{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/29571"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/29571","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays","abstract":"Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+ and Zn2+ are found capable of inducing folding between two pairs of stems while the active ions UO22+ and Pb2+ are not able to bring about the folding in any pairs of the stems. By correlating the enzymatic cleavage results, the Mg2+ and Zn2+ induced folding exerts a counter-productive effect on the activities. This result contradicts with the normal productive role that Mg2+ plays in the activation of ribozyme functions. At reduced ionic strength, even UO22+ and Pb2+ can induce folding due to the nonspecific electrostatic interaction from their divalent metal ion nature. And the progression of Mg2+ and Na+ concentration leads to an inactive-active-inactive transition in the DNAzyme function. Single molecule FRET is also used to obtain kinetics for low UO22+ concentration at reduced imaging buffer strength. Together with the biochemical characterization for the catalytic cores and optimal working conditions, a thorough understanding of this DNAzyme 39E is obtained, which might be helpful in the design of sensitive and selective DNAzymes. FRET is also used to gain step-wise kinetic information of adenosine aptamer structure-switching sensor. The kinetic information for individual steps (folding and releasing) obtained by monitoring FRET process between fluorophores labeled at several positions of the aptamer structure switching sensor provides direct evidence for sequential occurrences, as predicted by the structure switching principle. The information obtained here will facilitate sensors designed based on the structure-switching principle. Electrohydrodynamic jet (E-jet) printing is applied to the protein microarray field. With the development of multi-nozzle printing system, both single-protein array and multiple-protein arrays are successfully demonstrated. Several proteins, such as streptavidin, Green fluorescence protein (GFP), mCherry (a red fluorescence protein), et.al, have been printed, proving E-jet printing is generally applicable to many types of proteins. The printed streptavidin maintains its binding character with biotin, showing the printed streptavidin is still structurally intact and functionally active. What’s more, this printing technology has also been employed to immunology application. Immunoglobulin (Ig) G from several animal species are printed by E-jet printing, and their binding specificities to corresponding secondary antibody, anti IgG, are maintained. To prove this technique suitable for more practical applications, an inch-sized array with well controlled feature details has been completely in a short period of time. Overall, this technique will be a promising candidate for future protein microarray fabrication method.","abstract_html":"Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+ and Zn2+ are found capable of inducing folding between two pairs of stems while the active ions UO22+ and Pb2+ are not able to bring about the folding in any pairs of the stems. By correlating the enzymatic cleavage results, the Mg2+ and Zn2+ induced folding exerts a counter-productive effect on the activities. This result contradicts with the normal productive role that Mg2+ plays in the activation of ribozyme functions. At reduced ionic strength, even UO22+ and Pb2+ can induce folding due to the nonspecific electrostatic interaction from their divalent metal ion nature. And the progression of Mg2+ and Na+ concentration leads to an inactive-active-inactive transition in the DNAzyme function. Single molecule FRET is also used to obtain kinetics for low UO22+ concentration at reduced imaging buffer strength. Together with the biochemical characterization for the catalytic cores and optimal working conditions, a thorough understanding of this DNAzyme 39E is obtained, which might be helpful in the design of sensitive and selective DNAzymes. FRET is also used to gain step-wise kinetic information of adenosine aptamer structure-switching sensor. The kinetic information for individual steps (folding and releasing) obtained by monitoring FRET process between fluorophores labeled at several positions of the aptamer structure switching sensor provides direct evidence for sequential occurrences, as predicted by the structure switching principle. The information obtained here will facilitate sensors designed based on the structure-switching principle. Electrohydrodynamic jet (E-jet) printing is applied to the protein microarray field. With the development of multi-nozzle printing system, both single-protein array and multiple-protein arrays are successfully demonstrated. Several proteins, such as streptavidin, Green fluorescence protein (GFP), mCherry (a red fluorescence protein), et.al, have been printed, proving E-jet printing is generally applicable to many types of proteins. The printed streptavidin maintains its binding character with biotin, showing the printed streptavidin is still structurally intact and functionally