发展中的mRNA差别显示技术

随着ＰＣＲ技术的出现（１９８５）,在分子生物学界又相继出现了两个很有影响的新技术──ＲＡＰＤ技术（１９９０）和ｍＲＮＡ差示法（１９９２）,前者用于分子标记,后者用于基因分离。ｍＲＮＡ差示法的生物学基础是基因的差别表达,既：单个细胞中表达的基因仅占基因总数的１５％。这种基因的差别表达决定了生命的所有过程,如：发育和分化、对逆境的反应、细胞分裂、老化等,图一给出了该方法最初的技术路线。提取要比较的两种或两种以上样品的ｍＲＮＡｓ,分别逆转录成ｃＤＮＡｓ,经过ＰＣＲ扩增后,直接进行测序胶电泳即可识别有差别的ｍＲＮＡ。其中、关键的是ＰＣＲ扩增时两个引物的设计．３＇端引物Ｏｌｉｇｏ（ｄＴ）ＭＮ很容易与具有Ｎ＇Ｍ＇－ｐｏｌｙ（Ａ）－３＇末端的大多数ｍＲＮＡ结合,进行ｃＤＮＡ的逆转录合成。Ｍ、Ｎ提供锚定位点,防止３＇端引物在ｐｏｌｙ（Ａ）序列不同位置上的随机结合。５＇端为１０个碱基的随机引物。这个经验上的碱基数值较理论的６－７个碱基（表一）更能满足测序胶电泳要求的条件：分子大小在５００ｂｐ左右,每条泳道上条带数在１００条左右。该方法近年来又有如下改进：一、ＰＣＲ退火温度由４２℃改为４０℃,可在保证特异性的同时,增加泳道上的     

Easy In Vitro Synthesis of Optimised Functioning Reporter mRNA from Common eGFP Plasmid

The extensive growth in number and importance of experiments and clinical-aimed techniques based solely or majorly on the activity of RNA strands, e.g. CRSPR/Cas9 and siRNA, has put emphasis on the necessity of standardisation of experiments with RNA. Considering RNA degradation during its handling seems to be a major hindrance in all RNA-based tools, the assessment of its integrity is of utmost importance. Furthermore, evaluating whether the RNA to be transfected is intact requires time-consuming electrophoresis protocol. In view of the RNA lability and the necessity for controlling experiments performed with this molecule, the transfection of a reporter mRNA may be of aid in optimising experiments. Nevertheless, commercial reporter mRNAs are far less available than plasmids for such purpose. Thus, in this work, we aimed at the optimisation of an easily performed protocol to produce a suitable eGFP mRNA. By utilising molecular biology kits customarily employed in molecular biology laboratories working with RNA-based techniques and starting from any eGFP coding vector, we produced four mRNA molecules: (1) eGFP mRNA (non-polyadenylated); (2) Kozak-eGFP mRNA (non-polyadenylated, produced from the Kozak-containing amplicon); (3) eGFP-PolyA mRNA (polyadenylated); (4) Kozak-eGFP-PolyA mRNA (containing both signals, Kozak sequence and poly(A) tail). These mRNA molecules were transfected into HEK 293 FT cells, readily transfectable, and into the MDBK bovine lineage, which has been observed as difficult-to-transfect DNA constructs. eGFP expression could be detected both by flow cytometry and by fluorescence microscopy after transfection with the polyadenylated mRNAs. Upon cytometric analysis, we noted a marked difference among the mRNA groups (p?<?0.01), both in fluorescent population percentage and in florescence intensity. We showed here the necessity of the polyadenylation step in order to achieve cell expression of the eGFP observable under fluorescence microscopy. The presence of the Kozak sequence, as a 5′ element, seems to augment significantly the level of protein produced upon mRNA transfection. We presented here an easy protocol to allow production of functioning mRNAs from any DNA construct. The molecules produced may aid in the standardisation and controlling most of the RNA-related experiments as well as it gives proper guidance for researchers performing expression of other proteins through mRNA transfection.     

