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Thursday, February 23, 2012

Cloning Fact Sheet (1)

Introduction

The possibility of human cloning, raised when Scottish scientists at Roslin Institute created the much-celebrated sheep "Dolly" (Nature 385, 810-13, 1997), aroused worldwide interest and concern because of its scientific and ethical implications. The feat, cited by Science magazine as the breakthrough of 1997, also generated uncertainty over the meaning of "cloning" --an umbrella term traditionally used by scientists to describe different processes for duplicating biological material.

What is cloning? Are there different types of cloning?

When the media report on cloning in the news, they are usually talking about only one type called reproductive cloning. There are different types of cloning however, and cloning technologies can be used for other purposes besides producing the genetic twin of another organism. A basic understanding of the different types of cloning is key to taking an informed stance on current public policy issues and making the best possible personal decisions. The following three types of cloning technologies will be discussed: (1) recombinant DNA technology or DNA cloning, (2) reproductive cloning, and (3) therapeutic cloning.


Recombinant DNA Technology or DNA Cloning

The terms "recombinant DNA technology," "DNA cloning," "molecular cloning," and "gene cloning" all refer to the same process: the transfer of a DNA fragment of interest from one organism to a self-replicating genetic element such as a bacterial plasmid. The DNA of interest can then be propagated in a foreign host cell. This technology has been around since the 1970s, and it has become a common practice in molecular biology labs today.

Scientists studying a particular gene often use bacterial plasmids to generate multiple copies of the same gene. Plasmids are self-replicating extra-chromosomal circular DNA molecules, distinct from the normal bacterial genome (see image to the right). Plasmids and other types of cloning vectors were used by Human Genome Project researchers to copy genes and other pieces of chromosomes to generate enough identical material for further study.

To "clone a gene," a DNA fragment containing the gene of interest is isolated from chromosomal DNA using restriction enzymes and then united with a plasmid that has been cut with the same restriction enzymes. When the fragment of chromosomal DNA is joined with its cloning vector in the lab, it is called a "recombinant DNA molecule." Following introduction into suitable host cells, the recombinant DNA can then be reproduced along with the host cell DNA.

Plasmids can carry up to 20,000 bp of foreign DNA. Besides bacterial plasmids, some other cloning vectors include viruses, bacteria artificial chromosomes (BACs), and yeast artificial chromosomes (YACs). Cosmids are artificially constructed cloning vectors that carry up to 45 kb of foreign DNA and can be packaged in lambda phage particles for infection into E. coli cells. BACs utilize the naturally occurring F-factor plasmid found in E. coli to carry 100- to 300-kb DNA inserts. A YAC is a functional chromosome derived from yeast that can carry up to 1 MB of foreign DNA. Bacteria are most often used as the host cells for recombinant DNA molecules, but yeast and mammalian cells also are used.


Reproductive Cloning

Reproductive cloning is a technology used to generate an animal that has the same nuclear DNA as another currently or previously existing animal. Dolly was created by reproductive cloning technology. In a process called "somatic cell nuclear transfer" (SCNT), scientists transfer genetic material from the nucleus of a donor adult cell to an egg whose nucleus, and thus its genetic material, has been removed. The reconstructed egg containing the DNA from a donor cell must be treated with chemicals or electric current in order to stimulate cell division. Once the cloned embryo reaches a suitable stage, it is transferred to the uterus of a female host where it continues to develop until birth.

Dolly or any other animal created using nuclear transfer technology is not truly an identical clone of the donor animal. Only the clone's chromosomal or nuclear DNA is the same as the donor. Some of the clone's genetic materials come from the mitochondria in the cytoplasm of the enucleated egg. Mitochondria, which are organelles that serve as power sources to the cell, contain their own short segments of DNA. Acquired mutations in mitochondrial DNA are believed to play an important role in the aging process.

Dolly's success is truly remarkable because it proved that the genetic material from a specialized adult cell, such as an udder cell programmed to express only those genes needed by udder cells, could be reprogrammed to generate an entire new organism. Before this demonstration, scientists believed that once a cell became specialized as a liver, heart, udder, bone, or any other type of cell, the change was permanent and other unneeded genes in the cell would become inactive. Some scientists believe that errors or incompleteness in the reprogramming process cause the high rates of death, deformity, and disability observed among animal clones.


