Kristina Alejos | SUNY: University at Albany (original) (raw)

Uploads

Papers by Kristina Alejos

Research paper thumbnail of Orthogonal control of DNA nanoswitches with mixed physical and biochemical cues

Biophysical Journal, Feb 1, 2022

Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M... more Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M13 circular DNA and BtsCI enzyme were purchased from New England Biolabs (NEB). GelRed nucleic acid stain was purchased from Biotium, Fremont, CA, USA. Molecular biology grade agarose was purchased from Fisher BioReagents. The DNA oligonucleotides with photocleavable linkers (PCL) were chemically synthesized at 1.0-µmol scales by solid phase synthesis using an Oligo-800 synthesizer and provided by the Sheng lab at SUNY Albany. Linearization of M13 DNA 5 µl of 100 nM circular single-stranded M13 DNA, 2.5 µl of 10´ Cut Smart buffer, 0.5 µl of 100 µM BtsCI restriction-site complementary-oligonucleotide and 16 µl of deionized water were mixed and annealed from 95 °C to 50 °C in a T100™ Thermal Cycler (Bio-Rad, Hercules, CA, USA). 1 µl of the BtsCI enzyme (20,000 units/ml) was added to the mixture and incubated at 50 °C for 15 min. The mixture was brought up to 95 °C for 1 min to heat deactivate the enzyme followed by cooling down to 4 °C. Construction of nanoswitches Linearized single-stranded M13 DNA (20 nM) was mixed with 10-fold excess of the backbone oligonucleotides and detector strands and annealed from 90 °C to 20 °C at 1 °C min −1 in a thermal cycler. Following construction, the nanoswitches were diluted in 1´ PBS to a concentration of 400 pM. Nanoswitch locking and unlocking A typical reaction contained 160 pM nanoswitch with 2.5 nM target DNA or RNA in a 10 µl reaction

Research paper thumbnail of Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues

Research paper thumbnail of Orthogonal control of DNA nanoswitches with mixed physical and biochemical cues

Biophysical Journal, 2022

Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M... more Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M13 circular DNA and BtsCI enzyme were purchased from New England Biolabs (NEB). GelRed nucleic acid stain was purchased from Biotium, Fremont, CA, USA. Molecular biology grade agarose was purchased from Fisher BioReagents. The DNA oligonucleotides with photocleavable linkers (PCL) were chemically synthesized at 1.0-µmol scales by solid phase synthesis using an Oligo-800 synthesizer and provided by the Sheng lab at SUNY Albany. Linearization of M13 DNA 5 µl of 100 nM circular single-stranded M13 DNA, 2.5 µl of 10´ Cut Smart buffer, 0.5 µl of 100 µM BtsCI restriction-site complementary-oligonucleotide and 16 µl of deionized water were mixed and annealed from 95 °C to 50 °C in a T100™ Thermal Cycler (Bio-Rad, Hercules, CA, USA). 1 µl of the BtsCI enzyme (20,000 units/ml) was added to the mixture and incubated at 50 °C for 15 min. The mixture was brought up to 95 °C for 1 min to heat deactivate the enzyme followed by cooling down to 4 °C. Construction of nanoswitches Linearized single-stranded M13 DNA (20 nM) was mixed with 10-fold excess of the backbone oligonucleotides and detector strands and annealed from 90 °C to 20 °C at 1 °C min −1 in a thermal cycler. Following construction, the nanoswitches were diluted in 1´ PBS to a concentration of 400 pM. Nanoswitch locking and unlocking A typical reaction contained 160 pM nanoswitch with 2.5 nM target DNA or RNA in a 10 µl reaction

Research paper thumbnail of Orthogonal control of DNA nanoswitches with mixed physical and biochemical cues

Biophysical Journal, Feb 1, 2022

Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M... more Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M13 circular DNA and BtsCI enzyme were purchased from New England Biolabs (NEB). GelRed nucleic acid stain was purchased from Biotium, Fremont, CA, USA. Molecular biology grade agarose was purchased from Fisher BioReagents. The DNA oligonucleotides with photocleavable linkers (PCL) were chemically synthesized at 1.0-µmol scales by solid phase synthesis using an Oligo-800 synthesizer and provided by the Sheng lab at SUNY Albany. Linearization of M13 DNA 5 µl of 100 nM circular single-stranded M13 DNA, 2.5 µl of 10´ Cut Smart buffer, 0.5 µl of 100 µM BtsCI restriction-site complementary-oligonucleotide and 16 µl of deionized water were mixed and annealed from 95 °C to 50 °C in a T100™ Thermal Cycler (Bio-Rad, Hercules, CA, USA). 1 µl of the BtsCI enzyme (20,000 units/ml) was added to the mixture and incubated at 50 °C for 15 min. The mixture was brought up to 95 °C for 1 min to heat deactivate the enzyme followed by cooling down to 4 °C. Construction of nanoswitches Linearized single-stranded M13 DNA (20 nM) was mixed with 10-fold excess of the backbone oligonucleotides and detector strands and annealed from 90 °C to 20 °C at 1 °C min −1 in a thermal cycler. Following construction, the nanoswitches were diluted in 1´ PBS to a concentration of 400 pM. Nanoswitch locking and unlocking A typical reaction contained 160 pM nanoswitch with 2.5 nM target DNA or RNA in a 10 µl reaction

Research paper thumbnail of Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues

Research paper thumbnail of Orthogonal control of DNA nanoswitches with mixed physical and biochemical cues

Biophysical Journal, 2022

Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M... more Oligonucleotides were purchased from Integrated DNA Technologies (IDT) with standard desalting. M13 circular DNA and BtsCI enzyme were purchased from New England Biolabs (NEB). GelRed nucleic acid stain was purchased from Biotium, Fremont, CA, USA. Molecular biology grade agarose was purchased from Fisher BioReagents. The DNA oligonucleotides with photocleavable linkers (PCL) were chemically synthesized at 1.0-µmol scales by solid phase synthesis using an Oligo-800 synthesizer and provided by the Sheng lab at SUNY Albany. Linearization of M13 DNA 5 µl of 100 nM circular single-stranded M13 DNA, 2.5 µl of 10´ Cut Smart buffer, 0.5 µl of 100 µM BtsCI restriction-site complementary-oligonucleotide and 16 µl of deionized water were mixed and annealed from 95 °C to 50 °C in a T100™ Thermal Cycler (Bio-Rad, Hercules, CA, USA). 1 µl of the BtsCI enzyme (20,000 units/ml) was added to the mixture and incubated at 50 °C for 15 min. The mixture was brought up to 95 °C for 1 min to heat deactivate the enzyme followed by cooling down to 4 °C. Construction of nanoswitches Linearized single-stranded M13 DNA (20 nM) was mixed with 10-fold excess of the backbone oligonucleotides and detector strands and annealed from 90 °C to 20 °C at 1 °C min −1 in a thermal cycler. Following construction, the nanoswitches were diluted in 1´ PBS to a concentration of 400 pM. Nanoswitch locking and unlocking A typical reaction contained 160 pM nanoswitch with 2.5 nM target DNA or RNA in a 10 µl reaction

Log In