RU2018101666A - Новые ферменты и системы crispr - Google Patents
Новые ферменты и системы crispr Download PDFInfo
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- RU2018101666A RU2018101666A RU2018101666A RU2018101666A RU2018101666A RU 2018101666 A RU2018101666 A RU 2018101666A RU 2018101666 A RU2018101666 A RU 2018101666A RU 2018101666 A RU2018101666 A RU 2018101666A RU 2018101666 A RU2018101666 A RU 2018101666A
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- effector protein
- cpf1
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- 238000010354 CRISPR gene editing Methods 0.000 title claims 5
- 108091033409 CRISPR Proteins 0.000 title claims 3
- 108090000790 Enzymes Proteins 0.000 title claims 3
- 102000004190 Enzymes Human genes 0.000 title claims 3
- 210000004027 cell Anatomy 0.000 claims 48
- 238000000034 method Methods 0.000 claims 42
- 108090000623 proteins and genes Proteins 0.000 claims 28
- 102000004169 proteins and genes Human genes 0.000 claims 22
- 239000012636 effector Substances 0.000 claims 20
- 108091033319 polynucleotide Proteins 0.000 claims 8
- 102000040430 polynucleotide Human genes 0.000 claims 8
- 239000002157 polynucleotide Substances 0.000 claims 8
- 230000008685 targeting Effects 0.000 claims 8
- 150000007523 nucleic acids Chemical group 0.000 claims 7
- 108020004414 DNA Proteins 0.000 claims 6
- 102100035102 E3 ubiquitin-protein ligase MYCBP2 Human genes 0.000 claims 6
- 108020004707 nucleic acids Proteins 0.000 claims 6
- 102000039446 nucleic acids Human genes 0.000 claims 6
- 239000013598 vector Substances 0.000 claims 6
- 108091032973 (ribonucleotides)n+m Proteins 0.000 claims 5
- 239000002245 particle Substances 0.000 claims 5
- 108091028043 Nucleic acid sequence Proteins 0.000 claims 4
- 210000003527 eukaryotic cell Anatomy 0.000 claims 4
- 230000004048 modification Effects 0.000 claims 4
- 238000012986 modification Methods 0.000 claims 4
- 230000001105 regulatory effect Effects 0.000 claims 4
- MBLBDJOUHNCFQT-UHFFFAOYSA-N N-acetyl-D-galactosamine Natural products CC(=O)NC(C=O)C(O)C(O)C(O)CO MBLBDJOUHNCFQT-UHFFFAOYSA-N 0.000 claims 3
- 208000009869 Neu-Laxova syndrome Diseases 0.000 claims 3
- 108010077850 Nuclear Localization Signals Proteins 0.000 claims 3
- 239000002773 nucleotide Substances 0.000 claims 3
- 125000003729 nucleotide group Chemical group 0.000 claims 3
- 108020005004 Guide RNA Proteins 0.000 claims 2
- OVRNDRQMDRJTHS-KEWYIRBNSA-N N-acetyl-D-galactosamine Chemical compound CC(=O)N[C@H]1C(O)O[C@H](CO)[C@H](O)[C@@H]1O OVRNDRQMDRJTHS-KEWYIRBNSA-N 0.000 claims 2
- 241000605894 Porphyromonas Species 0.000 claims 2
- 230000005856 abnormality Effects 0.000 claims 2
- 210000004102 animal cell Anatomy 0.000 claims 2
- 238000003776 cleavage reaction Methods 0.000 claims 2
- 210000005260 human cell Anatomy 0.000 claims 2
- 238000000338 in vitro Methods 0.000 claims 2
- 230000007017 scission Effects 0.000 claims 2
- 241000894007 species Species 0.000 claims 2
- 210000000130 stem cell Anatomy 0.000 claims 2
- 239000013603 viral vector Substances 0.000 claims 2
- 241000093740 Acidaminococcus sp. Species 0.000 claims 1
- 101000860090 Acidaminococcus sp. (strain BV3L6) CRISPR-associated endonuclease Cas12a Proteins 0.000 claims 1
- 241000894006 Bacteria Species 0.000 claims 1
- 241000168061 Butyrivibrio proteoclasticus Species 0.000 claims 1
- 241001040999 Candidatus Methanoplasma termitum Species 0.000 claims 1
