一种用少量标本快速构建老年性白内障消减cDNA文库的方法

为从少量标本中获得含较多大片段的、高质量的老年性白内障消减cDNA文库,利用磁珠分离、生物素标记的改良消减杂交法获得差异cDNA,利用选择性PCR法扩增其中大片段差异cDNA,从而成功构建老年性白内障消减cDNA文库.在文库中随机挑取的22个克隆中,1 000 bp以上的片段有7个,占31.8%,750 bp以上有15个,占68.2%.所得cDNA片段较大,可以满足下一步研究需要.改良消减杂交法结合选择性PCR法可以从少量标本中快速有效地获得大片段高质量的消减cDNA文库.     

用改良消减杂交结合选择性PCR法构建老年性白内障消减cDNA文库

为构建含较多大片段的高质量的老年性白内障消减cDNA文库 ,利用生物素标记、磁珠分离的改良消减杂交法获得差异cDNA .利用选择性PCR法扩增其中大片段差异cDNA ,将其与T 载体进行T A连接并转化入大肠杆菌 ,成功构建老年性白内障消减cDNA文库 .共获得 4 0 0 0余个克隆 ,随机挑取的 2 2个克隆中 ,≥ 10 0 0bp的片段有 7个 ,占 31 8% ,≥ 75 0bp有 15个 ,占 6 8 2 % .将≥ 75 0bp的 15个克隆进行反向点杂交 ,排除其中假阳性克隆 ,阳性克隆经测序并与GenBank比较 ,得到 6个已知基因、1个新基因 ,6个已知基因中 4个为全长基因 ,说明所得cDNA片段较大 ,文库质量较高 .改良消减杂交法结合选择性PCR法可以快速有效地获得大片段高质量的消减cDNA文库 ,为进一步筛选、鉴定老年性白内障致病相关基因奠定了基础     

Cloning of open reading frames and promoters from the Saccharomyces cerevisiae genome: construction of genomic libraries of random small fragments

We have developed a novel efficient method, carrier-facilitated insertion, to insert small (150-600 bp) DNA fragments into plasmid vectors. This method employs a carrier segment of vector DNA to circumvent the difficulties in ligating two fragments together to generate a recombinant circle efficiently. We have used carrier-facilitated insertion to construct three genomic libraries of random (DNase I-generated) fragments from the Saccharomyces cerevisiae genome. One of these was an expression library, and the other two were promoter-cloning libraries. 87-90% of the Escherichia coli colonies in each library contained recombinant plasmids, and less than 3% of the recombinants contained more than one insert. Detection of open reading frames among the inserts in the expression library was accomplished by testing for beta-galactosidase activity. This methodology, unencumbered by the intrinsic disproportionality of cDNA libraries, can be used to identify and clone DNA that codes for a specific antigenic determinant. When used in combination with a method to detect and isolate random constitutive, repressible and inducible yeast promoters, these libraries should permit a comprehensive analysis of the yeast genome and its expression.     

团头鲂促性腺激素GtH Iβ亚基基因5′端启动子区克隆及表达载体构建

本研究利用改进的锚定PCR方法克隆了团头鲂(Megalobrama amblycephala)促性腺激素Iβ(GtH Iβ)亚基基因5′端侧翼序列,并在生物信息学方法分析的基础上构建了荧光素酶质粒表达载体。序列分析结果显示:克隆得到的GtHIβ亚基基因5′端侧翼序列长度为479bp,其中包括TATA盒、ARE、PRE、ERE、SF-1、Ptx1等可能对GtH Iβ亚基基因转录调控起重要作用的功能转录因子结合位点。利用PCR方法在基因组中扩增得到了3个缺失片段,并同全长片段一起分别连接至pGL3-Basic报告基因载体,成功构建了团头鲂GtH Iβ亚基基因5′端侧翼序列的表达载体,为进一步研究、分析其转录调控机制提供了基础。       

用人染色体14q24.3区带探针池直接分离表达顺序

本文报道了从显微切割的人染色体区带直接分离区带专一性表达序列的方法和结果。     

一种快速简便构建DNA病毒测序文库的方法

为了对1株中国棉铃虫核型多角体缺失病毒HZ-9进行基因组测序,采用了一种新的方法,通过超声波振断HaBacHZ9细菌人工染色体质粒（bacterial artificial chromosome plasmid,Bacmid）基因组DNA,用Taq酶在DNA片段两端加腺噤呤A,胶回收后得到预期的1—2kb的DNA片段,然后与pGEM-Teasy载体连接,构建了中国棉铃虫缺失病毒HaBacHZ9的亚克隆文库。结果随机挑选10个克隆子酶切分析,显示9个克隆子有1500bp左右的插入片断,并对HaBaeHZ9进行了全基因组测序。结论成功构建了HaBaeHZ9的DNA测序文库,为HZ-9功能基因组学研究奠定了基础,这是一种简单快速的构建DNA病毒测序文库的方法。     

Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones

 We report a strategy for developing codominant PCR-based genetic markers by using sequenced cDNA clones from loblolly pine (Pinus taeda L.). These clones were previously used as probes for detecting restriction fragment length polymorphisms (RFLPs) to generate linkage maps. After assessing the complexity of banding patterns from Southern blots, we selected clones representing relatively simple gene families, and then determined nucleotide sequences for about 200 bp at each end of the cDNA inserts. Specific PCR primers were designed to amplify samples of genomic DNA derived from two loblolly pine mapping populations. Polymorphisms were detected after digesting the amplified DNA fragments with a battery of restriction endonucleases, and most polymorphisms were inherited in a Mendelian fashion. These newly identified genetic markers are codominant and relatively simple to use. By assaying DNA from individuals used to construct RFLP maps, we show that most of these markers map to the same position as the RFLP loci detected using their corresponding cDNAs as probes, implying that these markers have been converted from RFLP to PCR-based methods. These PCR-based markers will be useful for genome mapping and population genetics. Received: 10 February 1998 / Accepted: 25 February 1998     

Identification of a new mutation in medium-chain acyl-CoA dehydrogenase (MCAD) deficiency.

A mutation involving an A-to-G nucleotide replacement at position 985 of the medium-chain acyl-CoA dehydrogenase (MCAD) cDNA was found in homozygous form in 18 unrelated MCAD-deficient families and in heterozygous form in 4 families. By PCR amplification and sequencing of cDNA from a compound heterozygote, we have detected a new mutation in an MCAD-deficient patient in whom one MCAD allele produces mRNA that is missing 4 bp in the MCAD cDNA, while the other allele carries the A-to-G-985 mutation. The presence of this 4-bp deletion was confirmed in the patient's genomic DNA by dot-blot hybridization with allele-specific oligonucleotide probes and by restriction analysis of PCR products. A rapid screening test for this 4-bp deletion was developed, based on mismatched primer PCR amplification. The deletion created a new restrictive-enzyme site which yielded two DNA fragments. The 4-bp deletion was not found in the three remaining MCAD chromosomes not harboring the A-to-G-985 mutation, nor it was present in 20 chromosomes from 10 unrelated normal Caucasians. The PCR-based method for screening these two mutations can detect over 93% of all MCAD mutations.     

Determination of the sequence of an expressible cDNA clone encoding ERp60/calregulin by the use of a novel nested set method

An analysis of the N-terminal sequence of the luminal endoplasmic reticulum protein, ERp60, showed that it was identical to the well-characterized Ca2+-binding protein, calregulin. A full-length, expressible cDNA clone encoding this protein was isolated from a mouse fibroblast cDNA library. A novel nested set strategy for the production of overlapping fragments for DNA sequencing was used to determine the complete nucleotide (nt) sequence of both strands of the ERp60 clone. This method utilizes a series of nonspecific deletion primers in conjunction with a specific site primer to generate the nested set fragments. This procedure possesses several advantages over other nested set techniques, since it does not require (i) the re-cloning of the DNA insert into other vectors, (ii) any prior knowledge of the restriction sites of the nt sequence, or (iii) the transformation and analysis of bacterial subclones. ERp60 has a 17-amino acid (aa) signal sequence and the mature protein contains 399 aa with a calculated M(r) of 46,347.     

A simple,rapid, efficient and inexpensive strategy for sequencing clones from cDNA libraries

In this report, we describe a simple, rapid, efficient and inexpensive strategy for sequencing inserted DNAs from clones of cDNA or gDNA libraries. This strategy uses PCR products directly amplified from transformed bacterial colonies, with universal primers within the vector. The method can be applied for sequencing cDNA or gDNA libraries with up to 4 ∼ 5 kb insert sizes, without overnight liquid culture or plasmid DNA preparation steps. We successfully used this method to analyze clones from full-length, enriched cDNA libraries. Although simple, following this strategy will significantly help researchers to avoid unnecessary steps in the analysis of a cDNA library.     

Hamster estrogen receptor cDNA: cloning and mRNA expression

Estrogen-induced hamster kidney tumor model serves as a useful model to study the biochemical and molecular mechanisms of hormonal carcinogenesis. In this model, we have demonstrated an increased expression of estrogen receptor mRNA and protein in estrogen-treated kidneys and in estrogen-induced tumors. The sequence information for hamster estrogen receptor gene is not known and has been investigated in this study. A hamster uterus cDNA library was constructed and the 5'-region of the hamster estrogen receptor cDNA cloned from this library using polymerase chain reaction (PCR) methodology. Additionally, hamster kidney polyadenylated RNA was reverse transcribed and PCR amplified using primers that were designed based on maximum homology between mouse, rat and human estrogen receptor cDNAs. These PCR amplified fragments were cloned into plasmid vectors and clones with the expected size of the insert subjected to Southern blot analysis using human estrogen receptor cDNA as a probe. The positive clones on Southern blot analysis and the PCR amplified products from these clones were subjected to DNA sequence analysis. Using this strategy, a full length, 1978 bp hamster estrogen receptor cDNA has been cloned which shows 87% homology with human, 90% with rat and 91% with mouse estrogen receptor cDNA. The deduced amino acid shares 88% homology with human, and 93% with rat and mouse estrogen receptors. Hamster estrogen receptor domain C (DNA binding domain) shows a 100% homology with a similar domain from mouse, rat, human, pig, sheep, horse and chicken estrogen receptor (Genebank reference ID: AF 181077).     