Therapeutic Cloning

Therapeutic cloning, also called "embryo cloning," is the production of human embryos for use in research. The goal of this process is not to create cloned human beings, but rather to harvest stem cells that can be used to study human development and to treat disease. Stem cells are important to biomedical researchers because they can be used to generate virtually any type of specialized cell in the human body. Stem cells are extracted from the egg after it has divided for 5 days. The egg at this stage of development is called a blastocyst. The extraction process destroys the embryo, which raises a variety of ethical concerns. Many researchers hope that one day stem cells can be used to serve as replacement cells to treat heart disease, Alzheimer's, cancer, and other diseases.

In November 2001, scientists from Advanced Cell Technologies (ACT), a biotechnology company in Massachusetts, announced that they had cloned the first human embryos for the purpose of advancing therapeutic research. To do this, they collected eggs from women's ovaries and then removed the genetic material from these eggs with a needle less than 2/10,000th of an inch wide. A skin cell was inserted inside the enucleated egg to serve as a new nucleus. The egg began to divide after it was stimulated with a chemical called ionomycin. The results were limited in success. Although this process was carried out with eight eggs, only three began dividing, and only one was able to divide into six cells before stopping.


How can cloning technologies be used?

Recombinant DNA technology is important for learning about other related technologies, such as gene therapy, genetic engineering of organisms, and sequencing genomes. Gene therapy can be used to treat certain genetic conditions by introducing virus vectors that carry corrected copies of faulty genes into the cells of a host organism. Genes from different organisms that improve taste and nutritional value or provide resistance to particular types of disease can be used to genetically engineer food crops. With genome sequencing, fragments of chromosomal DNA must be inserted into different cloning vectors to generate fragments of an appropriate size for sequencing.

If the low success rates can be improved (Dolly was only one success out of 276 tries), reproductive cloning can be used to develop efficient ways to reliably reproduce animals with special qualities. For example, drug-producing animals or animals that have been genetically altered to serve as models for studying human disease could be mass produced.

Reproductive cloning also could be used to repopulate endangered animals or animals that are difficult to breed. In 2001, the first clone of an endangered wild animal was born, a wild ox called a gaur. The young gaur died from an infection about 48 hours after its birth. In 2001, scientists in Italy reported the successful cloning of a healthy baby mouflon, an endangered wild sheep. The cloned mouflon is living at a wildlife center in Sardinia. Other endangered species that are potential candidates for cloning include the African bongo antelope, the Sumatran tiger, and the giant panda. Cloning extinct animals presents a much greater challenge to scientists because the egg and the surrogate needed to create the cloned embryo would be of a species different from the clone.

Therapeutic cloning technology may some day be used in humans to produce whole organs from single cells or to produce healthy cells that can replace damaged cells in degenerative diseases such as Alzheimer's or Parkinson's. Much work still needs to be done before therapeutic cloning can become a realistic option for the treatment of disorders.

CAM ASSAY

Shell-less embryo culture

Fertilized white leghorn chicken eggs (SPAFAS Inc., Norwich, CT) were received at day 0 and

incubated for 3 days at 37°C with constant humidity. On day 3, eggs were rinsed with 70% ethanol and

opened into 100 mm2 tissue culture coated Petri dishes under aseptic conditions. The embryos were then

returned to a humidified 38°C incubator2 for 7-9 additional days.

Mesh assay

Substrates

Vitrogen (Collagen Biomaterials, Palo Alto, CA) was diluted to a concentration of 1.46 mg/ml with

an equal volume of DMEM (HEPES buffer, no phenol red, GIBCO BRL, Gaithersberg, MD). This 1:1 mixture

made up half of the total volume to be pipetted onto the mesh (final concentration = 0.73 mg/ml). Matrigel

(Becton Dickinson, Bedford, MA) was diluted to a final concentration of 10 mg/ml with DMEM and directly

pipetted onto meshes. Nylon mesh with 250 μm2 openings were cut into 4 mm x 4 mm squares and

autoclaved. In preparation for polymerization, meshes were placed, under aseptic conditions, onto a nonbinding

surface (i.e., bacteriological Petri dish). The polymerization conditions for each substrate were

identical; after mixing the growth factors and/or compounds, 40 μl were pipetted onto each mesh in a

bacteriological Petri dish as described above. The Petri dish was placed in a humidified 37°C incubator with

5% CO2 for 30 minutes to allow polymerization followed by an incubation at 4°C for 2 hours.

