Method and apparatus for parallel synthesis of chain molecules such as dna

Abstract

Synthesis of chain molecules such as DNA is carried out in a conduit having an interior channel with an inlet end and an outlet end. At least one wall of the conduit is substantially transparent to selected wavelengths of light. Solid carrier particles are contained within the interior channel of the conduit. A plurality of controllable light sources are mounted at spaced locations along the length of the transparent wall of the conduit to allow selective illumination of separated sections of the particles within the conduit. When a light source is turned on, a photodeprotecting group is removed from the carrier particles in the section that is illuminated by the light source. A reagent containing a selected base is flowed through the conduit so that the base will attach to the carrier particles in those sections which have been exposed to light and deprotected.

1 . A method of synthesizing DNA chain molecules on carrier particles within an interior channel of a conduit, the method comprising:
 (a) illuminating optically isolated sections of the carrier particles within the channel, the carrier particles having protected groups selected from the group consisting of protected group linkers, protected nucleotide bases, protected oligonucleotides, and combinations thereof attached to their surfaces, whereby the illuminated protected groups are photodeprotected; and   (b) flowing a reagent comprising a nucleotide base over the carrier particles, whereby the nucleotide base becomes attached to the photodeprotected groups.   
     
     
         2 . The method of  claim 1  further including:
 (c) flowing a reagent comprising a protecting group over the surfaces of the carrier particles, whereby the attached nucleotide bases become protected; stopping the flow of reagent and illuminating selected optically isolated sections of the carrier particles within the channel, whereby the illuminated protected nucleotide bases on the carrier particles are photodeprotected; and   (d) flowing a reagent comprising a nucleotide base over the carrier particles, whereby the nucleotide base in the reagent becomes attached to photodeprotected nucleotide bases on the carrier particles.   
     
     
         3 . The method of  claim 2  wherein steps (c) and (d) are repeated multiple times to form oligomers of differing sequences at the optically isolated sections of carrier particles. 
     
     
         4 . The method of  claim 3  further including releasing the formed oligomers from the carrier particles and transporting the released oligomers in a fluid out of the conduit. 
     
     
         5 . The method of  claim 1  wherein the conduit comprises a thin walled capillary tube having an interior channel, the walls of the conduit being transparent, and wherein light sources are mounted at spaced positions along the length of the transparent wall of the conduit and are activated selectively to provide the selected illumination of optically isolated sections of the carrier particles in the conduit. 
     
     
         6 . The method of  claim 5  wherein the light sources are light emitting diodes which emit light of a selected wavelength when supplied with electricity. 
     
     
         7 . The method of  claim 6  wherein the light emitting diodes are mounted to the conduit such that a face of the light emitting diode from which light is emitted forms a portion of the transparent wall of the conduit. 
     
     
         8 . The method of  claim 6  wherein the sections are optically isolated by light blocking material mounted between adjacent light emitting diodes such that the light blocking material prevents light from one light emitting diode passing into a section of the channel that is to be illuminated by an adjacent light emitting diode. 
     
     
         9 . The method of  claim 1  wherein the carrier particles are formed as microspheres having a diameter in the range of 1 μm to 1000 μm. 
     
     
         10 . The method of claim I wherein the conduit has walls which are all transparent to light and further including a material adjacent to the conduit between the optically isolated sections which blocks the transmission of light through the walls of the conduit to minimize stray light. 
     
     
         11 . The method of  claim 1  wherein the section are optically isolated by separators between adjacent sections of particles that block light transmission and flow of carrier particles therethrough while allowing passage of liquid. 
     
     
         12 . The method of  claim 11  wherein the separators are formed of solid plugs having channels therethrough that allow flow of liquid but are sized to block passage of carrier particles. 
     
     
         13 . The method of  claim 11  wherein the separators comprise particles comprising a light absorbing or light blocking material.