You will have to escape the input strings before passing them to MySql.

The list of escape characters is:

Character   Escape Sequence
\0  An ASCII NUL (0x00) character.
\'  A single quote (“'”) character.
\"  A double quote (“"”) character.
\b  A backspace character.
\n  A newline (linefeed) character.
\r  A carriage return character.
\t  A tab character.
\Z  ASCII 26 (Control-Z). See note following the table.
\\  A backslash (“\”) character.
\%  A “%” character. See note following the table.
\_  A “_” character. See note following the table.

I've developed my own MySQL escape method in Java (if useful for anyone).

See class code below.

Warning: wrong if NO_BACKSLASH_ESCAPES SQL mode is enabled.

private static final HashMap<String,String> sqlTokens;
private static Pattern sqlTokenPattern;

static
{           
    //MySQL escape sequences: http://dev.mysql.com/doc/refman/5.1/en/string-syntax.html
    String[][] search_regex_replacement = new String[][]
    {
                //search string     search regex        sql replacement regex
            {   "\u0000"    ,       "\\x00"     ,       "\\\\0"     },
            {   "'"         ,       "'"         ,       "\\\\'"     },
            {   "\""        ,       "\""        ,       "\\\\\""    },
            {   "\b"        ,       "\\x08"     ,       "\\\\b"     },
            {   "\n"        ,       "\\n"       ,       "\\\\n"     },
            {   "\r"        ,       "\\r"       ,       "\\\\r"     },
            {   "\t"        ,       "\\t"       ,       "\\\\t"     },
            {   "\u001A"    ,       "\\x1A"     ,       "\\\\Z"     },
            {   "\\"        ,       "\\\\"      ,       "\\\\\\\\"  }
    };

    sqlTokens = new HashMap<String,String>();
    String patternStr = "";
    for (String[] srr : search_regex_replacement)
    {
        sqlTokens.put(srr[0], srr[2]);
        patternStr += (patternStr.isEmpty() ? "" : "|") + srr[1];            
    }
    sqlTokenPattern = Pattern.compile('(' + patternStr + ')');
}


public static String escape(String s)
{
    Matcher matcher = sqlTokenPattern.matcher(s);
    StringBuffer sb = new StringBuffer();
    while(matcher.find())
    {
        matcher.appendReplacement(sb, sqlTokens.get(matcher.group(1)));
    }
    matcher.appendTail(sb);
    return sb.toString();
}

Welcome to the world of string encoding formats!

tl;dr - The preferred method for handling quotes and escape characters when storing data in MySQL columns is to use parameterized queries and let the MySQLDatabase driver handle it. Alternatively, you can escape quotes and slashes by doubling them up prior to insertion.

Full example at bottom of link

standard SQL update

# as_json must have escape slashes and quotes doubled
query = """\
        UPDATE json_sandbox
        SET data = '{}'
        WHERE id = 1;
    """.format(as_json)

with DBConn(*client.conn_args) as c:
    c.cursor.execute(query)
    c.connection.commit()

parameterized SQL update

# SQL Driver will do the escaping for you
query = """\
        UPDATE json_sandbox
        SET data = %s
        WHERE id = %s;
    """

with DBConn(*client.conn_args) as c:
    c.cursor.execute(query, (as_json, 1))
    c.connection.commit()

Invalid JSON SQL

{
  "abc": 123,
  "quotes": "ain't it great",
  "multiLine1": "hello\nworld",
  "multiLine3": "hello\r\nuniverse\r\n"
}

Valid JSON SQL

{
  "abc": 123,
  "quotes": "ain''t it great",
  "multiLine1": "hello\\nworld",
  "multiLine3": "hello\\r\\nuniverse\\r\\n"
}

Python transform:

# must escape the escape characters, so each slash is doubled
# Some MySQL Python libraries also have an escape() or escape_string() method.
as_json = json.dumps(payload) \
    .replace("'", "''") \
    .replace('\\', '\\\\')

Full example

import json
import yaml

from DataAccessLayer.mysql_va import get_sql_client, DBConn

client = get_sql_client()

def encode_and_store(payload):
    as_json = json.dumps(payload) \
        .replace("'", "''") \
        .replace('\\', '\\\\')

    query = """\
            UPDATE json_sandbox
            SET data = '{}'
            WHERE id = 1;
        """.format(as_json)

    with DBConn(*client.conn_args) as c:
        c.cursor.execute(query)
        c.connection.commit()

    return

def encode_and_store_2(payload):
    as_json = json.dumps(payload)

    query = """\
            UPDATE json_sandbox
            SET data = %s
            WHERE id = %s;
        """

    with DBConn(*client.conn_args) as c:
        c.cursor.execute(query, (as_json, 1))
        c.connection.commit()

    return


def retrieve_and_decode():
    query = """
        SELECT * FROM json_sandbox
        WHERE id = 1
    """

    with DBConn(*client.conn_args) as cnx:
        cursor = cnx.dict_cursor
        cursor.execute(query)

        rows = cursor.fetchall()


    as_json = rows[0].get('data')

    payload = yaml.safe_load(as_json)
    return payload



if __name__ == '__main__':

    payload = {
        "abc": 123,
        "quotes": "ain't it great",
        "multiLine1": "hello\nworld",
        "multiLine2": """
            hello
            world
        """,
        "multiLine3": "hello\r\nuniverse\r\n"
    }


    encode_and_store(payload)
    output_a = retrieve_and_decode()

    encode_and_store_2(payload)
    output_b = retrieve_and_decode()

    print("original: {}".format(payload))
    print("method_a: {}".format(output_a))
    print("method_b: {}".format(output_b))

    print('')
    print(output_a['multiLine1'])

    print('')
    print(output_b['multiLine2'])

    print('\nAll Equal?: {}'.format(payload == output_a == output_b))