active. What’s more, this printing technology has also been employed to immunology application. Immunoglobulin (Ig) G from several animal species are printed by E-jet printing, and their binding specificities to corresponding secondary antibody, anti IgG, are maintained. To prove this technique suitable for more practical applications, an inch-sized array with well controlled feature details has been completely in a short period of time. Overall, this technique will be a promising candidate for future protein microarray fabrication method.","abstract_has_math":false,"creators":["He, Ying"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Materials Science & Engr","degree_department":null,"school":null,"contributors":["Lu, Yi","Rogers, John A.","Braun, Paul V.","Ha, Taekjip","Cheng, Jianjun"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-02-01T00:56:06Z","date_published":"2012-02-01T00:56:06Z","updated_at":"2026-07-22T22:25:27Z","subjects":["Functional DNA","Fluorescence resonance energy transfer (FRET)","Protein microarray","Deoxyribonucleic acid (DNA)"],"languages":["en"],"rights":["Copyright 2011 Ying He"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/29571","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Lu, Yi","Rogers, John A.","Braun, Paul V.","Ha, Taekjip","Cheng, Jianjun"]},{"key":"dc:creator","label":"Author","values":["He, Ying"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-02-01T00:56:06Z","2014-02-01T11:00:35Z","2011-12"]},{"key":"dc:type","label":"Dc Type","values":["Dissertation / Thesis","text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Materials Science & Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Functional DNA","Fluorescence resonance energy transfer (FRET)","Protein microarray","Deoxyribonucleic acid (DNA)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2011 Ying He"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/29571"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+ and Zn2+ are found capable of inducing folding between two pairs of stems while the active ions UO22+ and Pb2+ are not able to bring about the folding in any pairs of the stems. By correlating the enzymatic cleavage results, the Mg2+ and Zn2+ induced folding exerts a counter-productive effect on the activities. This result contradicts with the normal productive role that Mg2+ plays in the activation of ribozyme functions. At reduced ionic strength, even UO22+ and Pb2+ can induce folding due to the nonspecific electrostatic interaction from their divalent metal ion nature. And the progression of Mg2+ and Na+ concentration leads to an inactive-active-inactive transition in the DNAzyme function. Single molecule FRET is also used to obtain kinetics for low UO22+ concentration at reduced imaging buffer strength. Together with the biochemical characterization for the catalytic cores and optimal working conditions, a thorough understanding of this DNAzyme 39E is obtained, which might be helpful in the design of sensitive and selective DNAzymes. FRET is also used to gain step-wise kinetic information of adenosine aptamer structure-switching sensor. The kinetic information for individual steps (folding and releasing) obtained by monitoring FRET process between fluorophores labeled at several positions of the aptamer structure switching sensor provides direct evidence for sequential occurrences, as predicted by the structure switching principle. The information obtained here will facilitate sensors designed based on the structure-switching principle. Electrohydrodynamic jet (E-jet) printing is applied to the protein microarray field. With the development of multi-nozzle printing system, both single-protein array and multiple-protein arrays are successfully demonstrated. Several proteins, such as streptavidin, Green fluorescence protein (GFP), mCherry (a red fluorescence protein), et.al, have been printed, proving E-jet printing is generally applicable to many types of proteins. The printed streptavidin maintains its binding character with biotin, showing the printed streptavidin is still structurally intact and functionally active. What’s more, this printing technology has also been employed to immunology application. Immunoglobulin (Ig) G from several animal species are printed by E-jet printing, and their binding specificities to corresponding secondary antibody, anti IgG, are maintained. To prove this technique suitable for more practical applications, an inch-sized array with well controlled feature details has been completely in a short period of time. Overall, this technique will be a promising candidate for future protein microarray fabrication method.