Q. Base pairing, in RNA, is A–G and U–C.

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Q. In addition to the canonical base pairing, there often exists non-canonical base pairing such as _________ and ________ base paring.

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Q. Four main subtypes of secondary structures can be identified. They are hairpin loops, bulge loops, interior loops, and multi-branch loops.

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Q. The ______ refers to a structure with two ends of a single-stranded region (loop) connecting a base-paired region (stem).

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Q. The __________ refers to two single-stranded regions on opposite strands connecting two adjacent base-paired segments.

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Q. At present, there are essentially two types of method of RNA structure prediction. One is the minimum free energy approach and the Second one is a comparative approach.

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Q. Ab initio approach makes structural predictions based on ______

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Q. In ab initio approach, generally, when a base pairing is formed, the energy of the molecule is _________ because of attractive interactions between the two strands.

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Q. In ab initio methods, free energy can be calculated based on parameters empirically derived for small molecules.

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Q. The energy necessary to form individual base pairs is not quite affected by adjacent base pairs.

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Q. The attractive interactions lead to _________ energy.

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Q. If the base pair is adjacent to loops or bulges, the neighboring loops and bulges tend to ___________ the base-pair formation.

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Q. The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method.

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Q. Ab initio methods are energetically least favorable.

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Q. The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.

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Q. In dot matrix in ab initio methods, the diagonals _____________ to the main diagonal represent regions that can self hybridize.

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Q. In dot matrix in ab initio methods, one way to reduce the noise in the matrix is to select an appropriate window size of a maximum number of contiguous base matches.

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Q. In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a ____ secondary structure in a ________ molecule.

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Q. In ab initio methods, a quantitative approach such as dynamic programming can be used to assemble a final structure with optimal base-paired regions.

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Q. In dynamic programming, in ab initio methods, Often ________ base pairing and energy terms of the base pairing _____ incorporated into the scoring process.

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