DNA enzyme generated by a novel single-stranded DNA expression vector inhibits expression of the essential bacterial cell division gene ftsZ

Rapid emergence of antibiotic-resistant bacterial pathogens has created urgent demand for the discovery and development of new antibacterial agents directed toward novel targets. Antisense oligodeoxynucleotides (AS-ODN) and their modified forms have been utilized to block gene expression in bacterial cells, showing potential for developing highly specific and efficacious antibacterial agents. In this study, a tetracycline-regulated expression vector was developed for generating single-stranded DNA (ssDNA) of a desired target sequence in bacterial cells. This inducible ssDNA expression vector was tested for producing a DNA enzyme designed to specifically cleave ftsZ mRNA. Our results indicate that the expressed DNA enzyme molecules not only repress ftsZ gene expression and but also inhibit bacterial cell proliferation. Although we believe that the cleavage of ftsZ mRNA by the expressed DNA enzyme molecules is responsible for the inhibitory effects on ftsZ gene expression and bacterial cell proliferation, the antisense mechanism could also be responsible for the biological effects. The ability of this ssDNA expression system to selectively modulate gene expression may provide a powerful strategy in determining the contribution of a given gene product to bacterial growth or pathogenesis and opens a new venue for developing antibacterial agents.     

Detection of rare mRNA species in a complex RNA population by blot hybridization techniques: a comparative survey

The detection of very rare mRNA species in a complex RNA preparation by current RNA blotting techniques is not straightforward. To be able to determine the size of mRNA molecules representing 10(-6) to 10(-7) of the total mass of an RNA preparation, a quantitative comparison of the level of detection of denatured mRNA species electrophoretically separated on agarose gels, followed by transfer to either nitrocellulose or diazobenzyloxymethyl (DBM) paper and hybridization to specific cDNA probes was carried out. Different transfer procedures were analyzed. Optimal conditions have been found which allowed the detection of RNA bands containing as little as 5 pg of a specific sequence within a few days of autoradiography following hybridization with highly labeled [32P]cDNA probes. Using this procedure it was shown that the low amounts of alpha-fetoprotein (AFP) mRNA sequences present in adult rat liver are mature AFP mRNA molecules.     

Feasible and reliable quantification of mRNA in Arabidopsis thaliana using optical thin-film biosensor chips

mRNA quantification is very important in molecular biological researches.Traditional spectrophotometric method cannot distinguish DNA,rRNA and tRNA species from mRNA.Northern blot can be used for mRNA quantification but is known to be time consuming.To rapidly detect mRNA levels,we developed an optical thin-film biosensor chip based method,to quantify mRNA in samples.After total RNA was extracted,the mRNA with poly(A)tails was reverse transcribed with oligo(dT)20 primers and dNTPs mixed with digoxigenin(DIG...     

Effect of mutations and deletions in a bicistronic mRNA on the synthesis of influenza B virus NB and NA glycoproteins.

The mRNA derived from influenza B virus RNA segment 6 is functionally bicistronic and encodes the NB and NA glycoproteins in different, overlapping reading frames. NB protein synthesis is initiated at the 5'-proximal AUG codon, and 4 nucleotides downstream there is a second AUG codon which is used to initiate NA protein synthesis. The nucleotide sequence context of the first AUG codon conforms closely with the established 5'-CC(A/G)CCAUGG-3' consensus sequence (M. Kozak, Nucleic Acids Res. 15:8125-8148, 1987), which should favor initiation of NB protein synthesis at this site, yet NB and NA are found to accumulate in approximately equal amounts in infected cells. To determine the features important for allowing initiation at the second 5'-proximal AUG codon, we made changes in the 5'-terminal region of the mRNA, including deletions, insertions, and site-specific mutations. The recombinant DNA molecules were expressed in eucaryotic cells, and the accumulation of NB and NA was quantitated. The data indicate that changes in the immediate sequence around the first AUG codon do not make a large difference in the amounts of NB and NA that accumulate, but that when the first AUG codon is displaced from its normal position it is now quite efficient at preventing downstream initiation events. In addition, the data indicate that an element of the B/NB/NA mRNA 5' untranslated leader region acts in cis to enhance the expression of NB and NA.     

5''-Terminal sequences of eucaryotic mRNA can be cloned with high efficiency.

A method for cloning mRNAs has been used which results in a high yield of recombinants containing complete 5'-terminal mRNA sequences. It is not dependent on self-priming to generate double-stranded DNA and therefore the S1 nuclease digestion step is not required. Instead, the cDNA is dCMP-tailed at its 3'-end with terminal deoxynucleotidyl transferase (TdT). The synthesis of the second strand is primed by oligo(dG) hybridized to the 3'-tail. Double-stranded cDNA is subsequently tailed with dCTP and annealed to dGMP-tailed vector DNA. This approach overcomes the loss of the 5'-terminal mRNA sequences and the problem of artifacts which may be introduced into cloned cDNA sequences. Chicken lysozyme cDNA was cloned into pBR322 by this procedure with a transformation efficiency of 5 x 10(3) recombinant clones per ng of ds-cDNA. Sequence analysis revealed that at least nine out of nineteen randomly isolated plasmids contained the entire 5'-untranslated mRNA sequence. The data strongly support the conclusion that the 5'-untranslated region of the lysozyme mRNA is heterogeneous in length.     