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2011-11-10T23:00:09Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5)","Made available in DSpace on 2012-02-01T00:56:06Z (GMT). No. of bitstreams: 2 He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5) license.txt: 4056 bytes, checksum: 9b30fd403925d6410d151f788e6272f9 (MD5)","Item marked as restricted to the 'Administrator' Group (id=1) by William Ingram (wingram2@illinois.edu) on 2012-02-01T00:57:21Z Item is restricted until 2014-02-01T00:56:58Z","Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2014-02-01T11:00:35Z Item was in collections: Dissertations and Theses - Materials Science and Engineering (ID: 649) Graduate Theses and Dissertations at Illinois (ID: 204) No. of bitstreams: 3 He_Ying.pdf.txt: 459313 bytes, checksum: 156fdd79d002546b42a2c971bf135a42 (MD5) He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5) license.txt: 4056 bytes, checksum: 9b30fd403925d6410d151f788e6272f9 (MD5)","Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2014-02-01T11:00:35Z"]},{"key":"dc:title","label":"Title","values":["Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays"]}]}],"canonical_facts":{"dc:contributor":["Lu, Yi","Rogers, John A.","Braun, Paul V.","Ha, Taekjip","Cheng, Jianjun"],"dc:creator":["He, Ying"],"dc:date":["2012-02-01T00:56:06Z","2014-02-01T11:00:35Z","2011-12"],"dc:description":["Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+ and Zn2+ are found capable of inducing folding between two pairs of stems while the active ions UO22+ and Pb2+ are not able to bring about the folding in any pairs of the stems. By correlating the enzymatic cleavage results, the Mg2+ and Zn2+ induced folding exerts a counter-productive effect on the activities. This result contradicts with the normal productive role that Mg2+ plays in the activation of ribozyme functions. At reduced ionic strength, even UO22+ and Pb2+ can induce folding due to the nonspecific electrostatic interaction from their divalent metal ion nature. And the progression of Mg2+ and Na+ concentration leads to an inactive-active-inactive transition in the DNAzyme function. Single molecule FRET is also used to obtain kinetics for low UO22+ concentration at reduced imaging buffer strength. Together with the biochemical characterization for the catalytic cores and optimal working conditions, a thorough understanding of this DNAzyme 39E is obtained, which might be helpful in the design of sensitive and selective DNAzymes. FRET is also used to gain step-wise kinetic information of adenosine aptamer structure-switching sensor. The kinetic information for individual steps (folding and releasing) obtained by monitoring FRET process between fluorophores labeled at several positions of the aptamer structure switching sensor provides direct evidence for sequential occurrences, as predicted by the structure switching principle. The information obtained here will facilitate sensors designed based on the structure-switching principle. Electrohydrodynamic jet (E-jet) printing is applied to the protein microarray field. With the development of multi-nozzle printing system, both single-protein array and multiple-protein arrays are successfully demonstrated. Several proteins, such as streptavidin, Green fluorescence protein (GFP), mCherry (a red fluorescence protein), et.al, have been printed, proving E-jet printing is generally applicable to many types of proteins. The printed streptavidin maintains its binding character with biotin, showing the printed streptavidin is still structurally intact and functionally active. What’s more, this printing technology has also been employed to immunology application. Immunoglobulin (Ig) G from several animal species are printed by E-jet printing, and their binding specificities to corresponding secondary antibody, anti IgG, are maintained. To prove this technique suitable for more practical applications, an inch-sized array with well controlled feature details has been completely in a short period of time. Overall, this technique will be a promising candidate for future protein microarray fabrication method.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2011-11-10T23:00:09Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5)","Made available in DSpace on 2012-02-01T00:56:06Z (GMT). No. of bitstreams: 2 He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5) license.txt: 4056 bytes, checksum: 9b30fd403925d6410d151f788e6272f9 (MD5)","Item marked as restricted to the 'Administrator' Group (id=1) by William Ingram (wingram2@illinois.edu) on 2012-02-01T00:57:21Z Item is restricted until 2014-02-01T00:56:58Z","Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2014-02-01T11:00:35Z Item was in collections: Dissertations and Theses - Materials Science and Engineering (ID: 649) Graduate Theses and Dissertations at Illinois (ID: 204) No. of bitstreams: 3 He_Ying.pdf.txt: 459313 bytes, checksum: 156fdd79d002546b42a2c971bf135a42 (MD5) He_Ying.pdf: 9688889 bytes, checksum: 80f427efe44e15dd105eedc8a796e619 (MD5) license.txt: 4056 bytes, checksum: 9b30fd403925d6410d151f788e6272f9 (MD5)","Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2014-02-01T11:00:35Z"],"dc:identifier":["http://hdl.handle.net/2142/29571"],"dc:language":["en"],"dc:rights":["Copyright 2011 Ying He"],"dc:subject":["Functional DNA","Fluorescence resonance energy transfer (FRET)","Protein microarray","Deoxyribonucleic acid (DNA)"],"dc:title":["Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays"],"dc:type":["Dissertation / Thesis","text"],"thesis:degree_discipline":["Materials Science & Engr"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:27Z"}