A Brief Bibliography of Nucleic Acid Cloning/Colony Methods.

(see also Sequencing by Synthesis Notes, SBS and Polonies).


Reference  Clonality   # primers       Physical

           shown?      free/covalent   isolation


Sha'69       Y            0/0          Agar gel

Coh'73       Y            0/0          Cell-membranes & agar

Law'78       Y            0/0          Agar gel

Li '88       Y            2/0          Plastic tube (solution)

Che'91       Y            0/0          Agarose gel

Che'97       Y            0/0          Agarose gel (Example 2)

Che'97       N            0/0          Polyacrylamide gel (Example 3)

Far'98       Y            0/2          Glass surface

Taw'98       Y            2/0          Emulsion

Chu'99       Y            1/0          Excluded volume cloning on patterned glass arrays  

Mit'99       Y            1/1          Polyacrylamide gel (& replicas)

Vog'99       Y            2/0          Plastic tube (solution)

Che'00       Y            2/0          Polyacrylamide gel

Ade'00       N            0/2          Glass surface

Gha'01       Y            2/0          Emulsion

Dea'02       N            1/0          Plastic tube (solution)

Cos'04       Y            1/1          Bead surface & emulsion  

Drm'05       Y            1/1          Rolling Circle Replication in solution & binding exclusion   


Schroeter J, Cohn F, Koch R (1876-9) bacteria would grow on solid substrates as potato, coagulated egg white, meat, and bread and that colonies were capable of forming new colonies of the same colour. http://www.britannica.com/nobel/micro/325_28.html

Webber, HJ (1903) Science 16 Oct. 502/2 "Clons .. are groups of plants that are propagated by the use of any form of vegetative parts." (--from OED)

Shapiro J, Machattie L, Eron L, Ihler G, Ippen K, Beckwith J. (1969) Isolation of pure lac operon DNA. Nature. 224(221):768-74.

Cohen SN, Chang AC, Boyer HW, Helling RB. (1973) Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A. 70(11):3240-4. 

Lawn RM.  Fritsch EF.  Parker RC.  Blake G.  Maniatis T. (1978) The isolation and characterization of linked delta- and beta-globin genes from a cloned library of human DNA. Cell 15(4):1157-74.

Li HH, Gyllensten UB, Cui XF, Saiki RK, Erlich HA, Arnheim N. (1988) Amplification and analysis of DNA sequences in single human sperm and diploid cells. Nature. 335(6189):414-7.

Chetverin AB, Chetverina HV, Munishkin AV. (1991) On the nature of spontaneous RNA synthesis by Q beta replicase. J Mol Biol. 222(1):3-9.

Sykes PJ, Neoh SH, Brisco MJ, Hughes E, Condon J, Morley AA. (1992) Biotechniques. 13(3):444-9. Quantitation of targets for PCR by use of limiting dilution.

Chetverin, AB and Chetverina, HV (1992-1997) A method for amplification of nucleic acids in solid media.  US patent # 5,616,478

Brenner S, et al. (1994-1996) WO 1996012039 A1 Massively parallel sequencing of sorted polynucleotides,

Church GM & Mitra R. (1997-2002) (1997-2002) Patent US 6,432,360 Replica amplification of nucleic acid arrays . (excluded volume DNAs on patterned arrays)

Farinelli, Kawashima, E, L Mayer (1997-1998) Method of nucleic acid amplification. Patent WO9844151A1.

Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet. 19(3):225-32.

Tawfik DS, Griffiths AD. (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol.  Jul;16(7):652-6. 

Ohuchi S, Nakano H and Yamane T. (1998) In vitro method for the generation of protein libraries using PCR amplification of a single DNA molecule and coupled transcription/translation. Nucleic Acids Res 26:4339-4346.

Mitra, R. and Church, G.M. (1999) In situ localized amplification and contact replication of many individual DNA molecules.  Nucleic Acids Res. 27(24):e34; pp.1-6.

Vogelstein B, Kinzler KW. (1999) Digital PCR. Proc Natl Acad Sci USA. 96(16):9236-41.

Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E. (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 28(20):E87.

Brenner S, et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. Jun;18(6):630-4.

Ghadessy FJ, Ong JL, Holliger P. (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4552-7.

Dean FB, et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A.  99(8):5261-6. 

Chetverina HV, Samatov TR, Ugarov VI, Chetverin AB. (2002) Molecular colony diagnostics: detection and quantitation of viral nucleic acids by in-gel PCR. Biotechniques.  Jul;33(1):150-2, 154, 156. 

Nakano M, Komatsu J, Matsuura S, Takashima K, Katsura S, Mizuno A. (2003) Single-molecule PCR using water-in-oil emulsion. J Biotechnol.  2003 Apr 24;102(2):117-24.

Dressman D, Yan H, Traverso G, Kinzler KW, and Vogelstein B. (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A. 100(15):8817-22.(emulsion beads)

Drmanac R, Callow MJ, Drmanac S, Hauser BK, Yeung G. 2005-7. US Patent Appl.20070099208. Single molecule arrays for genetic and chemical analysis. (random rolling circle arrays)

Costa GL, Leamon JH, Rothberg JM, Weiner MP. 2004. US Patent Appl. 20040185484 Method for preparing single-stranded DNA libraries. (emulsion beads)