Growth Factors

VPF/VEGF165 (Peprotech, Rocky Hill, NJ) was resuspended at 100 ng/μl in HBSS (Sigma, St.

Louis, MO). For each mesh containing VPF/VEGF, 250 μg was used.

Placement of meshes

In a tissue culture enclosure, meshes were placed onto the periphery of the CAM of a day 12-14

embryo, excluding areas containing major vessels. The embryos were then returned to the humidified 38°C

incubator with 3% CO2 for 24 to 48 additional hours.

Visualization of vessels

Embryos were removed from the incubator and meshes were viewed under a dissecting

microscope for gross evaluation. For injection, borosilicate glass capillaries (OD 1.0 mm, ID 0.75 mm; Sutter

Instrument Company, Novato, CA) were prepared with P-87 micropipette puller (Sutter Instrument

Company). Needles were connected with Tygon tubing (ID 1/32", OD 3/32", wall 1/32") to a 3cc syringe

with a 20-gauge needle. The syringe was attached to an infusion pump (Harvard Apparatus, South Natick,

MA). Injection of 400 μl FITC dextran, MW 2,000,000 (Sigma, St. Louis, MO), into the umbilical vein was

performed at a rate of 200 μl per minute. The FITC dextran was allowed to circulate for 5 minutes and 3.7%

formaldehyde in PBS was applied directly on each mesh. The embryos were then incubated at 4°C for 5

minutes and the meshes were dissected off the CAM and fixed in 3.7% formaldehyde for 10 minutes to

overnight.

Quantification of vessels

After fixation, meshes were mounted on slides with 90% glycerol in 1 X PBS and visualized on an

inverted fluorescence microscope. A Nikon Diaphot with a Sony DXC-151A camera attached to the side

port was used for capture of images, which were transferred to a Power Macintosh 7100/66AV. NIH Image

1.61 (public domain program available on the Internet at http://rsb.info.nih.gov/nih-image/) was used to

capture and analyze images. For each mesh, 5 random staggered images (approximately 600 μm each) were

captured using "Capture Frames," followed by "Make Montage" in order to display all of the frames at once.

The areas of high intensity were highlighted using "Density Slice" with (LUT selected at 105) and measured

using the "Measure" function. When density slicing is used in an image, the "Measure" function calculates

the areas of highlighted pixels.

(Source: Arispe Lab

Angiogenic Models-chorioallantoic membrane assay

Biomacromolecules - CAM preparation

CAM preparation. IPW research units. Prof. D. Neri · Prof. H. Wunderli - Allenspach · Prof. U. Spichiger - Keller · Prof. H.P. Merkle · Prof. U. Quitterer ...
www.pharma.ethz.ch/institute_groups/biomacromolecules/protocols/cam

Chorioallantoic Membrane Vascular Assay (CAMVA)

Chorioallantoic Membrane Vascular Assay (CAMVA). Theory: Vascular damage (i.e. ghost vessels, capillary injection, or. hemorrhaging) of the chorioallantoic ...
www.iivs.org/pages/methods/CAMVAsummarysheet.pdf

The gelatin sponge–chorioallantoic membrane assay

The gelatin sponge–chorioallantoic membrane assay. Here we present a method for the quantification of angiogenesis and antiangiogenesis in the chick embryo ...
www.natureprotocols.com/2006/06/23/the_gelatin_spongechorioallant.php

THE CHICK CHORIOALLANTOIC MEMBRANE AS A MODEL TISSUE FOR SURGICAL Retinal Research Simulation.
factors in ocular tissues of normal rabbits on chorioallantoic. membrane assay. Tohoku J Exp Med 1988;154:63–70. 10. Prost M. Experimental studies on the ...
www.stanford.edu/~palanker/publications/CAM%20as%20retinal%20model.pdf

Chorioallantoic membrane assay: vascularized 3-dim.

PubMed is a service of the US National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for ...
www.ncbi.nlm.nih.gov/pubmed/11547121

Assessment of Angiogenic Factors The Chick Chorioallantoic Membrane Assay.

Assessment of Angiogenic Factors The Chick Chorioallantoic Membrane Assay. By: Adam Jones3, Chisato Fujiyama3, Stephen Hague3, Roy Bicknell4 ...
www.springerprotocols.com/Abstract/doi/10.1385/1-59259-137-X:119

Chicken chorioallantoic membrane assay (Cytokines & Cells ...

