Replication of DNA microarrays from zip code masters.

Haohao Lin; Joohoon Kim; Li Sun; Richard M Crooks

doi:10.1021/ja0578799

Home/Archive/PubMed

PubMed · 16522108

Replication of DNA microarrays from zip code masters.

Haohao Lin·Joohoon Kim·Li Sun·Richard M Crooks

View original source ↗Export metadata ↓

Abstract

This report describes a mechanical method for efficient and accurate replication of DNA microarrays from a zip code master. The zip code master is a DNA array that defines the location of oligonucleotides consisting of two parts: a code sequence, which is complementary to one or more of the zip codes, and the functional sequence, which is terminated with biotin. Following hybridization of the zip code to the code sequence, a replica surface functionalized with streptavidin is brought into conformal contact with the surface of the master. When the two surfaces are separated, the functional and code sequences are transferred to the replica, and the zip code remains on the surface of the master. Using this approach it is possible to prepare replica arrays having any configuration from a single, universal master array. Here we demonstrate that this approach can be used to replicate master arrays having up to three different sequences, that feature sizes as small as 100 microm can be replicated, and that master arrays can be used to prepare multiple replicas.

Explore related subjects

Biotin DNA Microscopy, Fluorescence Oligonucleotide Array Sequence Analysis Oligonucleotides Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Haohao Lin, Joohoon Kim, Li Sun, Richard M Crooks. 2006-03-15. Replication of DNA microarrays from zip code masters.. https://doi.org/10.1021/ja0578799

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Biotin deficiency inhibits heme synthesis and impairs mitochondria in human lung fibroblasts.

Four of the 5 biotin-dependent carboxylases (BDC) are in the mitochondria. BDC replace intermediates in the Krebs [tricarboxylic acid (TCA)] cycle that are regularly removed for the synthesis of key metabolites such as heme or amino acids. Heme, unlike amino acids, is not recycled to regenerate these intermediates, is not utilized from the diet, and must be synthesized in situ. We studied whether biotin deficiency (BD) lowers heme synthesis and whether mitochondria would be disrupted. Biotin-deficient medium was prepared by using bovine serum stripped of biotin with charcoal/dextran or avidin. Biotin-deficient primary human lung fibroblasts (IMR90) lost their BDC and senesced before biotin-sufficient cells. BD caused heme deficiency; there was a decrease in heme content and heme synthesis, and biotin-deficient cells selectively lost mitochondrial complex IV, which contains heme-a. Loss of complex IV, which is part of the electron transport chain, triggered oxidant release and oxidative damage, hallmarks of heme deficiency. Restoring biotin to the biotin-deficient medium prevented the above changes. Old cells were more susceptible to biotin shortage than young cells. These findings highlight the biochemical connection among biotin, heme, and iron metabolism, and the mitochondria, due to the role of biotin in maintaining the biochemical integrity of the TCA cycle. The findings are discussed in relation to aging and birth defects in humans.

Biotin↗

PubMed2007

Synthesis and use of the protein phosphatase affinity matrices microcystin-sepharose and microcystin-biotin-sepharose.

Microcystin-based affinity matrices have been utilized to demonstrate the association of signaling proteins with protein phosphatases and for the purification of low-abundance microcystin-sensitive protein phosphatases. Here, we describe the procedure for the synthesis and use of microcystin-Sepharose and microcystin-biotin-Sepharose.

Biotin↗

PubMed2006

Endotoxin detection in a competitive electrochemical assay: synthesis of a suitable endotoxin conjugate.

A biotin-lipopolysaccharide (biotin-LPS) conjugate was synthesized from LPS smooth from Salmonella minnesota, yielding a conjugate with a biotin/LPS ratio equal to 1:1 and endotoxic activity of 0.08 EU ng(-1). The conjugate was used in an amperometric competitive assay to determine endotoxins with endotoxin-neutralizing protein (ENP) as the recognition element. The assay is performed on a modified electrode, involving the covalent binding of carboxymethyl dextran (CMDex) to a cystamine-modified gold electrode and then the covalent binding of the recognition protein, ENP, to CMDex. The assay is carried out by incubating the modified electrode in an LPS sample to which biotin-LPS was added. Both species compete for the recognition sites on the modified surface. After the incubation stage and a careful rinsing, the electrode is immersed in a solution containing neutravidin-horseradish peroxidase conjugate (N-HRP), which binds to the sites containing biotin-LPS on the electrode. The system is rinsed and a current signal is generated by the addition of hydrogen peroxide and a redox mediator. The assay is able to detect LPS from Salmonella minnesota at concentrations as low as 0.1 ng ml(-1), equivalent to 0.07 EU ml(-1).

Biotin↗