- 241000223283 Candidatus Peregrinibacteria bacterium GW2011_GWA2_33_10 Species 0.000 claims 1
- 102000053602 DNA Human genes 0.000 claims 1
- 241000702421 Dependoparvovirus Species 0.000 claims 1
- 241000589602 Francisella tularensis Species 0.000 claims 1
- 241000589599 Francisella tularensis subsp. novicida Species 0.000 claims 1
- 101000860092 Francisella tularensis subsp. novicida (strain U112) CRISPR-associated endonuclease Cas12a Proteins 0.000 claims 1
- 241000448224 Lachnospiraceae bacterium MA2020 Species 0.000 claims 1
- 241000448225 Lachnospiraceae bacterium MC2017 Species 0.000 claims 1
- 241000689670 Lachnospiraceae bacterium ND2006 Species 0.000 claims 1
- 241000713666 Lentivirus Species 0.000 claims 1
- 241001148627 Leptospira inadai Species 0.000 claims 1
- 241001465754 Metazoa Species 0.000 claims 1
- 241001193016 Moraxella bovoculi 237 Species 0.000 claims 1
- OVRNDRQMDRJTHS-CBQIKETKSA-N N-Acetyl-D-Galactosamine Chemical compound CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1O OVRNDRQMDRJTHS-CBQIKETKSA-N 0.000 claims 1
- 241000182952 Parcubacteria group bacterium GW2011_GWC2_44_17 Species 0.000 claims 1
- 241000878522 Porphyromonas crevioricanis Species 0.000 claims 1
- 241001302521 Prevotella albensis Species 0.000 claims 1
- 241001037426 Smithella sp. Species 0.000 claims 1
- 241001531273 [Eubacterium] eligens Species 0.000 claims 1
- 230000001580 bacterial effect Effects 0.000 claims 1
- 241000385540 bacterium 10 Species 0.000 claims 1
- 241000496058 bacterium ND2006 Species 0.000 claims 1
- 230000015572 biosynthetic process Effects 0.000 claims 1
- 230000005782 double-strand break Effects 0.000 claims 1
- 210000001808 exosome Anatomy 0.000 claims 1
- 229940118764 francisella tularensis Drugs 0.000 claims 1
- 238000001727 in vivo Methods 0.000 claims 1
- 230000001939 inductive effect Effects 0.000 claims 1
- 150000002632 lipids Chemical class 0.000 claims 1
- 239000002502 liposome Substances 0.000 claims 1
- 238000004519 manufacturing process Methods 0.000 claims 1
- 239000002184 metal Substances 0.000 claims 1
- 230000008929 regeneration Effects 0.000 claims 1
- 238000011069 regeneration method Methods 0.000 claims 1
- 241000701161 unidentified adenovirus Species 0.000 claims 1
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Claims (62)
1. Сконструированная не встречающаяся в природе система на основе коротких палиндромных повторов, регулярно расположенных группами (CRISPR)-CRISPR-ассоциированного фермента (Cas) (CRISPR-Cas), содержащая
a) одну или несколько полинуклеотидных последовательностей CRISPR-Cas V типа, предусматривающих направляющую РНК, которая содержит направляющую последовательность, связанную с последовательностью прямого повтора, где направляющая последовательность способна гибридизироваться с целевой последовательностью, или одну или несколько нуклеотидных последовательностей, кодирующих одну или несколько полинуклеотидных последовательностей CRISPR-Cas V типа, и
b) эффекторный белок Cpf1 или одну или несколько нуклеотидных последовательностей, кодирующих эффекторный белок Cpf1;
где одна или несколько направляющих последовательностей гибридизируются с указанной целевой последовательностью, причем указанная целевая последовательность находится в направлении 3' от мотива, смежного с протоспейсером (PAM), и при этом указанная направляющая РНК образует комплекс с эффекторным белком Cpf1.
