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(12) Patent Application Publication (10) Pub. No.: US 2005/0221316A1 Pedersen Et Al

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US 2005O221.316A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0221316A1 PederSen et al. (43) Pub. Date: Oct. 6, 2005 (54) METHOD FOR SYNTHESISING Jun. 20, 2002 (US)........................................... 10175539 TEMPLATED MOLECULES Jun. 20, 2002 (DK)................................ PA 2002 OO952 Jun. 20, 2002 (US)........................................... 60389885 (76) Inventors: Henrik Pedersen, Bagsvaerd (DK); Sep. 12, 2002 (US)........................................... 60409968 Anette Holtmann, Ballerup (DK); Sep. 12, 2002 (DK). PA 2002 O1347 Thomas Franch, Copenhagen N. (DK); Alex Haahr, Veksoe Sjaelland (DK); Publication Classification Jakob Felding, Charlottenlund (DK) 51)1) Int. Cl.Cl." .............................. C12O 1/68 ; C12P 19/34 Correspondence Address: (52) U.S. Cl. ............................................... 435/6; 435/91.2 BROWDY AND NEIMARK, P.L.L.C. 624 NINTH STREET, NW (57) ABSTRACT SUTE 300 The invention relates to a method for Synthesizing templated WASHINGTON, DC 20001-5303 (US) molecules attached to the templated which directed the Synthesis thereof. The method involves a template, a Scaf (21) Appl. No.: 10/507,121 fold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The (22) PCT Filed: Mar. 14, 2003 scaffold functional entity and the functional entity of the (86) PCT No.: PCT/DK03/00172 building block are both provided with complementary dimerization domains allowing the functional entities to (30) Foreign Application Priority Data come into close proximity when the complementary domains interact with to each other. The method may be Mar. 15, 2002 (DK). PA 2002 0415 used for generating libraries of templated molecules which Jun. 15, 2002 (US)........................................... 60364,056 may be Selected for biological activity. Patent Application Publication Oct. 6, 2005 Sheet 1 of 21 US 2005/0221316 A1 Fig.1 0, 1 mM TSAT 1 mM TSA 10 mM TSAT AB CO DEF AB CO DEF A B C O D E F Est; . f tf a y Fig.2 Y. mM TSAT o Patent Application Publication Oct. 6, 2005 Sheet 2 of 21 US 2005/0221316A1 Fig. 3 P Ah5 L M N -- 3 m 3 e 323 - a 3 - 2 TM EDC - 22 S - P o r Fig. 4 Exp. Q Exp. R pH 75 6 7 8 9 10 75 6 7- - -8 9 • 'E.10 Patent Application Publication Oct. 6, 2005 Sheet 3 of 21 US 2005/0221316A1 Fig.5 Exp. S Exp. T pH 75 10 7,510 A Fig. 6 s s e E is arrama UAVA Us We X Y Patent Application Publication Oct. 6, 2005 Sheet 4 of 21 US 2005/0221316A1 Fig. 7 Fig. 8 Ah-36 25 48,253° 585 - 63,165,6 +l-Ah38 • ,- Patent Application Publication Oct. 6, 2005 Sheet 5 of 21 US 2005/0221316A1 Fig. 9A tncubation temperatur 2 3. 4, 5 6 7 8 9 10 1 12 +-Ah38 - - - - - - - - - - - - - - - - - - - - - - - r is -r a 'i A. the new , Fig. 9B incubation temperatur 1 2 3. 4. 5 6 7 8 --Ah38 - - - - - - - - - - - a - ... a . to Patent Application Publication Oct. 6, 2005 Sheet 6 of 21 US 2005/0221316A1 Fig.10A 7.7 °C 15.4°C 21,0°C Experiment 10- 1 2 3 4 5 6 7 8 1 2 3 4 5 6 78 1 2 3 4 56 78 s . enting his Fig. 10B 26,0°C 10°C-35° C (99) Experiment 10- 1 2 3 4 5 67 8 1 2 3 4 5 6 7 8 Patent Application Publication Oct. 6, 2005 Sheet 7 of 21 US 2005/0221316A1 Fig.11 30°C 55°C Experiment 11- 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 A - . s . " Patent Application Publication Oct. 6, 2005 Sheet 8 of 21 US 2005/0221316A1 Fig. 12 Zipperbox, 5-10 nt Templa Patent Application Publication Oct. 6, 2005 Sheet 9 of 21 US 2005/0221316A1 Figure 13 A. i : 's same- Hm-- y B. Yrwriterwrx Patent Application Publication Oct. 6, 2005 Sheet 10 of 21 US 2005/0221316A1 Figure 14 The Zipper box principle. a X by s: X LOW temperature (zipper boxes aSSociate) a m-X X b \Y X and Y react is Medium temperature (dissociate zipper boxes) l LOW temperature (associate zipper boxes) X and Y react a H a Patent Application Publication Oct. 6, 2005 Sheet 11 of 21 US 2005/0221316A1 Patent Application Publication Oct. 6, 2005 Sheet 12 of 21 US 2005/0221316A1 Patent Application Publication Oct. 6, 2005 Sheet 13 of 21 US 2005/0221316A1 \/queuu?JedXEºqueuu?JedXE g+cz1987& §*Fuopean?**· •O.,L'OZ:|eueT.• ?...pº?B|duue1{? /|-61-I Patent Application Publication Oct. 6, 2005 Sheet 16 of 21 US 2005/0221316A1 9G7Z? ****-åº E|êued å« C]|êueelC)No.ued 9gº£Z|G7€.