Chicken chorioallantoic membrane assay. The following COPE entries contain this entry term or one of its hypertext synonyms: ...
www.copewithcytokines.de/cope.cgi?key=Chicken%20chorioallantoic%20membrane%20assay

THE SHELL-LESS CHIC CAM ASSAY: A MODEL FOR STUDYING MELANOMA

ANGIOTROPISM AND EXTRAVASCULAR MIGRATORY METASTASIS
http://www.med.miami.edu/mnbws/documents/06Lugassy.pdf

Chorioallantoic Membrane Vascular Assay - Alternative Ocular Irritation Testing

Chorioallantoic Membrane Vascular Assay Alternative Ocular Irritation. Day 7 - Vascular development of the Chorioallantoic Membrane. ASSAY HIGHLIGHTS: ...
www.camva.com/

The gelatin sponge-chorioallantoic membrane assay.

The gelatin sponge–chorioallantoic membrane assay ... quantification of angiogenesis and antiangiogenesis in the chick embryo chorioallantoic membrane (CAM) ...
www.nature.com/nprot/journal/v1/n1/abs/nprot.2006.13.html

angiogenic models

Classical angiogenesis assays include the chick chorioallantoic membrane, rabbit cornea assay, sponge implant models, matrigel plugs and conventional tumor ...
www.med.unibs.it/~airc/sandra/models.html

Evaluating Compounds Affecting Angiogenesis.indd

ASSAY. In a typical angiogenesis evaluation using the CAM assay,. fertilized chick eggs are incubated at 37°C and specific. humidity (60%) for 3 to 4 days. ...
www.sri.com/biosciences/pdf/EvaluatingCompoundsAffectingAngiogenesis.pdf

Animal models Protocols

A list of animal model protocols from scientific journals, patents and/or laboratory websites.

Animal Model for Assessing Therapeutic Efficacy of .alpha.-Amino Acid Prodrugs for Treating Alzheimer's Disease. US Patent#7,531,572 Protocol

Animal Model for Assessing Therapeutic Efficacy of .alpha.-Amino Acid Prodrugs for Treating Huntington's Disease. US Patent#7,531,572 Protocol

Animal Model for Assessing Therapeutic Efficacy of .alpha.-Amino Acid Prodrugs for Treating Spasticity. US Patent#7,531,572 Protocol

Animal Model for Assessing Therapeutic Efficacy of .alpha.-Amino Acid Prodrugs for Treating Anxiety. US Patent#7,531,572 Protocol

Animal Model for Assessing Therapeutic Efficacy of Prodrugs of 3-Aminopropylphosphinic Acid Analogs for Treating Depression. US Patent#7,585,996 Protocol

Animal Model for Assessing Therapeutic Efficacy of Prodrugs of 3-Aminopropylphosphinic Acid Analogs for Treating Alzheimer's Disease. US Patent#7,585,996 Protocol

Animal Model for Assessing Therapeutic Efficacy of Prodrugs of 3-Aminopropylphosphinic Acid Analogs for Treating Anxiety. US Patent#7,585,996 Protocol

Animal Model for Assessing Therapeutic Efficacy of Prodrugs of 3-Aminopropylphosphinic Acid Analogs for Treating Epilepsy. US Patent#7,585,996 Protocol

Animal Model of Nippostrongylus brasiliensis ... - Current Protocols Abstract Abstract: Animal models of Nippostrongylus brasiliensis and Heligmosomoides polygyrus infection are powerful tools for the investigation of the ... www.currentprotocols.com

Animal Models - Lab Protocol lab, laboratory, laboratory protocols, biology, life science, pcr, northern blot ... Animal Models, fsdf, 2009.07.05. Animal Models, fdsfdsfdxxx, 2009.07.05 ... www.labprotocol.com/index.php?kid=26...Animal+Models

Animal Models for Assessing Therapeutic Efficacy of .alpha.-Amino Acid Prodrugs for Treating Parkinson's Disease. US Patent#7,531,572 Protocol

Animal models for depression-like and - Nature.com 13 Dec 2007 ... Animal models for depression-like and anxiety-like behavior .... This protocol is related to the following articles: ... www.nature.com/protocolexchange/protocols/344

