细胞分子生物学新方法



细胞分子生物学新方法
方法学是现代医学和分子生物学的基础。现代医学生物学的研究进展和一切重大发现无一都离不开新技术和新方法。Nature杂志和核酸研究等国际上重要刊物都开辟了“methods”专栏和专刊。为此，CMBI专门搜集了近两年来发表在相关杂志上的细胞分子生物学新方法的文献，供大家参考。更多的文献请用相关关键词通过CMBI文献查询获取。
Whole-genome experimental identification of insertion-deletion polymorphisms of interspersed repeats by a new general approach Using DSP, a reversible cross-linker, to fix tissue sections for immunostaining, microdissection and expression profiling Use of pteridine nucleoside analogs as hybridization probes Use of mRNA-and protein-destabilizing elements to develop a highly responsive reporter system Use of a restriction enzyme-digested PCR product as substrate for helicase assays Two-step total gene synthesis method Two-photon fluorescence cross-correlation spectroscopy as a potential tool for high-throughput screening of DNA repair activity Tris-borate is a poor counterion for RNA Triplet nucleotide removal at random positions in a target gene Transposon-mediated generation of targeting vectors for the production of gene knockouts Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation Transformation of isolated mammalian mitochondria by bacterial conjugation Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces The power of real-time PCR Tetracycline-inducible gene regulation in mycobacteria Targeted ‘knockdown’ of spliceosome function in mammalian cells Targeted disruption of transcriptional regulatory function of p53 by a novel efficient method for introducing a decoy oligonucleotide into nuclei Tagging genes with cassette-exchange sites Systematic analysis of bicistronic reporter assay data Synthesis of unimolecularly circular G-quadruplexes as prospective molecular probes Surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes Suppression of vascular endothelial growth factor expression at the transcriptional and post-transcriptional levels Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells Submicron patterning of DNA oligonucleotides on silicon Subcellular localization as a limiting factor for utilization of decoy oligonucleotides Structure and RNA binding of the third KH domain of poly(C)-binding protein 1 Structural analysis of hepatitis C RNA genome using DNA microarrays Stringent doxycycline-dependent control of gene activities using an episomal one-vector system Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription Spatially and temporally controlled gene transfer by electroporation into adherent cells on plasmid DNA-loaded electrodes Small circular DNAs for synthesis of the human telomere repeat SiteFinding-PCR-a simple and efficient PCR method for chromosome walking Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs Site-directed, Ligase-Independent Mutagenesis (SLIM) siRNA target site secondary structure predictions using local stable substructures siRNA relieves chronic neuropathic pain Single-particle tracking for DNA tether length monitoring Single small-interfering RNA expression vector for silencing multiple transforming growth factor-β pathway components Single nucleotide extension technology for quantitative site-specific evaluation of metC-C in GC-rich regions Single copy shRNA configuration for ubiquitous gene knockdown in mice Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions Simple and highly efficient BAC recombineering using galK selection Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray Sequence dependence of cross-hybridization on short oligo microarrays Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes Selection of genomic sequences that bind tightly to Ff gene 5 protein Selection of functional human antibodies from retroviral display libraries Screening of retroviral cDNA libraries for factors involved in protein phosphorylation in signaling cascades Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses sc-An ES cell system for rapid, spatial and temporal analysis of gene function in vitro and in vivo RNAPol-ChIP-a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription RNAi-A bi-functional siRNA construct induces RNA interference RNA stem–loop enhanced expression of previously non-expressible genes RNA silencing in plants by the expression of siRNA duplexes RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays Reversibly switchable DNA nanocompartment on surfaces Reverse Sanger sequencing of RNA by MALDI-TOF mass spectrometry after solid phase purification Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features Real-time PCR genotyping using displacing probes Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry Real-time measurement of in vitro transcription Real-time investigation of nucleic acids phosphorylation process using molecular beacons Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo Quantitative high-throughput analysis of transcription factor binding specificities Quantitative detection of siRNA and single-stranded oligonucleotides Quantitative analysis of highly parallel transfection in cell microarrays Protein–DNA footprinting by endcapped duplex oligodeoxyribonucleotides Protein-mediated error correction for de novo DNA synthesis Protein evolution by codon-based random deletions Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts Production of viral vectors using recombinase-mediated cassette exchange Preparation of DNA-modified nanoparticles and preliminary study for colorimetric SNP analysis using their selective aggregations PPC-an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations PieceMaker-selection of DNA fragments for selector-guided multiplex amplification Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells PCR amplification from single DNA molecules on magnetic beads in emulsion Partial 13C isotopic enrichment of nucleoside monophosphates Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids One-step random mutagenesis by error-prone rolling circle amplification Oligonucleotide-assisted cleavage and ligation Offset recombinant PCR Nucleotide exchange and excision technology (NExT) DNA shuffling Magnetic Resonance Imaging of Neuronal Function in the Spinal Cord novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [-32P]ATP in RNA structural investigation Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions New separation-free assay technique for SNPs using two-photon excitation fluorometry Negatively charged self-assembling DNA-poloxamine nanospheres for in vivo gene transfer Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation Multiplex PCR Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments MSRE-PCR for analysis