\, s: OZ(61-) P iii. Patent Application Publication Oct. 6, 2005 Sheet 17 of 21 US 2005/0221316A1 va CN S O i. v OO v N V ve LO r w v C?) ve CN 8 ves s ve v O v E O i OO N CO O r Crd s CN re Patent Application Publication Oct. 6, 2005 Sheet 18 of 21 US 2005/0221316A1 81LI919 ZZ(61-) Patent Application Publication Oct. 6, 2005 Sheet 19 of 21 US 2005/0221316A1 KOOOGOCJOC]ºgSa?saod ---- ----?? queuu?JedXEºpueVqueuu?uedXEOpueo z9#7/860||Z|ZL||069/G(7ºZ| di (S N S dos Patent Application Publication Oct. 6, 2005 Sheet 20 of 21 US 2005/0221316A1 jueu?edx=-pueEqueuu?JedXEHpue9 Patent Application Publication Oct. 6, 2005 Sheet 21 of 21 US 2005/0221316A1 US 2005/0221316 A1 Oct. 6, 2005 METHOD FOR SYNTHESISING TEMPLATED identified but also directed by the nucleic acid tag. The MOLECULES approach is based on the traditional Split-and-combine Strat egy for Synthesis of combinatorial libraries comprising two TECHNICAL FIELD OF THE INVENTION or more Synthetic Steps. Plurality nucleic acid templates are used, each having at one end a chemical reactive site and 0001. The present invention relates to a method for dispersed throughout the Stand a plurality of codons regions, Synthesising templated molecules. The method implies a each of Said codon regions in turn Specifying different high local concentration of reactive groups intended to codons. Separately, each of the Strands, identified by a first participate in a formation of a linkage, thus increasing the codon region, is reacted at the chemical reaction sites with probability of linkage formation. The invention also relates Specific Selected reagents. Subsequently, all the Strands are to a library, that is a plurality of templated molecules, pooled and Subjected to a Second partitioning based on a wherein each of the. templated molecules are attached to the Second codon region. The split-and-combine method is template which directed the synthesis thereof. conducted an appropriate number of times to produce a library of typically between 10 and 10 different com BACKGROUND pounds. The Split-and-combine method is cumberSome and 0002 The generation of molecules carrying new proper generates only a relatively Small library. ties remains a challenging task. Recently, a number of 0006 Gartner ZJ and Liu D R (J. Am. Chem. Soc. 2001, procedures have been Suggested that should allow a more 123, 6961-6963) discloses a method in which DNA is used efficient generation and Screening of a larger number of to direct chemical reactions Sequence-specifically. It is molecules. The approaches taken involve the encoding and/ shown that the proximity effect provided by DNA-templated or templating of molecules other than natural biopolymers Synthesis can be used to promote chemical reactions. When such as peptide, RNA and DNA. These approaches allow the more than a single chemical entity is to participate in the researcher to generate and Screen a huge number of mol formation of an encoded molecule, it is necessary to have a ecules in a short time. This should lead to better molecules building block Spaced from a reactive site of the template by carrying the desired properties. one or more codons. Typically, the distance between the 0003. The central dogma of biology describes the one building block and the reactive site of the template amounts way flow of information from DNA to RNA to protein. to Several nucleotides, e.g. 30 nucleotides, which implies Recently, methods Such as phage display, peptides-on-plas that the reaction at the largest distance from the template mids, ribosome display and mRNA-protein fusion have been reactive site is less promoted relative to a chemical entity developed, allowing the transfer of information from the carried by a building block annealed to a codon next to the level of protein/peptide to RNA or DNA. This has enabled reactive Site. the use of molecular evolution to be applied on huge numbers of peptides that are exposed to an enrichment 0007. The present invention aims at suggesting a solution process, where after the enriched pool of molecules for increasing the local concentration of reactants to promote (enriched for a particular feature, Such as binding to receptor the probability of a reaction. protein) are amplified, by exploiting information flow from the peptide to DNA and then amplifying the DNA. SUMMARY OF THE INVENTION 0004 More recently, approaches have been developed 0008. The present invention provides a method for syn that allow the encoding of polypeptides and other biochemi thesising a templated molecule, Said method comprising the cal polymers. An example of this approach is disclosed in Steps of U.S. Pat No. 5,723,598, which pertains to the identification of a biochemical polymer that participates in a preselected 0009 a) providing at least one template comprising binding interaction with a target to form a binding reaction of one or more codons, complex.
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