Animal Models for SLE | Current Protocols Abstract Abstract: Systemic lupus erythematosus (SLE) in humans is ... www.currentprotocols.com

Animal Models of Acute and Chronic Graft-Versus-Host Disease effective regimen in blocking T cell function in GVHD. Supplement 27. Current Protocols in Immunology. 4.3.4. Animal Models of. Acute and. Chronic ... onlinelibrary.wiley.com/doi/10.1002/0471142735.im0403s27/pdf

Animal Models of Depression. US Patent#7,531,572 Protocol

Animal Models of Pain. US Patent#7,531,572 Protocol

Animal Models of Painful Diabetic Neuropathy ... - Current Protocols Abstract Abstract: Painful peripheral neuropathy is a common secondary ... www.currentprotocols.com/protocol/ns0918

Animal Models of Retroviral Encephalopathies. 6 Jul 2009 ... Protocols, methods, and experimental design for pharmacology, drug development, drug screens, pharmacokinetics, ADME, preclinical models of ... www.scientistsolutions.com

Animal Models to Assess the Efficacy of .alpha.-Amino Acid Prodrugs for Treating Social Phobia. US Patent#7,531,572 Protocol

Anti-Hepatitis B Virus Effect of N-nonyl-DNJ Alone in a Woodchuck Model. US Patent#7,612,093 Protocol

Antiviral Study to Test the Activity of N-nonyl-DNJ in Combination with 3TC in a Woodchuck Model of Hepatitis B Virus Infection. US Patent#7,612,093 Protocol

Auditory Startle and Prepulse Inhibition of Startle (PPI) Animal Model of Schizophrenia. US Patent#7,531,572 Protocol

Chemically induced mouse models of intestinal inflammation. 15 Mar 2007 ... Animal models of intestinal inflammation are indispensable for our .... Additionally, a protocol to generate colitis-associated colorectal ... www.nature.com

Chronic Constriction Injury Model (CCI Model) US Patent#6,936,628 Protocol

Esophageal injury model in vivo tissue reconstitution. J Clin Invest. 2008 Dec;118(12):3860-9 Protocol

Establishment of rat liver transplantation model. Hepatobiliary Pancreat Dis Int. 2008 Feb;7(1):29-33 Protocol

Experimental Orthotopic Tumor Models. Proc Natl Acad Sci U S A. 2008 March 18; 105(11): 4329 4334 Protocol

Experimental protocols for CMD animal models Experimental protocols for CMD animal models. Raffaella Willmann. Raffaella Willmann studied Biology in Italy and obtained her PhD in Biochemistry in ... www.treat-nmd.eu/research/preclinical/cmd-sops/

Haloperidol-induced Catalepsy in the Rat. US Patent#7,572,802 Protocol

Hemiparkinsonian Rat Model. Stem Cells Vol. 26 No. 8 August 2008, pp. 2183 -2192 Protocol

Human Ovarian Cancer Animal Model. PLoS One. 2009; 4(10): e7670. Protocol

In Vivo Data Rat Penile Erection Model. US Patent#7,470,691 Protocol

In vivo model of airway inflammation. PLoS ONE 4(11): e7525. Protocol

In vivo model of airway inflammation. PLoS ONE 4(11): e7525. Protocol

Induction of PD in Rats. US Patent#6,914,056 Protocol

Lymphadema Animal Model. US Patent#7,476,384 Protocol

Method for Making Atopic Dermatitis Model Mice. US Patent Application#20090246181 Protocol

Method for Making Atopic Dermatitis Model Mice. US Patent Application#20090246181 Protocol

Middle cerebral artery occlusion (MCAO) model. Journal of Neuroscience, November 19, 2008, 28(47):12433-12444 Protocol

Mouse Model for Hepatic Repopulation. Stem Cells Vol. 26 No. 5 May 2008, pp. 1117 -1127 Protocol

Mouse Models of Periventricular Leukomalacia This video protocol demonstrate establishing mouse models of periventricular leukomalacia (PVL), the predominant form of brain injury in premature infants. http://www.jove.com/Details.php?ID=2074

Murine model of ascending Urinary Tract Infection. PLoS Pathog. 2009 September; 5(9): e1000586. Protocol