2. Сконструированная не встречающаяся в природе векторная система на основе коротких палиндромных повторов, регулярно расположенных группами (CRISPR)-CRISPR-ассоциированного фермента (Cas) (CRISPR-Cas), содержащая один или несколько векторов, содержащих
a) первый регуляторный элемент, функционально связанный с одной или несколькими нуклеотидными последовательностями, кодирующими одну или несколько полинуклеотидных последовательностей CRISPR-Cas V типа, предусматривающих направляющую РНК, которая содержит направляющую последовательность, связанную с последовательностью прямого повтора, где направляющая последовательность способна гибридизироваться с целевой последовательностью,
b) второй регуляторный элемент, функционально связанный с нуклеотидной последовательностью, кодирующей эффекторный белок Cpf1;
где компоненты (a) и (b) находятся в одном и том же или в разных векторах системы,
где, будучи транскрибированными, одна или несколько направляющих последовательностей гибридизируются с указанной целевой последовательностью, причем указанная целевая последовательность находится в направлении 3' от мотива, смежного с протоспейсером (PAM), и при этом указанная направляющая РНК образует комплекс с эффекторным белком Cpf1.
3. Система по п. 1 или 2, где целевые последовательности находятся в клетке.
4. Система по п. 3, где клетка предусматривает эукариотическую клетку.
5. Система по п. 1 или 2, где, будучи транскрибированными, одна или несколько направляющих последовательностей гибридизируются с целевой последовательностью, и при этом направляющая РНК образует комплекс c эффекторным белком Cpf1, который вызывает расщепление отдаленно от целевой последовательности.
6. Система по п. 5, где указанное расщепление приводит к образованию ступенчатого двухнитевого разрыва с "липким" 5'-концом длиной 4 или 5 нуклеотидов.
7. Система по п. 1 или 2, где PAM предусматривает 5'-мотив с высоким содержанием T.
8. Система по п. 1 или 2, где эффекторный белок представляет собой эффекторный белок Cpf1, происходящий от одного из видов бактерий, приведенных на фигуре 64.
9. Система по п. 8, где эффекторный белок Cpf1 происходит от вида бактерий, выбранного из группы, состоящей из Francisella tularensis 1, Francisella tularensis subsp. novicida, Prevotella albensis, Lachnospiraceae bacterium MC2017 1, Butyrivibrio proteoclasticus, Peregrinibacteria bacterium GW2011_GWA2_33_10, Parcubacteria bacterium GW2011_GWC2_44_17, Smithella sp. SCADC, Acidaminococcus sp. BV3L6, Lachnospiraceae bacterium MA2020, Candidatus Methanoplasma termitum, Eubacterium eligens, Moraxella bovoculi 237, Leptospira inadai, Lachnospiraceae bacterium ND2006, Porphyromonas crevioricanis 3, Prevotella disiens и Porphyromonas macacae.
10. Система по п. 9, где последовательность PAM представляет собой TTN, где N представляет собой A/C/G или T, а эффекторный белок представляет собой FnCpf1, или где последовательность PAM представляет собой TTTV, где V представляет собой A/C или G, а эффекторный белок представляет собой PaCpf1p, LbCpf1 или AsCpf1.
11. Система по п. 1 или 2, где эффекторный белок Cpf1 содержит один или несколько сигналов ядерной локализации.
12. Система по п. 1 или 2, где последовательности нуклеиновой кислоты, кодирующие эффекторный белок Cpf1, являются кодон-оптимизированными для экспрессии в эукариотической клетке.
13. Система по п. 1 или 2, где компоненты (a) и (b) или нуклеотидные последовательности находятся в одном векторе.
14. Способ модифицирования представляющего интерес целевого локуса, включающий доставку системы по п. 1 или 2 в указанный локус или клетку, содержащую локус.
15. Способ модифицирования представляющего интерес целевого локуса, причем способ включает доставку в указанный локус не встречающейся в природе или сконструированной композиции, содержащей эффекторный белок Cpf1 и один или несколько компонентов на основе нуклеиновой кислоты, где эффекторный белок Cpf1 образует комплекс с одним или несколькими компонентами на основе нуклеиновой кислоты, и после связывания указанного комплекса с представляющим интерес целевым локусом, который находится в направлении 3' от мотива, смежного с протоспейсером (PAM), эффекторный белок индуцирует модификацию представляющего интерес целевого локуса.
