Microarrays pp 165-187 | Cite as

Choice of Polymer Matrix, Its Functionalization and Estimation of Functional Group Density for Preparation of Biochips

  • Shweta Mahajan
  • Bhashyam Vaijayanthi
  • Gopal Rembhotkar
  • Kailash Chand Gupta
  • Pradeep Kumar
Part of the Methods in Molecular Biology™ book series (MIMB, volume 381)


Oligonucleotide microarray has become an important and powerful tool for various genomic analyses, where, unlike conventional methods, one can identify simultaneously a large number of targets in a given sample. Postsynthesis immobilization, the most widely used method, involves the noncovalent and covalent fixing of suitably modified oligonucleotides on the solid supports. Among the various functional groups aminoalkyl, hydroxyalkyl, mercaptoalkyl, aldehyde, epoxy, and carboxyl the most frequently used functional groups on the polymeric surfaces. Because glass and polypropylene, the most widely used materials, are nonporous in nature, the functional groups density on the surface remains very low. In order to know the exact concentration of a ligand to be immobilized, it is essential to estimate the accessible functional groups on these surfaces. For this purpose, sensitive methods are required to estimate exact density of available functional groups on the surfaces. Apart from physical methods, a number of sensitive chemical methods, by making use of high extinction coefficient of 4,4′-dimethoxytrityl cation (ε 498 = 70,000 Lmol−11cm−1), have been reported to estimate accessible functional groups on the glass based polymer supports. In this chapter, use of these reagents for spectrophotometric determination of functional group density on glass microslides and polypropylene film has been discussed.

Key Words

DMPA DMTr-Cl DTNPME estimation functional group density functionalization glass microslide polypropylene film SDTB spectrophotometric methods 


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Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Shweta Mahajan
    • 1
  • Bhashyam Vaijayanthi
    • 2
  • Gopal Rembhotkar
    • 1
  • Kailash Chand Gupta
    • 1
  • Pradeep Kumar
    • 1
  1. 1.Nucleic Acids Research LaboratoryInstitute of Genomics and Integrative BiologyDelhiIndia
  2. 2.Department of Chemistry, Gargi CollegeUniversity of DelhiDelhiIndia

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