of gene-specific DNA methylation Molecular dynamics imaging in micropatterned living cells Molecular beacons with a homo-DNA stem molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs Modified branched peptides with a histidine-rich tail enhance in vitro gene transfection Mithramycin forms a stable dimeric complex by chelating with Fe(II) Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression Miniature RT–PCR system for diagnosis of RNA-based viruses Microarray segmentation methods significantly influence data precision MethylQuant-a sensitive method for quantifying methylation of specific cytosines within the genome Methylation-Specific MLPA (MS-MLPA) Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization method for cloning and sequencing long palindromic DNA junctions metaSHARK-software for automated metabolic network prediction from DNA sequence and its application Measurement of DNA mismatch repair activity in live cells MARA-a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays Mapping the B-A conformational transition along plasmid DNA mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy Magnetically assisted DNA assays Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR L1 retrotransposon-mediated stable gene silencing KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system Joining of long double-stranded RNA molecules through controlled overhangs Investigations on DNA intercalation and surface binding by SYBR Green Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs Instant evaluation of the absolute initial number of cDNA copies from a single real-time PCR curve Induction and characterization of taxol-resistance phenotypes with a transiently expressed artificial transcriptional activator library Inducible suppression of Fgfr2 and Survivin in ES cells using a combination of the RNA interference (RNAi) Increasing the efficiency of SAGE adaptor ligation bydirected ligation chemistry In vitro selection of restriction endonucleases by in vitro compartmentalization In vitro selection of Jun-associated proteins using mRNA display In situ oligonucleotide synthesis on poly(dimethylsiloxane) In situ imaging and isolation of proteins using dsDNA oligonucleotides Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools Improved microarray methods for profiling the yeast knockout strain collection Improved methods for the generation of human gene knockout and knockin cell lines Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules Hypervariable genes—experimental error or hidden dynamics Human pol II promoter prediction Human base excision repair enzymes apurinic-apyrimidinic endonuclease1 (APE1), DNA polymerase β and poly(ADP-ribose) polymerase how to search for general rules in RNA recombination High-throughput two-hybrid analysis High-throughput polyribosome fractionation High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry High sensitivity EndoV mutation scanning through real-time ligase proofreading Headloop suppression PCR and its application to selective amplification of methylated DNA sequences Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH Genomic DNA as a cohybridization standard for mammalian microarray measurements Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays Genome-wide selection of unique and valid oligonucleotides Genome-wide estimation of transcript concentrations from spotted cDNA microarray data Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis Genome amplification of single sperm using multiple displacement amplification Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags Gene trap and gene inversion methods for conditional gene inactivation in the mouse Gene silencing in alveolar type II cells using cell-specific promoter in vitro and in vivo Four new type I restriction enzymes identified in Escherichia coli clinical isolates Expressible molecular colonies Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins Evaluation of vector-primed cDNA library production from microgram quantities of total RNA Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease Enhanced microarray performance using low complexity representations of the transcriptome End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes Emerging tools for real-time labinteractions on functional protein microarrays Efficient and seamless DNA recombineering using a thymidylate synthase A selection system Effective transcriptome amplification for expression profiling on sense-oriented oligonucleotide microarrays effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides Dual FRET molecular beacons for mRNA detection in living cells DNA microarrays on nanoscale-controlled surface DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene DNA analysis with multiplex microarray-enhanced PCR Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay Direct molecular haplotyping by melting curve analysis of hybridization probes Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes Direct isolation of specific RNA-interacting proteins using a novel affinity medium Direct detection of methylation in genomic DNA Diagnostic application of padlock probes—multiplex detection of plant pathogens using universal microarrays Development of an automated in vitro selection protocol to obtain RNA-based aptamers-identification of a biostable substance P antagonist Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs Determination of tumor necrosis factor receptor-associated factor trimerization in living cells by CFPYFPmRFP FRET detected by flow cytometry Detection of single DNA molecules by multicolor quantum-dot end-labeling Detection of protein–DNA interaction with a DNA probe Detection and discovery of RNA modifications using microarrays Detection and characterization of horizontal transfers in prokaryotes using genomic signature Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH Detecting seeded motifs in DNA sequences Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered Covalent antibody display—an in vitro antibody-DNA library selection system Correcting errors in synthetic DNA through consensus shuffling Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor Control of siRNA expression using the Cre–loxP recombination system Conditional knockdown of Fgfr2 in mice using Cre-LoxP induced RNA interference Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction Competitive enzymatic reaction to control allele-specific extensions Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop Combining SELEX with quantitative