16. Способ по п. 15, где представляющий интерес целевой локус находится в клетке.
17. Способ по п. 16, где клетка является эукариотической клеткой.
18. Способ по п. 16, где клетка является клеткой животного или человека.
19. Способ по п. 16, где клетка является растительной клеткой.
20. Способ по п. 15, где представляющий интерес целевой локус содержится в молекуле ДНК in vitro.
21. Способ по п. 15, где указанную не встречающуюся в природе или сконструированную композицию, содержащую эффекторный белок Cpf1 и один или несколько компонентов на основе нуклеиновой кислоты, доставляют в клетку в виде одной или нескольких полинуклеотидных молекул.
22. Способ по п. 15, где представляющий интерес целевой локус предусматривает ДНК.
23. Способ по п. 22, где ДНК является релаксированной или суперспирализованной.
24. Способ по п. 15, где композиция содержит один компонент на основе нуклеиновой кислоты.
25. Способ по п. 24, где один компонент на основе нуклеиновой кислоты предусматривает направляющую последовательность, связанную с последовательностью прямого повтора.
26. Способ по п. 15, где модификация представляющего интерес целевого локуса представляет собой разрыв нити.
27. Способ по п. 26, где разрыв нити предусматривает ступенчатый двухнитевой разрыв ДНК с "липким" 5'-концом длиной 4 или 5 нуклеотидов.
28. Способ по п. 26, где представляющий интерес целевой локус является модифицированным посредством интеграции ДНК-вставки в ступенчатый двухнитевой разрыв ДНК.
29. Способ по п. 15, где эффекторный белок Cpf1 содержит один или несколько сигналов ядерной локализации (NLS).
30. Способ по п. 21, где одна или несколько полинуклеотидных молекул содержатся в одном или нескольких векторах.
31. Способ по п. 21, где одна или несколько полинуклеотидных молекул содержат один или несколько регуляторных элементов, функционально сконфигурированных для обеспечения экспрессии эффекторного белка Cpf1 и/или компонента(компонентов) на основе нуклеиновой кислоты, где один или несколько регуляторных элементов необязательно предусматривают индуцируемые промоторы.
32. Способ по п. 21, где одна или несколько полинуклеотидных молекул или один или несколько векторов содержатся в системе доставки.
33. Способ по п. 21, где систему или одну или несколько полинуклеотидных молекул доставляют посредством частиц, везикул или одного или нескольких вирусных векторов.
34. Способ по п. 33, где частицы предусматривают липид, сахар, металл или белок.
35. Способ по п. 33, где везикулы предусматривают экзосомы или липосомы.
36. Способ по п. 33, где один или несколько вирусных векторов предусматривают одно или несколько из аденовируса, одного или нескольких лентивирусов или одного или нескольких аденоассоциированных вирусов.
37. Способ по п. 15, который представляет собой способ модифицирования клетки, линии клеток или организма путем манипуляции с одной или несколькими целевыми последовательностями в представляющих интерес локусах генома.
38. Клетка, полученная в результате осуществления способа по п. 37, или ее потомство, где клетка содержит модификацию, не присутствующую в клетке, в отношении которой не осуществляли способ.
39. Клетка по п. 38 или ее потомство, где клетка, в отношении которой не осуществляли способ, содержит аномалию, а клетка, полученная в результате осуществления способа, характеризуется устраненной или скорректированной аномалией.
40. Продукт клетки, полученный из клетки или ее потомства по п. 38, где продукт является модифицированным по своей природе или количеству по сравнению с продуктом клетки, полученным из клетки, в отношении которой не осуществляли способ.
41. Продукт клетки по п. 40, где клетка, в отношении которой не осуществляли способ, содержит аномалию, и при этом продукт клетки отражает аномалию, которая устраняется или корректируется с помощью способа.
42. In vitro, ex vivo или in vivo клетка-хозяин или линия клеток или их потомство, содержащие систему по п. 1 или 2.
43. Клетка-хозяин или линия клеток или их потомство по п. 42, где клетка является эукариотической клеткой.
44. Клетка-хозяин или линия клеток или их потомство по п. 43, где клетка является клеткой животного.