Murine Model of Hindlimb Ischemia This video demonstrates the methodology for the murine model of unilateral hindimb ischemia. The specific materials and procedures for creating and evaluating the model are described, including the assessment of limb perfusion by laser Doppler imaging. This protocol can also be utilized for the transplantation and non-invasive tracking of cells. http://www.jove.com/details.stp?id=1035

Myocardial Infarction Model and Bulk Cell Transplantation. PLoS ONE. 2008; 3(3): e1789. Protocol

Osteoporosis Induction in Animal Model So, there was a need to have protocol in animal model to let the ... aim of this research was to make such protocol in animal model. ... www.scipub.org/fulltext/AJAV/AJAV52139-145.pdf

PCP-Induced Hyperactivity Animal Model of Schizophrenia. US Patent#7,531,572 Protocol

Production of a Parkinsonian Rat Model, Cell Transplantation, and Behavioral Testing. Proc Natl Acad Sci U S A. 2008 March 4; 105(9): 3392 3397 Protocol

Rat Cryoinjury Model. Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6063-8 Protocol

Rat model of chronic myocardial infarction. J Formos Med Assoc. 2008 Feb;107(2):165-74 Protocol

Rat model of myocardial infarction. J Cell Mol Med. 2008 Mar 28 Protocol

Rescue of Ischemia in Rabbit Lower Limb Model. US Patent#7,476,384 Protocol

Small Animal Models of Hemorrhagic Shock. 6 Jul 2009 ... Protocols and methods for immunology, antigen presentation ... www.scientistsolutions.com

Spinal Cord Injury Model and Transplantation. PLoS ONE 4(11): e7706. Protocol

Springer Protocols: Animal Models Animal Models. Protocols in Animal Models ... Fluorescent In Situ Hybridization Protocols in Drosophila Embryos and Tissues ... www.springerprotocols.com/.../browse?...Protocol...Animal%20Models...Animal%20Models

Stem ceII mobilisation- Mice model. WO/2008/104090 Protocol

Tissue Samples from a Murine Model of Induced Cardiovascular Defects. PLoS ONE. 2009; 4(1): e4221 Protocol

Tissue Samples from a Murine Model of Induced Cardiovascular Defects. PLoS ONE. 2009; 4(1): e4221 Protocol

Transplantation of Pancreatic Islets Into the Kidney Capsule of Diabetic Mice A protocol to cleanly and easily deliver islets or cells under the kidney capsule of diabetic or normal mice. http://www.jove.com/index/details.stp?ID=404

A PCR-based strategy for cloning short hairpin sequences: “PCR shagging"

A PCR-based strategy for cloning short hairpin sequences:
“PCR shagging”.
Our overall approach is to use an RNA polymerase III promoter to drive
expression of encoded short hairpin RNA (shRNA). For this purpose we use the U6
snRNA promoter and maintain the transcript initiating “G” nucleotide of the U6snRNA
transcript. There by, hairpin sequences will start with a “G”. Termination is mediated
by a run of Ts at the end of the hairpin.
The major difference between our hairpins those reported by others is that we
went through a battery of tests of hairpin length and structure, and found that hairpins of
27 to 29nt in length are more effective than hairpins of 19nt and 21nt. Additionally, we
use a few G-U pairing in the hairpin stem (which are permitted in dsRNA alpha helices)
to stabilize hairpins during propogation in bacteria.
We have developed a fast and effective, PCR-based strategy to clone shRNA
sequences. In this strategy, short hairpin RNA (shRNA) sequences are converted into a
single ~73nt primer sequences onto which are added 21nt of homology to the human U6
snRNA promoter. Such primers have performed flawlessly so far in PCR reactions
(n>40) and subsequent cloning.
PCR
TA/Topo
Cloning
HindIII site
Transient transfection Subcloning (eg Invitrogen’s Gateway
system)
U6 promoter
U6 promoter Ts
U6 promoter Ts
There are several steps in generating hairpin primers. First, a 29nt “sense” sequence
which ends with a “C” is picked out from the coding sequence of gene of interest.
Second, the actual hairpin is constructed in a 5’->3 orientation with respect to the
intended transcript.
Anti-sense Loop Sense Term
ggctatgaagagatacgccctggttccGaagcttGggaaccagggcgtatctcttcatagccTTTTTTG
Predicted shRNA structure
5’->3’ Anti-sense strand
-------| GAA
GGCUAUGAAGAGAUACGCCCUGGUUCC G
CCGAUACUUCUCUAUGCGGGACCAAGG C
UU^ GUU
3’<-5’ Sense strand
Third, a few stem pairing are changed to G-U by altering the sense strand sequence. G-U
base pairing seems to be essential for stability of short hairpins in bacteria and does
not interfere with silencing. Finally, the hairpin construct is converted to its “reverse
complement” onto which is added 21nt of homology to the Human U6 promoter.
Hairpin portion of the primer (~69nt)
CAAAAAAggctatgaagagaCacgccctgAttccCaagcttCggaaccagggcgtatctcttcatagcc
+
U6 promoter reverse primer sequence
Ggt gtt tcg tcc ttt cca caa
Final primer (5’->3’, just as it would be ordered)
CAAAAAAggctatgaagagaCacgccctgAttccCaagcttCggaaccagggcgtatctcttcatagcc
Ggt gtt tcg tcc ttt cca caa
All of the aforementioned steps are automated using a program developed by Ravi
Sachidanandam and Jeremiah Faith (CSHL) where either accession numbers from
GenBank or raw sequences are required to generate hairpin PCR primers.
[Note: Don’t let the G-U pairings represented in the primer fool you into thinking
the primer is incorrect. ]
A link to the hairpin primer generation program, the “RNAi oligo retriever”, can be
found at:
www.cshl.org/public/SCIENCE/hannon.html
Make sure that you enter accession numbers and sequences which match cDNA or
exon sequences!

