
BioStratum, Inc.
Fay Sharpe Fagan Minnich & McKee LLP
Slobodyansky Elizabeth
LandOfFree
Method for determining the nucleotide sequence of the gene... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method for determining the nucleotide sequence of the gene..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for determining the nucleotide sequence of the gene... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3151521