Improved detection of small deletions in complex pools of DNA

About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are engaged in a project to derive deletion alleles in every gene in this set. Our standard methods make use of nested PCR to hunt for animals in mutagenized populations that carry deletions at a given locus. The deletion bearing animals exist initially in mixed populations where the majority of the animals are wild type at the target. Therefore, the production of the PCR fragment representing the deletion allele competes with the production of the wild type fragment. The size of the deletion fragment relative to wild type determines whether it can compete to a level where it can be detected above the background. Using our standard conditions, we have found that when the deletion is <600 bp, the deletion fragment does not compete effectively with the production of the wild type fragment in PCR. Therefore, although our standard methods work well to detect mutants with deletions >600 bp, they do not work well to detect mutants with smaller deletions. Here we report a new strategy to detect small deletion alleles in complex DNA pools. Our new strategy is a modification of our standard PCR based screens. In the first round of the nested PCR, we include a third PCR primer between the two external primers. The presence of this third primer leads to the production of three fragments from wild type DNA. We configure the system so that two of these three fragments cannot serve as a template in the second round of the nested PCR. The addition of this third primer, therefore, handicaps the amplification from wild type template. On the other hand, the amplification of mutant fragments where the binding site for the third primer is deleted is unabated. Overall, we see at least a 500-fold increase in the sensitivity for small deletion fragments using our new method. Using this new method, we report the recovery of new deletion alleles within 12 C.elegans genes.     

Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology

Two cDNAs encoding new DNA-binding proteins (Dbps) have been cloned using a human placenta lambda gt11 recombinant cDNA library and DNA fragments as probes. Hybrid proteins expressed by the lambda gt11 cDNA library were blotted onto nitrocellulose filters, and incubated with three different radio-labeled DNA probes containing the human epidermal growth factor (EGF) receptor enhancer or the human c-erbB-2 promoter. Two kinds of clones, named dbpA and dbpB, showed high affinities for the DNA probes. The comparison of the nucleotide and the deduced amino acid (aa) sequences between these two cDNAs indicated that 100 of 109 aa located in the central region of these two Dbps were identical. The dbpA and dbpB-coded proteins also had an affinity for other cDNA probes such as the human c-ski gene, but not for poly(dI-dC).poly(dI-dC), suggesting that the sequence(s) recognized by the dbpA and dbpB-coded proteins may occur frequently, or that these proteins bind to DNA non-specifically in a different manner from that of histones. A simple method, described in this paper, can be used to isolate cDNA clones encoding Dbps. Strategies used for the detection of sequence-specific and non-specific Dbps are discussed.     

Identification of the alternative splice products encoded by the human protein phosphatase inhibitor-1 gene

We have isolated three major cDNA fragments of protein phosphatase inhibitor-1 from human brain and liver by RT-PCR. The 536 bp fragment encoded the wild-type of inhibitor-1 while two other fragments were alternative splice products of the inhibitor-1 gene, which was confirmed by partial genomic DNA sequencing. The 380 bp fragment encoded an in-frame 51-residue-deleted inhibitor-1, named inhibitor-1alpha, and the deletion occurred from residue 84 to 134 of inhibitor-1. The 316 bp fragment termed inhibitor-1beta was derived from an internal deletion of 536 bp fragment. This deletion resulted in an out of frame shift, allowing the 316 bp fragment that encoded the partial sequence of inhibitor-1. Based on the reported mRNA sequence of inhibitor-1 and evidence from our RT-PCR, we suggested that inhibitor-1beta consisted of 132 amino acids of which the N-terminal 61 amino acid sequences were identical to inhibitor-1 while the sequence after residue-61 was markedly different.     

cDNA文库法制备HCV-1诊断芯片探针的应用性研究

探讨利用eDNA文库法制备HCV-1诊断基因芯片探针的可行性．用限制性内切酶Sau3AI消化HCVla及lb全长eDNA,所得的酶切片段72℃补平加A,AT克隆,PCR初步鉴定,并测序．结果显示：HCV两个亚型1a、1b的全长eDNA得到57个大小相对一致(200-1000bp)的片段,平均每个亚型约28个,PCR及序列分析表明,所扩增的片段均属于HCV-1的特异基因,可做为HCV-1诊断基因芯片探针．利用eDNA文库法收集片段是一种快速、简便制备芯片探针的实用方法．