Methods:

THE PROTOCOL
Ordering Primers
Since very little primer is required for the PCR reaction they can be ordered .05μmol
scale from Sigma-Genosys or whomever. We find that PAGE purification is costly and
unnecessary (PCR will fill in shorted primers!).


PCR
We use a pGEM1 plasmid containing the human U6 locus (N. Hernandez, CSHL) as the
template for the PCR reaction. This vector contains ~500bp of upstream U6 promoter
sequence. Since an SP6 sequence flanks the upstream portion of the U6 promoter, we
use an SP6 oligo as the universal primer in U6-hairpin PCR reactions.
SP6 sequence: GATTTAGGTGACACTATAG
We have had consistently good results using Taq polymerase for PCR with 4% DMSO
and 50pmoles of each primers. (For pENTR/D-Topo cloning [see below], I add .1uL
of Vent to polish the ends.)
PCR conditions: 95° for 3 min; 30 cycles of 95° for 30 sec, 55° for 30 sec, & 72° for 1
min; followed by one cycle of 72° for 10 min.
The PCR product will be ~600bp in length.


CLONING
We currently use two cloning technologies available from Invitrogen: T-A and
directional topoisomerase-mediated cloning kits (catalog #K2040-10, K2400-20). The
directional cloning kit is designed for Invitrogen’s Gateway system. We use both kits
according to the manufacture’s instructions. If using Topo-cloning, do NOT gel purify
PCR products – it reduces the efficiency of the Topo-reaction.
pENTR/D-Topo SP6 primer: CACC GATTTAGGTGACACTATAG
For convenient identification of clones containing the proper insert (20-100% for Topocloning),
a HindIII site has been designed into the loop of the hairpin. A second HindIII
site exists 5’ of U6 promoter. Digesting clones with HindIII releases a ~500bp fragment.
SP6-U6 promoter PCR product sequence (with out hairpin)*.
SP6—HindIII—BamHI—U6 promoter

An Introduction to Genetic Analysis for DNA Protein interactions

An Introduction to Genetic Analysis. Table of Contents

On almost every page of Introduction to Genetic Analysis, we recreate the landmark experiments in genetics and have the students analyze the data and draw ...
www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=iga.TOC

Modern Genetic Analysis. Table of Contents

Modern Genetic Analysis was written for instructors and students who need a textbook that supports the 'DNA first' approach. Griffiths, Anthony JF; Gelbart, ...
www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mga.TOC

Springer Protocols: Abstract: Genetic Analysis of DNA-Protein Interactions Using a Reporter Gene Assay in Yeast.

High-resolution genetic analysis of DNA-protein interactions is particularly problematic in metazoans. We have devised an approach that makes use of the ...
www.springerprotocols.com/Abstract/doi/10.1385/1-59259-208-2:431

Genetic analysis of prokaryotic and eukaryotic DNA-binding Proteins in E. Coli.

Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the {sigma}70 Subunit ... system for studying protein-DNA and protein-protein interactions ...
nar.oxfordjournals.org/cgi/content/abstract/26/16/3700

Quantifying DNA−protein interactions by double-stranded DNA .

Moreover, measuring DNA−protein interactions in different buffer ..... Parallel analysis of genetic selections using whole genome oligonucleotide arrays. ...
www.nature.com/nbt/journal/v17/n6/full/nbt0699_573.html

Genetic Analysis, Using P22 Challenge Phage, of the Nitrogen Activator Protein DNA-Binding Site in the Klebsiella Aerogenes Put Operon.

If a mutation in the site prevents the DNA-protein interaction, ant is expressed ..... Genetic analysis of pathogenic bacteria: a laboratory manual. ...
jb.asm.org/cgi/content/full/180/3/571?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=p

Quantitative prediction of NF-kappa B DNA- protein interactions ...

Genetics Quantitative prediction of NF- kappa B DNA- protein interactions. Irina A. Udalova dagger , Dagger ,§, Richard Mott dagger , Dagger ...
www.pnas.org/cgi/content/abstract/99/12/8167

Genomic analysis of protein–DNA interactions in bacteria: insights into transcription and chromosome organization

Jun 16, 2007 ... Genomic analysis of protein–DNA interactions in bacteria: ... and genetic approaches have been used to study protein–DNA interactions. ...
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2958.2007.05781.x

Development of genetic analysis technique using stable isotope marking molecular switch

Development of genetic analysis technique using stable isotope marking ... of them is a development of fast analysis method of the DNA-protein interaction, ...

http://sciencelinks.jp/j-east/article/200517/000020051705A0653408.php

Genetic Analysis of Yeast RPA1 Reveals Its Multiple Functions in DNA Metabolism...

The Phosphorylation Domain of the 32-kDa Subunit of Replication Protein A (RPA) Modulates RPA-DNA Interactions: EVIDENCE FOR AN INTERSUBUNIT INTERACTION ...
www.genetics.org/cgi/content/abstract/148/3/989

Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli

Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Saeed Tavazoie1 & George M. Church

http://www.nature.com/nbt/journal/v16/n6/abs/nbt0698-566.html

From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression

In defining the underlying ideas of DNA-protein interactions, one can, ..... although this genetic analysis tells us little about the relative shapes or ...

http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.34.040204.144521

ScienceDirect - Genetic Analysis: Biomolecular Engineering.

ScienceDirect - the world's leading platform offers over 2000 high quality peer-reviewed full-text journals and books on science, technology and medicine.
www.sciencedirect.com/science/journal/10503862

Protein-DNA interactions

Genetic analysis. Isolation of mutants in the DNA binding site help to ... under low ionic-strength conditions, which favor strong DNA-protein interactions. ...
www.biochem.arizona.edu/classes/bioc568/protein_dna_interactions.htm

DPInteract

Robison, K., and Church, G. DPInteract: A database on DNA-protein interactions. ... SeqAnalRef, a bibliography on biological sequence analysis ...
arep.med.harvard.edu/dpinteract/

Animal Perfusion Solution

4% Paraformaldehyde (For ICC & 5' Nucleutidase staining)

100 ml 250 ml 300 ml 500 ml 1000ml

Paraformaldehyde 4g 10g 12g 20g 40g

ddH2O 80ml 200ml 240ml 400ml 800ml

heat mixture (do not exceed 65 C) with stirring

add a few drops 50% NaOH to clear solution, add:

NaCl 0.8g 2g 2.4g 4g 8g

KCl 0.02g 0.05g 0.06g 0.1g 0.2g

Na2HPO4 0.061g 0.152g 0.182g 0.305g 0.61

KH2PO4 0.02g 0.05g 0.06g 0.1g 0.2g

pH solution to 7.0-7.5 with paper pH strips

Volume to 100ml 250ml 300ml 500ml 1000ml

Filter entire solution

Cool on ice

2% Paraformaldehyde (200 ml)

Paraformaldehyde 4g

ddH2O 160ml

heat mixture (do not exceed 65 C) with stirring

add a few drops 50% NaOH to clear solution, add:

NaCl 1.6 g

KCl 0.04 g

Na2HPO4 0.122 g

KH2PO4 0.04 g

pH solution to 7.0-7.5 with paper pH strips

Volume to 200 ml

Filter entire solution

Cool on ice

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