Feasible and reliable quantification of mRNA in Arabidopsis thaliana using optical thin-film biosensor chips

mRNA quantification is very important in molecular biological researches.Traditional spectrophotometric method cannot distinguish DNA,rRNA and tRNA species from mRNA.Northern blot can be used for mRNA quantification but is known to be time consuming.To rapidly detect mRNA levels,we developed an optical thin-film biosensor chip based method,to quantify mRNA in samples.After total RNA was extracted,the mRNA with poly(A)tails was reverse transcribed with oligo(dT)20 primers and dNTPs mixed with digoxigenin(DIG)-11-dUTP.The transcribed first strand cDNA was hybridized with oligo(dA)20 nucleotide probes spotted on optical thin-film biosensor chips.Excess first strand cDNA,single-strand RNA,and mis-matcbed DNA/DNA hybrids were removed by washing.The perfect-matched DNA/DNA hybrid was detected with anti-DIG-AP(alkaline phosphatase)conjugate and then incubated with NBT/BCIP substrate for color development.The range of the color is from purplish red to blue,according to the cDNA mass deposited on chip surface.Detection of mRNA levels from Arabidopsis samples proved that this method is feasible for mRNA quantification,and has great potential for application in mRNA quantification in various organisms.     

BCL2 and BAX mRNA concentration profile in fibrillary astrocytoma

A high level of the BCL2 protein and the lack of apoptosis promoting protein BAX are beginning to be treated as markers of cellular resistance to anti-neoplastic drugs. The object of the study were specimens from stereotactic biopsy of Astrocytoma fibrillare in the central brain area, inaccessible to conventional surgery. The cytological preparations have been evaluated with histopathological and immunohistochemical methods in order to determine the origin of the tumour and assess cell proliferation activity. The molecular analysis conducted in order to determine the sensitivity of the tumour to radio- or chemotherapy included the determination of the number of mRNA BCL2 alpha and beta molecules and of BAX in 1 microg total RNA obtained from microscope slides. A higher expression of BAX than of BCL2-alpha is a prognosis for a positive result of chemo- or radiotherapy. A trace number of mRNA BCL2-beta molecules and a smaller number of mRNA BCL2-alpha molecules than mRNA BAX is a good prognosis for therapy.     

Determination of best-fit potential parameters for a reactive force field using a genetic algorithm

The ReaxFF interatomic potential, used for organic materials, involves more than 600 adjustable parameters, the best-fit values of which must be determined for different materials. A new method of determining the set of best-fit parameters for specific molecules containing carbon, hydrogen, nitrogen and oxygen is presented, based on a parameter reduction technique followed by genetic algorithm (GA) minimization. This work has two novel features. The first is the use of a parameter reduction technique to determine which subset of parameters plays a significant role for the species of interest; this is necessary to reduce the optimization space to manageable levels. The second is the application of the GA technique to a complex potential (ReaxFF) with a very large number of adjustable parameters, which implies a large parameter space for optimization. In this work, GA has been used to optimize the parameter set to determine best-fit parameters that can reproduce molecular properties to within a given accuracy. As a test problem, the use of the algorithm has been demonstrated for nitromethane and its decomposition products.     

Isolation and translation of mRNA coding for the variant surface antigens of Paramecium.

In the poly(A)+RNA isolated from the ciliate Paramecium primaurelia is found a discrete and abundant mRNA species of high molecular weight (corresponding to about 9,000 nucleotides). This mRNA species has size and abundance characteristics that identify it tentatively as the message coding for the variant cell-surface antigens. After microinjection of the high molecular weight mRNA into amphibian oocytes, polypeptides are synthesized that are immunoprecipitated specifically with antibodies directed against the homologous Paramecium antigen. On collecting the culture medium of oocytes microinjected with Paramecium mRNA, newly-synthesized complete antigen molecules (Mr approximately 300,000) can be recovered by immunoprecipitation.