Compositions and methods for enhanced synthesis of nucleic acid molecules

A method for synthesizing a nucleic acid molecule, comprising:

• (a) mixing a nucleic acid template with one or more compounds having a chemical formula selected from the group consisting of formula I or formula IL or a salt thereof, wherein said compound is not betaine:
• Formula I:
• where A is
• where X is
• where N is positively charged;
• wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula I;
• wherein Z may be the same as or different from Y;
• wherein each Y and Z are independently selected from the group consisting of —OH, —NH2, —SH, —PO3H, —CO2H, —SO3H and hydrogen;
• wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;
• wherein R4, R5, and R6 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;
• wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;
• wherein R1, R2 and R3 may be the same or different and are independently selected from the group consisting of:
• with the proviso that no more than two of A, R1, R2 and R3 are selected from the group consisting of hydrogen, methyl, ethyl and propyl;
• and
• with the proviso that if one, and only one, of R1, R2 and R3 is ═O, then A is none of hydrogen, methyl, ethyl and propyl;
• wherein each R7 and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;
• g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R1, R2, and R3 are ═O, then the other is not ═O;
• Formula II:
• wherein Formula II is saturated or unsaturated;
• wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;
• wherein X is selected from the group consisting of N, C, O, P and S;
• wherein Y is selected from the group consisting of O, N, S, P, C, —O—NH—, —O—CH2—NH—, —O—CH2—O—, —NH—CH2—NH—, —O—CH(CH3)—NH—, —NH—CH(CH3)—NH—, —O—CH(CH3)—O—, —NH—C(CH3)2—NH—, —O—S—, —O—CH2—S—, —NH—S—, —NH—CH2—S—, and other mercaptan, phosphate, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• with the proviso that if either X or Y is N, then the other is not C;
• wherein R1, R2, R3, R4, R5, R6, R7 and R8 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• and
• wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, to form a mixture;
• and
• (b) incubating said mixture under conditions whereby a first nucleic acid molecule complementary to all or a portion of said template is made, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

A method for amplifying a nucleic acid molecule, comprising:

• (a) mixing a nucleic acid template with one or more compounds having a chemical formula selected from the group consisting of formula I or formula II, or a salt thereof, wherein said compound is not betaine:
• Formula I:
• where A is
• where X is
• where N is positively charged;
• wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula II;
• wherein Z may be the same as or different from Y;
• wherein each Y and Z are independently selected from the group consisting of —OH, —NH2, —SH, —PO3H, —CO2H, —SO3H and hydrogen;
• wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;
• wherein R4, R5, and R6 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;
• wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;
• wherein R1, R2 and R3 may be the same or different and are independently selected from the group consisting of:
• with the proviso that no more than two of A, R1, R2 and R3 are selected from the group consisting of hydrogen, methyl, ethyl and propyl;
• and
• with the proviso that if one, and only one, of R1, R2 and R3 is ═O, then A is none of hydrogen, methyl, ethyl and propyl;
• wherein each R7 and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amnino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;
• g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R1, R2, and R3 are ═O, then the other is not ═O;
• Formula II:
• wherein Formula II is saturated or unsaturated;
• wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;
• wherein X is selected from the group consisting of N, C, O, P and S;
• wherein Y is selected from the group consisting of O, N, S, P, C, —O—NH—, —O—CH2—NH—, —O—CH2—O—, —NH—CH2—NH—, —O—CH(CH3NH—, —NH—CH(CH3)—NH—, —O—CH(CH3)—O—, —NH—C(CH3)2—NH—, —O—S—, —O—CH2—S—, —NH—S—, —NH—CH2—S—, and other mercaptan, phosphato, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• with the proviso that if either X or Y is N, then the other is not C;
• wherein R1, R2, R3, R4, R5, R6, R7 and R8 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• and
• wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, to form a mixture;
• and
• (b) incubating said mixture under conditions whereby a nucleic acid molecule complementary to all or a portion of said template is amplified, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

A method for sequencing a nucleic acid molecule, comprising:

• (a) mixing a nucleic acid molecule to be sequenced with one or more primers, one or more compounds having a chemical formula selected from the group consisting of formula I or formula II, or a salt thereof, wherein said compound is not betaine:
• Formula I:
• where A is
• where X is
• where N is positively charged;
• wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula I;
• wherein Z may be the same as or different from Y;
• wherein each Y and Z are independently selected from the group consisting of —OH, —NH2,—SH, —PO3H, —CO2H, —SO3H and hydrogen;
• wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;
• wherein R4, R5, and R6 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;
• wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;
• wherein R1, R2 and R3 may be the same or different and are independently selected from the group consisting of:
• with the proviso that no more than two of A, R1, R2 and R3 are selected from the group consisting of hydrogen, methyl, ethyl and propyl;
• and
• with the proviso that if one, and only one, of R1, R2 and R3 is ═O, then A is none of hydrogen, methyl, ethyl and propyl;
• wherein each R7 and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;
• g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R1, R2, and R3 are ═O, then the other is not ═O;
• Formula II:
• wherein Formula II is saturated or unsaturated;
• wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;
• wherein X is selected from the group consisting of N, C, O, P and S;
• wherein Y is selected from the group consisting of O, N, S, P, C,—O—NH—, —O—CH2—NH—, —O—CH2—O—, —NH—CH2—NH—, —O—CH(CH3)NH—, —NH—CH(CH3)—NH—, —O—CH(CH3)—O—, —NH—C(CH3)2—NH—, —O—S—, —O—CH2—S—, —NH—S—, —NH—CH2—S—, and other mercaptan, phosphate, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• with the proviso that if either X or Y is N, then the other is not C;
• wherein R1, R2, R3, R4, R5, R6, R7 and R8 may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;
• and
• wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, one or more nucleotides and one or more terminating agents to form a mixture;
• (b) incubating said mixture under conditions whereby a population of molecules complementary to all or a portion of said molecule to be sequenced is synthesized;
• and
• (c) separating said population to determine the nucleotide sequence of all or a portion of said molecule to be sequenced, wherein the bases of said nucleic acid molecule to be sequenced comprise greater than about 60% guanine and cytosine.