Cas9 Sandbox: Difference between revisions

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== DNA Interaction ==

Target DNA contains a protospacer adjacent motif on the non-complementary strand, which constitues the <scene name='71/714945/Pam_interaction/8'>Cas9 interaction at the PAM sequence</scene>. This canonical sequence of 5’-NGG-3’ is recognized by Cas9 and is essential for genetic interference and editing, therefore, it will not cleave the target sequence if the PAM sequence is absent. The double Guanine of the non-complementary sequence strand interacts via hydrogen bonding from the major groove through two conserved arginine residues on the carboxy-terminus of Cas9 <ref>PMID:25079318</ref>. The minor groove of the PAM sequence interacts with a serine, through a hydrogen bridge to the last guanine, and lysine residue on the complementary target strand of the middle guanine.

Target DNA contains a protospacer adjacent motif on the non-complementary strand, which constitues the <scene name='71/714945/Pam_interaction/12'>Cas9 interaction at the PAM sequence</scene>. This canonical sequence of 5’-NGG-3’ is recognized by Cas9 and is essential for genetic interference and editing, therefore, it will not cleave the target sequence if the PAM sequence is absent. The double Guanine of the non-complementary sequence strand interacts via hydrogen bonding from the major groove through two conserved arginine residues on the carboxy-terminus of Cas9 <ref>PMID:25079318</ref>. The minor groove of the PAM sequence interacts with a serine, through a hydrogen bridge to the last guanine, and lysine residue on the complementary target strand of the middle guanine.

The deoxyribose-phosphate backbone of the non-complementary strand is arranged in close proximity to various hydrogen bonding atoms, some of which are accomplished through water molecules, and ionic interactions. A phosphate lock loop provides local strand separation upstream of the PAM sequence when a Lysine and Serine residue stabilize target DNA. The PAM sequence recognition of Cas9 is an integral function of its specific binding, subsequent base pair melting and cleavage of target DNA.

Cas9 Sandbox: Difference between revisions

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@@ Line 18: / Line 18: @@
 == DNA Interaction ==
-Target DNA contains a protospacer adjacent motif on the non-complementary strand, which constitues the <scene name='71/714945/Pam_interaction/8'>Cas9 interaction at the PAM sequence</scene>. This canonical sequence of 5’-NGG-3’ is recognized by Cas9 and is essential for genetic interference and editing, therefore, it will not cleave the target sequence if the PAM sequence is absent. The double Guanine of the non-complementary sequence strand interacts via hydrogen bonding from the major groove through two conserved arginine residues on the carboxy-terminus of Cas9 <ref>PMID:25079318</ref>.  The minor groove of the PAM sequence interacts with a serine, through a hydrogen bridge to the last guanine, and lysine residue on the complementary target strand of the middle guanine.
+Target DNA contains a protospacer adjacent motif on the non-complementary strand, which constitues the <scene name='71/714945/Pam_interaction/12'>Cas9 interaction at the PAM sequence</scene>. This canonical sequence of 5’-NGG-3’ is recognized by Cas9 and is essential for genetic interference and editing, therefore, it will not cleave the target sequence if the PAM sequence is absent. The double Guanine of the non-complementary sequence strand interacts via hydrogen bonding from the major groove through two conserved arginine residues on the carboxy-terminus of Cas9 <ref>PMID:25079318</ref>.  The minor groove of the PAM sequence interacts with a serine, through a hydrogen bridge to the last guanine, and lysine residue on the complementary target strand of the middle guanine.
 The deoxyribose-phosphate backbone of the non-complementary strand is arranged in close proximity to various hydrogen bonding atoms, some of which are accomplished through water molecules, and ionic interactions. A phosphate lock loop provides local strand separation upstream of the PAM sequence when a Lysine and Serine residue stabilize target DNA. The PAM sequence recognition of Cas9 is an integral function of its specific binding, subsequent base pair melting and cleavage of target DNA.