45. Клетка-хозяин или линия клеток или их потомство по п. 33, где клетка является клеткой человека.
46. Клетка-хозяин, линия клеток или их потомство по п. 31, предусматривающие стволовую клетку или линию стволовых клеток.
47. Клетка-хозяин или линия клеток или их потомство по п. 30, где клетка является растительной клеткой.
48. Способ получения растения с модифицированным представляющим интерес признаком, кодируемым представляющим интерес геном, причем указанный способ включает приведение растительной клетки в контакт с системой по п. 1 или п. 2 или осуществление в отношении растительной клетки способа по п. 15, за счет чего обеспечивается либо модифицирование, либо введение указанного представляющего интерес гена, и регенерацию растения из указанной растительной клетки.
49. Способ идентификации представляющего интерес признака у растения, причем указанный представляющий интерес признак кодируется представляющим интерес геном, причем указанный способ включает приведение растительной клетки в контакт с системой по п. 1 или 2 или осуществление в отношении растительной клетки способа по п. 15, за счет чего обеспечивается идентификация указанного представляющего интерес гена.
50. Способ по п. 49, дополнительно включающий введение идентифицированного представляющего интерес гена в растительную клетку, или линию растительных клеток, или растительную зародышевую плазму и получение из них растения, в результате чего растение содержит представляющий интерес ген.
51. Способ по п. 50, где у растения проявляется представляющий интерес признак.
52. Частица, содержащая систему по п. 1 или 2.
53. Частица по п. 52, где частица содержит эффекторный белок Cpf1 в комплексе с направляющей РНК.
54. Система или способ по пп. 1, 2 или 15, где комплекс, направляющая РНК или белок конъюгированы по меньшей мере с одним сахарным фрагментом, необязательно N-ацетилгалактозамином (GalNAc), в частности, с трехразветвленным GalNAc.
55. Система или способ по пп. 1, 2 или 15, где концентрация Mg2+ составляет от приблизительно 1 мМ до приблизительно 15 мМ.
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| RU2720769C1 (ru) * | 2019-12-13 | 2020-05-13 | Федеральное бюджетное учреждение науки «Центральный научно-исследовательский институт эпидемиологии» Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека (ФБУН ЦНИИ Эпидемиологии Роспотребнадзора) | Способ получения препарата рибонуклеопротеинового комплекса CRISPR/CAS и препарат для детекции провирусной ДНК вируса иммунодефицита человека, интегрированной в геном человека, в ультранизких концентрациях |
| RU2720768C1 (ru) * | 2019-12-13 | 2020-05-13 | Федеральное бюджетное учреждение науки "Центральный научно-исследовательский институт эпидемиологии" Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека (ФБУН ЦНИИ Эпидемиологии Роспотребнадзора) | Система CRISPR-Cas для детекции провирусной ДНК вируса иммунодефицита человека, интегрированной в геном человека, в ультранизких концентрациях |
| RU2720767C1 (ru) * | 2019-12-13 | 2020-05-13 | Федеральное бюджетное учреждение науки «Центральный научно-исследовательский институт эпидемиологии» Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека (ФБУН ЦНИИ Эпидемиологии Роспотребнадзора) | Способ обнаружения провирусной ДНК вируса иммунодефицита человека, интегрированной в геном человека, в ультранизких концентрациях и специфические олигонуклеотиды для использования в способе |
| RU2743861C1 (ru) * | 2020-04-15 | 2021-03-01 | Федеральное бюджетное учреждение науки "Центральный научно-исследовательский институт эпидемиологии" Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека (ФБУН ЦНИИ Эпидемиологии Роспотребнадзора) | Система CRISPR-Cas для выявления гена антибиотикоустойчивости blaVIM-2 (металло-бета-лактамаза класс B VIM-2) Pseudomonas aeruginosa в ультранизких концентрациях |
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| WO2021211010A1 (ru) * | 2020-04-15 | 2021-10-21 | Федеральное Бюджетное Учреждение Науки "Центральный Научно-Исследовательский Институт Эпидемиологии" Федеральной Службы По Надзору В Сфере Защиты Прав Потребителей И Благополучия Человека | Crispr/cas для выявления гена антибиотикоустойчивости bla vim-2 |
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