assays to rapidly obtain accurate models of protein–DNA interactions Combinatorial codon-based amino acid substitutions ChIP Display-novel method for identification of genomic targets of transcription factors Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle The multiple uses of fluorescent proteins to visualize cancer in vivo BiSearch= primer-design and search tool for PCR on bisulfite-treated genomes Bigenic Cre-loxP, putk conditional genetic ablation Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples Attachment of oligonucleotide probes to poly carbodiimide-coated glass for microarray applications Atelocollagen-mediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo ArrayOme-a program for estimating the sizes of microarray-visualized bacterial genomes Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis Analysis of scanning force microscopy images of protein-induced DNA bending using simulations Analysis of host response to bacterial infection using error model based gene expression microarray experiments An ultrasensitive site-specific DNA recombination assay based on dual-color fluorescence cross-correlation spectroscopy An ultrasensitive photoelectrochemical nucleic acid biosensor An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes An efficient system to establish multiple embryonic stem cell lines carrying an inducible expression unit An efficient one-step site-directed and site-saturation mutagenesis protocol Amino-functionalized DNA Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA Advances in functional protein microarray technology A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids A universal transgene silencing method based on RNA interference a specific signature for nucleic acid structures A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences A simple, bead-based approach for multi-SNP molecular haplotyping A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes A simple method for displaying recalcitrant proteins on the surface of bacteriophage lambda A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins A novel real-time PCR assay for quantitative analysis of methylated alleles A novel PCR strategy for high-efficiency, automated site-directed mutagenesis A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm A novel method of identifying genetic mutations using an electrochemical DNA array a novel method for surveying allelic sequence variation A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system A novel 4-base-recognizing RNA cutter that can remove the single 3' terminal nucleotides from RNA molecules A new approach to SNP genotyping with fluorescently labeled mononucleotides A multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo A multi-enzyme model for pyrosequencing A microarray configuration to quantify expression levels and relative abundance of splice variants A method to monitor replication fork progression in mammalian cells A method to find tissue-specific novel sites of selective adenosine deamination A high-throughput screening of genes that encode proteins transported into the endoplasmic reticulum A high-throughput method to monitor the expression of microRNA precursors A high-throughput assay for Tn5 Tnp-induced DNA cleavage A GFP-based reporter system to monitor nonsense-mediated mRNA decay A GFP-based assay for rapid screening of compounds affecting ARE-dependent mRNA turnover A gene truncation strategy generating N-and C-terminal deletion variants of proteins for functional studies A FRET-based analysis of SNPs without fluorescent probes A dual-light reporter system to determine the efficiency of protein–protein interactions in mammalian cells A dual-fluorescence reporter system for high-throughput clone characterization and selection by cell sorting A complementation method for functional analysis of mammalian genes A colorimetric method for point mutation detection using high-fidelity DNA ligase A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA 2(I) collagen gene regulation by protein kinase C signaling in human dermal fibroblasts Zooming in on electron tomography Use of quantum dots for live cell imaging The Overnight Express Autoinduction System-High-density cell growth and protein expression while you sleep Single-molecule DNA nanomanipulation-Improved resolution through use of shorter DNA fragments Simple bioseparations using self-cleaving elastin-like polypeptide tags Culture of human embryonic stem cells Reverse MAPPIT-screening for protein-protein interaction modifiers in mammalian cells Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system Real-time imaging of ligand-induced IKK activation in intact cells and in living mice Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry proteomics gets parallel Profiling DNA methylation patterns using genomic tiling microarrays Production of endoribonuclease-prepared short interfering RNAs for gene silencing in mammalian cells Probing the kinome ProbeLibrary-A new method for faster design and execution of quantitative real-time PCR Prime time for real-time PCR Mass spectrometry-gaining mass appeal in proteomics imaging of multiple endogenous proteins using Quantum dots Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro Highly efficient molecular delivery into mammalian cells using carbon nanotube spearing high-resolution measurements of single-vesicle fusion and release Go with the microflow Gene expression profiling in single cells within tissue Flow cytometry smaller and better direct visualization of DNA methyltransferase activity in living cells Determination of absolute protein numbers in single synapses by a GFP-based calibration technique Detection of femtogram amounts of biogenic amines using self-assembled DNA-protein nanostructures Conjugation of fluorophores to tubulin Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations Cell type–specific expression profiling in plants via cell sorting of protoplasts from fluorescent Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis Analysis of exocytotic events recorded by amperometry An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways A Tn7-based broad-range bacterial cloning and expression system A streamlined platform for high-content functional proteomics of primary human specimens A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases A microfluidic culture platform for CNS axonal injury, regeneration and transport A microfluidic chemostat for experiments with bacterial and yeast cells

Last Modified: 2005-12-18