Next-nearest-neighbor sequence determinants of antisense DNA

A method for designating a nucleotide sequence of n nucleotides as n next-nearest-neighbor nucleotide triplets comprising:

• (a) treating the n nucleotide sequence as a closed sequence, with the ends of said sequence meeting to form a circle;
• (b) reading the nucleotide sequence three nucleotides at a time, moving up one nucleotide along the sequence, and then reading the next three nucleotides, for n steps;
• and
• (c) interpreting the n readings of three nucleotides each as being equal to n next-nearest-neighbor nucleotide triplets.

A method for assigning parameters of antisense effectiveness to 64 next-nearest-neighbor nucleotide triplets from measurements of the antisense effectiveness of at least 64 nucleotide sequences, wherein the sequences are considered to be closed sequences without end effects comprising:

• (a) constructing a matrix X having N rows and M columns, wherein said matrix X has one row for each of a minimum of N=64 nucleotide sequences and one column for each of the possible M=64 types of next-nearest-neighbor nucleotide triplets for sequences containing the common four nucleotides, A, U, G, and C, wherein the numbers in the matrix columns are the numbers of each type of next-nearest-neighbor nucleotide triplet in the sequence in the given row;
• (b) constructing a matrix Y with N rows and 1 column, wherein the numbers in the rows are measured values for the biological antisense effectiveness of the N sequences;
• (c) dividing the rows of matrices X and Y by the respective errors in the measured values;
• (d) constructing a matrix P having M rows and 1 column, wherein the numbers in the rows are the 64 parameters of antisense effectiveness assigned to the next-nearest-neighbor nucleotide triplets;
• (e) checking that the matrices satisfy the condition that X multiplied by P equals Y, via matrix multiplication;
• and
• (f) solving equation X multiplied by P equals Y via the singular value decomposition method, wherein said equation is solved for P.

A method for assigning parameters to 49 combinations of next-nearest-neighbor nucleotide triplets from measurements of antisense effectiveness of at least 49 sequences, wherein the sequences are considered to be closed sequences without end effects comprising:

• (a) constructing a matrix X having N rows and M columns, wherein said matrix X has one row for each of a minimum of N=49 nucleotide sequences and there is one column for each of the possible M=49 independent combinations of next-nearest-neighbor nucleotide triplets for sequences containing the common four nucleotides A, U, G, and C, wherein the numbers in the matrix columns are the numbers of each type of independent next-nearest-neighbor nucleotide combination in the sequence in the given row;
• (b) constructing a matrix Y having N rows and 1 column, wherein the numbers in the rows are the measured values for the biological antisense effectiveness of the N sequences;
• (c) dividing the rows of matrices X and Y by the respective errors in the measured values;
• (d) constructing a matrix P having M rows and 1 column, wherein the numbers in the rows are the 49 parameters of antisense effectiveness assigned to the independent next-nearest-neighbor nucleotide combinations;
• (e) checking that the matrices satisfy the condition that X multiplied by P equals Y, via matrix multiplication;
• and
• (f) solving the equation X multiplied by P equals Y via the singular value decomposition method, wherein said equation is solved for P.